Propka: Difference between revisions

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{{Infobox script-repo
|type      = script
|filename  = propka.py
|author    = [[User:Tlinnet|Troels E. Linnet]]
|license  = BSD
}}
== Acknowledgement ==
== Acknowledgement ==
The PROPKA method is developed by the [http://propka.ki.ku.dk/~luca/wiki/index.php/JansPage Jensen Research Group] , Department of Chemistry, University of Copenhagen.
propka.py contact and relies on the result from the [http://propka.ki.ku.dk propka] server


propka.py contact and relies on the result from the [http://propka.ki.ku.dk propka] server
The PROPKA method is developed by the [http://propka.ki.ku.dk/~luca/wiki/index.php/JansPage Jensen Research Group] , Department of Chemistry, University of Copenhagen. <br />


== Introduction ==
== Introduction ==
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It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.
It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.


If is not possible to get the mechanize module to work, one can go to the [http://propka.ki.ku.dk/ propka] server, upload a .pdb file, and download the .pka file. <br />
If you put the mechanize folder and the propka.py script somewhere in your pymol search path, then getting the pka values is made super easy. By the way, did you know, that you don't have to prepare the .pdb file by adding/removing hydrogens? The [http://propka.ki.ku.dk/ propka] server uses its own internal hydrogen placement algorithm.
By setting: "method=file" and point to the .pka file "file_name=.\Results_propka\4ins_.pka", one can process the .pka result file and get the pymol command file.
 
<syntaxhighlight lang="python">
import propka
fetch 4ins, async=0
propka
</syntaxhighlight>
 
If there is no web connection, it is possible to process a result file from a previous run or from a downloaded propka webpage result. This can be a handsome feature in a teaching/seminar situation, since it speeds up the pymol result or that an available web connection can be doubtful. Just point to the .pka file: Remember the dot "." which means "current directory".
<syntaxhighlight lang="python">
import propka
load 4ins.pdb
propka pkafile=./Results_propka/4ins"LOGTIME".pka, resi=18.25-30, resn=cys
</syntaxhighlight>


The last possibility, is just to ask for the pka values of a recognized PDB id. This is done with the "getpropka" function.
The last possibility, is just to ask for the pka values of a recognized PDB id. This is done with the "getpropka" function.
<syntaxhighlight lang="python">
import propka
getpropka source=ID, PDBID=4ake, logtime=_, showresult=yes
</syntaxhighlight>


== Dependency of python module: mechanize ==
== Dependency of python module: mechanize ==
The script needs mechanize to run.
The script needs mechanize to run. The module is included in the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].
* On windows, it is not easy to make additional modules available for pymol. So put in into your working folder.
* On windows, it is not easy to make additional modules available for pymol. So put in into your working folder.
* The easy manual way:
* The easy manual way:
Line 24: Line 47:


=== Examples ===
=== Examples ===
<source lang="python">
Read about the proteins here:<br>
run ./propka.py
http://www.proteopedia.org/wiki/index.php/4ins <br>
http://www.proteopedia.org/wiki/index.php/1hp1 <br>
 
<syntaxhighlight lang="python">
import propka
 
fetch 4ins, async=0
fetch 4ins, async=0
propka molecule=4ins, chain=*, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes, showresult=no
propka       OR
propka 4ins  OR
propka 4ins, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes


import propka
fetch 1hp1, async=0
fetch 1hp1, async=0
propka molecule=1hp1, chain=A, resi=308.513, resn=CYS, logtime=_, verbose=no, showresult=no
propka molecule=1hp1, chain=A, resi=305-308.513, resn=CYS, logtime=_


getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=no
import propka
</source>
getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=yes
</syntaxhighlight>


<gallery heights="240px" widths="340px">
<gallery heights="240px" widths="340px">
Image:propka4ins.png|propka used on 4INS.
Image:Propka1HP1.png|propka used on 1HP1.
Image:propka1hp1.png|propka used on 1HP1.
Image:Propka1HP1-ATP.png|propka used on 1HP1, zoom on ATP ligand.
Image:Results_log.png|An appending logfile ./Results_propka/_Results.log saves the input commands and the result for the residues specified with resi= and resn=
Image:Propka1HP1-ZN.png|propka used on 1HP1, zoom on ZN ligand metal center.
</gallery>
<gallery heights="240px" widths="340px">
Image:Propka4INS.png|propka used on 4INS.
Image:Pymolpropkamenu.png|The easy menu does it easy to click on/off ligands and bonds
Image:Resultslog.png|An appending logfile ./Results_propka/_Results.log saves the input commands and the result for the residues specified with resi= and resn=
</gallery>
</gallery>
pka atoms are created and renamed for their pka value. That makes it easy to "click" the atom in pymol and instantly see the pka value.
pka atoms are created and renamed for their pka value. That makes it easy to "click" the atom in pymol and instantly see the pka value.


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If one wants to see the specified result, the logfile ./Results_propka/_Results.log saves the link to the propka server. Here one can see in an interactive Jmol appp, the interactions to the pka residues.
If one wants to see the specified result, the logfile ./Results_propka/_Results.log saves the link to the propka server. Here one can see in an interactive Jmol appp, the interactions to the pka residues.


== Example Pymol Script ==
== Use of script ==
<source lang="python">
<syntaxhighlight lang="python">
### Point to your directory with the script.
cd /home/tlinnet/test
#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/propka
cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\predict_reactivity\propka


run ./propka.py
import propka


### Fetch 4ins from web. async make sure, we wait to have completed
### The fastest method is just to write propka. Then the last pymol molecule is assumed and send to server. verbose=yes makes the script gossip mode.
fetch 4ins, async=0
fetch 4ins, async=0
propka molecule=4ins, chain=*, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes, showresult=no
propka


### If there is problems to get the mechanize module working, get the result .pka file at the propka webpage manually.
### Larger protein
### Then run with method=file and point to .pka file.
fetch 1hp1, async=0
#fetch 4ins, async=0
propka logtime=_, resi=5-10.20-30, resn=CYS.ATP.TRP, verbose=yes
#hide everything, 4ins
#show cartoon, 4ins
#propka method=file, molecule=4ins, resi=18.25-30, resn=cys, file_name=.\Results_propka\4ins_.pka


### Some more examples. This molecule has 550 residues, so takes a longer time.
### Fetch 4ins from web. async make sure, we dont execute script before molecule is loaded. The resi and resn prints the interesting results right to command line.
#fetch 1hp1, async=0
fetch 4ins, async=0
#propka molecule=1hp1, chain=A, resi=308.513, resn=CYS, logtime=_, verbose=no, showresult=no
propka chain=*, resi=5-10.20-30, resn=ASP.CYS, logtime=_


### One can also just make a lookup for a protein. Use function: getpropka
### If there is no web connection, one can process a local .pka file. Either from a previous run or from a downloaded propka webpage result.
### Note. This does only print the result to the pymol command line
### Then run and point to .pka file with: pkafile=./Results_propka/pkafile.pka Remember the dot "." in the start, to make it start in the current directory.
#getpropka source=ID, PDBID=4ake, logtime=_, server_wait=3.0, verbose=no, showresult=yes
load 4ins.pdb
#getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=no
propka pkafile=./Results_propka/4ins_.pka, resi=18.25-30, resn=cys,
</source>
=== Input paramaters ===
<source lang="python">
# method : method=upload is default. This sends .pdb file and request result from propka server.
## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
# molecule : name of the molecule. Ending of file is assumed to be .pdb
# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
# resi : Select by residue number, which residues should be printed to screen and saved to the log file: \Results_propka\_Results.log.
## Separate with "." or make ranges with "-". Ex: resi=35.40-50
# resn : Select by residue name, which residues should be printed to screen and saved to the log file: \Results_propka\_Results.log.
## Separate with "." Ex: resn=cys.tyr
# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
## Normal it usefull to set it empty. Ex: logtime=_
# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
# file_name: only used for: propka method=file  . Write the path to .pka file
# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds.
# version=v3.1 is default. This is what version of propka which would be used.
## Possible: 'v3.1','v3.0','v2.0'. If a newer version is available than the current v3.1, a error message is raised to make user update the script.
# source : source=upload is default and is set at the propka webpage. Can only be used for in the function "getpropka".
# getpropka source=ID, PDBID=4ake , one can print to the command line, the pka value for any official pdb ID. No files are displayed in pymol.
</source>
 
== Python Code ==
<source lang="python">
#-------------------------------------------------------------------------------
# Name: propka for pymol
# Purpose: To fetch and display the pka values for protein of intetest
#
# Author: Troels E. Linnet
#
# Created: 14/08/2011
# Copyright: (c) Troels E. Linnet 2011
# Contact:      tlinnet snabela gmail dot com
# Licence: Free for all
#-------------------------------------------------------------------------------
"""
    The PROPKA method is developed by the
  Jensen Research Group
Department of Chemistry
University of Copenhagen
 
Please cite these references in publications:
Hui Li, Andrew D. Robertson, and Jan H. Jensen
"Very Fast Empirical Prediction and Interpretation of Protein pKa Values"
Proteins, 2005, 61, 704-721.


Delphine C. Bas, David M. Rogers, and Jan H. Jensen
### Some more examples. This molecule has 550 residues, so takes a longer time. We select to run the last molecule, by writing: molecule=1hp1
"Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes"
Proteins, 2008, 73, 765-783.
 
Mats H.M. Olsson, Chresten R. Soendergard, Michal Rostkowski, and Jan H. Jensen
"PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions"
Journal of Chemical Theory and Computation, 2011 7 (2), 525-537
 
Chresten R. Soendergaard, Mats H.M. Olsson, Michaz Rostkowski, and Jan H. Jensen
"Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values"
Journal of Chemical Theory and Computation, 2011 in press
"""
#-------------------------------------------------------------------------------
# The script needs mechanize to run.
# On windows, it is not easy to make additional modules available for pymol. So put in into your working folder.
#1)The easy manual way:
#a)Go to: http://wwwsearch.sourceforge.net/mechanize/download.html
#b)Download mechanize-0.2.5.zip. http://pypi.python.org/packages/source/m/mechanize/mechanize-0.2.5.zip
#c)Extract to .\mechanize-0.2.5  then move the in-side folder "mechanize" to your folder with propka.py. The rest of .\mechanize-0.2.5 you don't need.
#You can also see other places where you could put the "mechanize" folder. Write this in pymol to see the paths where pymol is searching for "mechanize"
# import sys; print(sys.path)
 
#-------------------------------------------------------------------------------
"""
Example for pymol script to start the functions. For example: trypropka.pml
Execute with pymol or start pymol and: File->Run->trypropka.pml
##############################################################################################################################################################################################################################
 
### Point to your directory with the script.
#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/predict_reactivity/propka
cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\predict_reactivity\propka
 
run ./propka.py
 
### Fetch 4ins from web. async make sure, we wait to have completed
fetch 4ins, async=0
fetch 4ins, async=0
propka molecule=4ins, chain=*, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes, showresult=no
fetch 1hp1, async=0
propka molecule=1hp1, chain=A, resi=300-308.513, resn=CYS.ATP.TRP, logtime=_, verbose=no, showresult=no
propka molecule=1hp1, pkafile=./Results_propka/1hp1_.pka, verbose=yes
</syntaxhighlight>


### If there is problems to get the mechanize module working, get the result .pka file at the propka webpage manually.
=== Input paramaters ===
### Then run with method=file and point to .pka file.
<syntaxhighlight lang="text">
#fetch 4ins, async=0
############################################Input parameters: propka############################################
#hide everything, 4ins
############# The order of input and changable things:
#show cartoon, 4ins
propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL")
#propka method=file, molecule=4ins, resi=18.25-30, resn=cys, file_name=.\Results_propka\4ins_.pka
 
### Some more examples. This molecule has 550 residues, so takes a longer time.
#fetch 1hp1, async=0
#propka molecule=1hp1, chain=A, resi=308.513, resn=CYS, logtime=_, verbose=no, showresult=no
 
### One can also just make a lookup for a protein. Use function: getpropka
### Note. This does only print the result to the pymol command line
#getpropka source=ID, PDBID=4ake, logtime=_, server_wait=3.0, verbose=no, showresult=yes
#getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=no
 
#########input paramaters#########
# method : method=upload is default. This sends .pdb file and request result from propka server.
# method : method=upload is default. This sends .pdb file and request result from propka server.
## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
## If one points to an local .pka file, then method is auto-changed to method=file. This is handsome in off-line environment, ex. teaching or seminar.
# pkafile: Write the path to .pka file. Ex: pkafile=./Results_propka/4ins_.pka
# molecule : name of the molecule. Ending of file is assumed to be .pdb
# molecule : name of the molecule. Ending of file is assumed to be .pdb
# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
# resi : Select by residue number, which residues should be printed to screen and saved to the log file: \Results_propka\_Results.log.
# resi : Select by residue number, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." or make ranges with "-". Ex: resi=35.40-50
## Separate with "." or make ranges with "-". Ex: resi=35.40-50
# resn : Select by residue name, which residues should be printed to screen and saved to the log file: \Results_propka\_Results.log.
# resn : Select by residue name, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." Ex: resn=cys.tyr
## Separate with "." Ex: resn=cys.tyr
# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
Line 189: Line 135:
# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
# file_name: only used for: propka method=file  . Write the path to .pka file
# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds.
# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds.
# version=v3.1 is default. This is what version of propka which would be used.
# version=v3.1 is default. This is what version of propka which would be used.
## Possible: 'v3.1','v3.0','v2.0'. If a newer version is available than the current v3.1, a error message is raised to make user update the script.
## Possible: 'v3.1','v3.0','v2.0'. If a newer version is available than the current v3.1, a error message is raised to make user update the script.
# source : source=upload is default and is set at the propka webpage. Can only be used for in the function "getpropka".
############################################Input parameters: getpropka############################################
# getpropka source=ID, PDBID=4ake , one can print to the command line, the pka value for any official pdb ID. No files are displayed in pymol.
############# The order of input and changable things:
getpropka(PDB="NIL",chain="*",resi="0",resn="NIL",source="upload",PDBID="",logtime=time.strftime("%Y%m%d%H%M%S",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no")
# PDB: points the path to a .pdb file. This is auto-set from propka function.
# source : source=upload is default and is set at the propka webpage.
# source=ID, PDBID=4ake , one can print to the command line, the pka value for any official pdb ID. No files are displayed in pymol.
# PDBID: is used as the 4 number/letter pdb code, when invoking source=ID.
</syntaxhighlight>
 
== Examples ==
=== Example 1 - Mutagenesis analysis - part 1 ===
This script was developed with the intention of making analysis of possible mutants easier. For example, the reactivity of Cysteines in FRET maleimide labelling is determined by the fraction of the Cysteine residue which is negatively charged (C-). This fraction is related to its pKa value and the pH of the buffer: f(C-)=1/(10(pK-pH)+1). So, one would be interested in having the lowest possible pKa value as possible. Ideally lower than the pH of the buffer. To analyse where to make the best mutant in your protein, you could do the following for several residues. We do the mutagenesis in the command line, since we then could loop over the residues in the protein.<br>
So, in a loop with defined residues, this could look like the following code. Note, now we are quite happy for the result log file, since it collects the pka for the mutants.
 
{{Template:PymolScriptRepoDownload|examples/propka_1.pml}}
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_1.pml" highlight="python" />


##############################################################################################################################################################################################################################
=== Example 2 - Mutagenesis analysis - part 2 ===
To only loop over surface residues, you might want to find these with the script [[FindSurfaceResidues]].


"""
{{Template:PymolScriptRepoDownload|examples/propka_2.pml}}
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_2.pml" highlight="python" />


try: from pymol import cmd; runningpymol='yes'
A little warning though. You need to be carefull about the rotamer you're choosing. It can happen that the first rotamer ends up being in physically non-reasonable contact distance to other residues, so atoms become overlayed. Also, the mutagenesis wizard can have the funny habit of sometimes not adding hydrogens to terminal -C or -N after mutating a residue.
except: runningpymol='no'; pass
import time, platform, os


def propka(method="upload",molecule="NIL",chain="*",resi="0",resn="NIL",logtime=time.strftime("%Y%m%d%H%M%S",time.localtime()),server_wait=10.0,version="v3.1",verbose="no",showresult="no",file_name="NIL"):
=== Example 3 - Scan a range of proteins ===
### First we have to be sure, we give reasonable arguments
Could be done with this script
assert method in ['upload', 'file'], "'method' has to be either: method=upload or method=file"
assert molecule not in ['NIL'], "You always have to provide molecule name. Example: molecule=4ins"
### To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
if resi != "0": resi_range = ResiRange(resi)
else: resi_range=resi
### Also works for residue names. They are all converted to bigger letters. Example: resn="cys.Tyr"
if resn != "NIL": resn_range = ResnRange(resn); resn_range = [resn.upper() for resn in resn_range]
else: resn_range = resn
### Make chain range, and upper case.
chain = ChainRange(chain)
### Make result directory. We also the absolut path to the new directory.
Newdir = createdirs()
if method=="upload":
### We try to load mechanize. If this fail, one can always get the .pka file manual and the run: method=file
try: import mechanize; importedmechanize='yes'
except ImportError: print("Import error. Is a module missing?"); print(sys.exc_info()); print("Look if missing module is in your python path\n%s")%sys.path;importedmechanize='no'; import mechanize
### The name for the new molecule
newmolecule = "%s%s"%(molecule,logtime)
### Create the new molecule from original loaded and for the specified chains. Save it, and disable the old molecule.
cmd.create("%s"%newmolecule, "%s and chain %s"%(molecule,chain))
cmd.save("%s%s.pdb"%(Newdir,newmolecule), "%s"%newmolecule)
cmd.disable("%s"%molecule)
### Let the new molecule be shown in cartoon.
cmd.hide("everything", "%s"%newmolecule)
cmd.show("cartoon", "%s"%newmolecule)
### Make the absolut path to the newly created .pdb file.
PDB="%s%s.pdb"%(Newdir,newmolecule);source="upload"; PDBID=""
### Request server, and get the absolut path to the result file.
file_name = getpropka(source,PDB,chain,resi,resn,PDBID,logtime,server_wait,version,verbose,showresult)
### Open the result file and put in into a handy list.
list_results = importpropkaresult(file_name)
if method=="file":
assert file_name not in ['NIL'], "You have to provide path to file. Example: file_name=./Results_propka/4ins_2011.pka"
assert ".pka" in file_name, 'The propka result file should end with ".pka" \nExample: file_name=./Results_propka/4ins_2011.pka \nfilename_name=%s'%(file_name)
### The name for the molecule we pass to the writing script of pymol commands
newmolecule = "%s"%molecule
### We open the result file we have got in the manual way and put in into a handy list.
list_results = importpropkaresult(file_name)
### Now create the pymol command file. This should label the protein. We get back the absolut path to the file, so we can execute it.
result_pka_pymol_name = writepymolcmd(newmolecule,file_name)
### Now run our command file.
cmd.do("@%s"%result_pka_pymol_name)
### Then we print the interesting residues to the screen.
printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult)
if runningpymol !='no': cmd.extend("propka",propka)


def getpropka(source="upload",PDB="NIL",chain="*",resi="0",resn="NIL",PDBID="",logtime=time.strftime("%Y%m%d%H%M%S",time.localtime()),server_wait=10.0,version="v3.1",verbose="no",showresult="no"):
{{Template:PymolScriptRepoDownload|examples/propka_3.pml}}
try: import mechanize; importedmechanize='yes'
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_3.pml" highlight="python" />
except ImportError: print("Import error. Is a module missing?"); print(sys.exc_info()); print("Look if missing module is in your python path \n %s"%sys.path);importedmechanize='no'


url = "http://propka.ki.ku.dk/"
== ScriptVersion ==
assert version in ['v2.0', 'v3.0', 'v3.1'], "'version' has to be either: 'v2.0', 'v3.0', 'v3.1'"
Current_Version=20111202
propka_v_201108 = 3.1
assert source in ['ID', 'upload', 'addr', 'input_file'], "'source' has to be either: 'ID', 'upload', 'addr', 'input_file'"
if source=="upload": assert PDB not in ['NIL'], "You always have to provide PDB path. Example: PDB=.\Results_propka\4ins2011.pdb"
if source=="ID": assert len(PDBID)==4 , "PDBID has to be 4 characters"
### To print out to screen for selected residues. Can be separated with "." or make ranges with "-". Example: resi="4-8.10"
if resi != "0": resi_range = ResiRange(resi)
else: resi_range=resi
### Also works for residue names. They are all converted to bigger letters. Example: resn="cys.Tyr"
if resn != "NIL": resn_range = ResnRange(resn); resn_range = [resn.upper() for resn in resn_range]
else: resn_range = resn
### Start the browser
br = mechanize.Browser()
### We pass to the server, that we are not a browser, but this python script. Can be used for statistics at the propka server.
br.addheaders = [('User-agent', 'pythonMechanizeClient')]
### To turn on debugging messages
#br.set_debug_http(True)
### To open the start page.
page_start = br.open(url)
read_start = page_start.read()
if verbose == 'yes': print(br.title()); print(br.geturl())
### To get available forms
page_forms = [f.name for f in br.forms()]
if verbose == 'yes': print(page_forms)
### Select first form
br.select_form(name=page_forms[0])
### Print the parameters of the 'version' RadioControl button and current value
if verbose == 'yes': print(br.find_control(name='version')), br.find_control(name='version').value
### This is to check, that the current script is "up-to-date".
        propka_v_present = float(br.find_control(name='version').value[0].replace('v',''))
        if propka_v_present > propka_v_201108:
raise UserWarning('\nNew version of propka exist.\nCheck/Update your script.\nPresent:v%s > Script:v%s'%(propka_v_present,propka_v_201108))
### Change the parameters of the 'version' radio button and then reprint the new value. Input has to be in a list [input].
br.form['version'] = [version]
if verbose == 'yes': print(br.find_control(name='version').value)
### Print the parameters of the 'source' RadioControl button and current value
if verbose == 'yes': print(br.find_control(name='source'), br.find_control(name='source').value)
### Change the parameters of the 'source' radio button and then reprint the new value. Input has to be in a list [input].
br.form['source'] = [source]
if verbose == 'yes': print(br.find_control(name='source').value)
### This step was the must strange and took a long time. For finding the information and the double negative way.
### One have to enable the pdb button. Read more here: http://wwwsearch.sourceforge.net/old/ClientForm/  ("# All Controls may be disabled.....)
PDBID_control = br.find_control("PDBID")
PDB_control = br.find_control("PDB")
if verbose == 'yes': print(PDBID_control.disabled, PDB_control.disabled)
if source == "ID": PDBID_control.disabled=False; PDB_control.disabled=True
if source == "upload": PDBID_control.disabled=True; PDB_control.disabled=False
if verbose == 'yes': print(PDBID_control.disabled, PDB_control.disabled)
### We create the result dir, and take with us the 'path' to the result dir.
Newdir = createdirs()
### Open all the files, and assign them.
if source == "upload": filename = PDB
if source == "ID": filename = PDBID
files = openfiles(Newdir, filename, logtime, source)
result_pka_file=files[0];result_input_pka_file=files[1];result_log=files[2];filepath=files[3];result_pka_file_name=files[4];result_pka_file_stripped=files[5]
## Print the parameters of the 'PDBID' TextControl button and current value
if source == "ID" and verbose == 'yes': print(br.find_control(name='PDBID')); print(br.find_control(name='PDBID').value)
## Change the parameters of the 'PDBID' TextControl and then reprint the new value. Input has just to be a string.
if source == "ID": br.form["PDBID"] = PDBID
if source == "ID" and verbose == 'yes': print(br.find_control(name='PDBID').value)
## Print the parameters of the 'PDB' TextControl button and current value
if source == "upload" and verbose == 'yes': print(br.find_control(name='PDB')); print(br.find_control(name='PDB').value)
## Change the parameters of the 'PDB' FileControl and then reprint the new value. Input has just to be a string.
if source == "upload": PDBfilename=PDB; PDBfilenamepath=PDB
if source == "upload": br.form.add_file(open(PDBfilename), 'text/plain', PDBfilenamepath, name='PDB')
if source == "upload" and verbose == 'yes': print(br.find_control(name='PDB')); print(br.find_control(name='PDB').value)
## Now reprint the current selected form, so we see that we have the right values.
if verbose == 'yes': print(br.form)
### Make "how" we would like the next request. We would like to "Click the submit button", but we have not opened the request yet.
req = br.click(type="submit", nr=0)
### Have to pass by a mechanize exception. Thats the reason for the why True
### The error was due to: br.open(req)
###### mechanize._response.httperror_seek_wrapper: HTTP Error refresh: The HTTP server returned a redirect error that would lead to an infinite loop.
###### The last 30x error message was:
###### OK
### I haven't been able to find the refresh problem or extend the time. So we make a pass on the raised exception.
try:
print("Now sending request to server")
br.open(req)
### If there is raised an exception, we jump through to the result page after some sleep.
        except mechanize.HTTPError:
### We can extract the jobid from the current browser url.
jobid = br.geturl()[32:-5]
### We notice how the script at the server presents the final result page.
url_result = url + "pka/" + jobid + ".html"
### Now we continue to try to find the result page, until we have succes. If page doesn't exist, we wait a little.
while True:
print("Result still not there. Waiting %s seconds more"%server_wait)
time.sleep(float(server_wait))
### To pass the "break" after the exception, we make a hack, wait and then go to the result page, which is the jobid.
try:
page_result = br.open(url_result)
read_result = page_result.read()
### If we don't receive a error in getting the result page, we break out of the while loop.
break
### If the page doesn't exist yet. We go back in the while loop.
except mechanize.HTTPError:
### Wait another round
pass
### If we get a timeout, we also wait.
except mechanize.URLError:
### Wait another round
pass
htmlresult="The detailed result is now available at: %s"%br.geturl()
print(htmlresult)
read_result = br.response().read()
## Now save the available links from the current page. But only links that satisfy the expression.
links_result = []
for l in br.links(url_regex='http://propka.ki.ku.dk/pka'):
links_result.append(l)
### Now follow the link to the .propka_input resultpage
if len(links_result) > 1: br.follow_link(links_result[1])
### Now get the page text for the current link
if len(links_result) > 1: read_result1 = br.response().read()
### Save the result
if len(links_result) > 1: result_input_pka_file.write(read_result1)
### Now follow the link to the .pka resultpage
if len(links_result) > 1: br.back()
result_input_pka_file.close()
### Now follow first link. "Should be" available for all versions of propka.
br.follow_link(links_result[0])
### Now get the page for the current link
read_result0 = br.response().read()
### Save the result and close file.
result_pka_file.write(read_result0)
result_pka_file.close()
### Now get the result in a list, which is sorted
list_results = importpropkaresult(result_pka_file_name)
### Print to log file
result_log.write("# executed: %s \n# logtime: %s \n# source=%s \n# PDB=%s \n# chain=%s \n# PDBID=%s \n# server_wait=%s version=%s verbose=%s showresult=%s \n# resi=%s resn=%s\n# %s \n"%(time.strftime("%Y%m%d%H%M%S",time.localtime()),logtime,source,PDB,chain,PDBID,server_wait,version,verbose,showresult,resi,resn,htmlresult))
### Print to screen
printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult)
### Now write to log
for l in list_results:
if resi != "0" and int(l[1]) in resi_range:
result_log.write("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]) + '\n')
if resn != "NIL" and l[0] in resn_range and int(l[1]) not in resi_range:
result_log.write("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]) + '\n')
result_pka_file_stripped.write("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]) + '\n')
result_pka_file_stripped.close()
result_log.close()
return(result_pka_file_name)
if runningpymol !='no': cmd.extend("getpropka",getpropka)


def writepymolcmd(newmolecule,file_name):
== Changelog ==
list_results = importpropkaresult(file_name)
* 20111202
files_pka_pymol = openpymolfiles(file_name)
*# This code has been put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].
result_pka_pymol=files_pka_pymol[0];result_pka_pymol_name=files_pka_pymol[1]
dictio = {'ASP':'CG', 'GLU':'CD', 'ARG':'CZ', 'LYS':'NZ', 'HIS':'CG', 'CYS':'SG', 'TYR':'OH', 'C-':'C', 'N+':'N'}
### Now start write to the file.
pkamolecule="pka%s"%(newmolecule)
### Try to make silent, and not auto zoom the new objects
result_pka_pymol.write("feedback disable,all,actions\n")
result_pka_pymol.write("feedback disable,all,results\n")
result_pka_pymol.write("set auto_zoom, off\n")
### Create a new empty pymol pka molecule
result_pka_pymol.write("cmd.create('%s','None')\n"%(pkamolecule))
for l in list_results:
name=dictio[l[0]];resi=l[1];chain=l[2];pka=l[3];buried=l[4]
if "*" in pka: pka = pka.replace("*",""); comment="*:Coupled residues detected"
else: comment=""
### Make the selection for which atom to copy
newselection = ("%s and chain %s and resi %s and name %s"%(newmolecule,chain,resi,name))
### Copy the atom, call it by the residue name
result_pka_pymol.write("cmd.create('%s','%s',quiet=1)\n"%(resi,newselection))
### Alter the name and the b value of the newly created atom
result_pka_pymol.write("cmd.alter('%s','b=%s')\n"%(resi,pka))
result_pka_pymol.write("cmd.alter('%s','vdw=0.5')\n"%(resi))
result_pka_pymol.write("cmd.alter('%s','name=%s%s%s')\n"%(resi,'"',pka,'"'))
createselection = ("%s and chain %s and resi %s"%(resi,chain,resi))
result_pka_pymol.write("cmd.create('%s','%s or (%s)',quiet=1)\n"%(pkamolecule,pkamolecule,createselection))
### Remove the temporary atoms
result_pka_pymol.write("cmd.remove('%s')\n"%(resi))
### Delete the temporary molecule/selection
result_pka_pymol.write("cmd.delete('%s')\n"%(resi))


result_pka_pymol.write("cmd.show('spheres','%s')\n"%(pkamolecule))
* 20110823
result_pka_pymol.write("cmd.spectrum('b','rainbow',selection='%s',minimum='0',maximum='14')\n"%(pkamolecule))
*# Fixed some issues with selection algebra of Ligands.
result_pka_pymol.write("cmd.alter('name 99.9','vdw=0.8')\n")
*# Now colors Ligands automatically to purple scheme.
result_pka_pymol.write("cmd.show('spheres','name 99.9')\n")
result_pka_pymol.write("cmd.color('sulfur','name 99.9')\n")
result_pka_pymol.write("set auto_zoom, on\n")
result_pka_pymol.write("feedback enable,all,actions\n")
result_pka_pymol.write("feedback enable,all,results\n")
result_pka_pymol.close()
return(result_pka_pymol_name)


def openpymolfiles(file_name):
* 20110822
result_pka_pymol_name = file_name.replace(".pka",".pml")
*# Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
result_pka_pymol = open(result_pka_pymol_name, "w")
*# Bonds to N-terminal and C-terminal did not show up. Fixed.
return(result_pka_pymol, result_pka_pymol_name)
*# If one just write "propka", the "last" molecule in the pymol object list is now assumed, instead of the first. This makes mutagenesis analysis easier.
*# The pka difference from assumed standard values are now also displayed. Standard values are set to: pkadictio = {'ASP':3.9, 'GLU':4.3, 'ARG':12.0, 'LYS':10.5, 'HIS':6.0, 'CYS':8.3, 'TYR':10.1}
*# The menu size is made bigger, so it can fit the long names for the bonding partners. There's also a slider that you can drag using the mouse
*#:--it's the tiny tab between the command line and the movie controls. Drag that left or right.


def printpropkaresult(list_results, resi, resi_range, resn, resn_range, showresult):
* 20110821
for l in list_results:
*# The resn function was made wrong, only taking the last item of list. Fixed.
if resi != "0" and int(l[1]) in resi_range:
*# resn= can now also be print to screen/log for ligands like ATP. Ex: resn=CYS.ATP.TRP
if showresult != 'yes': print("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]))
*# Ligands are now also written to the "stripped-file". "./Results_propka/PDB.stripped"
if resn != "NIL" and l[0] in resn_range and int(l[1]) not in resi_range:
*# Bonds are now also made for Ligands.
if showresult != 'yes': print("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]))
if showresult == 'yes': print("%3s %3s %s %6s %3s %5s %3s %4s %s"%(l[0],l[1],l[2],l[3],l[4],l[5],l[6],l[7],l[8]))


def importpropkaresult(result_pka_file_name):
* 20110820
result_pka_file = open(result_pka_file_name, "r")
*# If one points to a result .pka file, then "method" is automatically set to "method=file".
list_results = []
*# Added the ability for pka values for ligands
for l in result_pka_file:
*# Bonds are now generated for the pka atoms.
if not l.strip():
*# The color scheme is changed from "rainbow" to "red_white_blue". This is easier to interpret.
continue
** CC: COULOMBIC INTERACTION. Color is red.
else:
** SH: SIDECHAIN HYDROGEN BOND. Color is brightorange.
### To search for the right lines
** BH: BACKBONE HYDROGEN BOND. Color is lightorange.
if l.strip().split()[0] in ['ASP', 'GLU', 'ARG', 'LYS', 'HIS', 'CYS', 'TYR', 'C-', 'N+'] and len(l.strip().split())>20:
list_results.append([l.strip().split()[0], l.strip().split()[1], l.strip().split()[2], l.strip().split()[3], l.strip().split()[4], l.strip().split()[6], l.strip().split()[7], l.strip().split()[8], l.strip().split()[9]])
### Sort the result after the residue number and then chain.
list_results.sort(key=lambda residue: int(residue[1]))
list_results.sort(key=lambda chain: chain[2])
result_pka_file.close()
return(list_results)


def createdirs():
* 20110817
if platform.system() == 'Windows': Newdir = os.getcwd()+"\Results_propka\\"
*# If just invoking with "propka", it will select the first molecule. And now it is possible also to write. "propka all".
if platform.system() == 'Linux': Newdir = os.getcwd()+"/Results_propka/"
*# Removed the "raise UserWarning" if the script is oudated. Only a warning message is printed.
if not os.path.exists(Newdir): os.makedirs(Newdir)
return(Newdir)


def openfiles(Newdir, filename, logtime, source):
* 20110816
if source == "upload":
*# Made the execution of the pymol command script silent, by only using cmd.API. This will raise a Warning, which can be ignored.
result_pka_file_name = filename.replace(".pdb",".pka")
*# Built-in a Script version control, to inform the user if the propka script is updated on this page
result_pka_input_file_name = filename.replace(".pdb",".propka_input")
*# The alternate attribute for the labeling atoms are reset. It was found pymol objected altering names for atoms which had alternate positions/values.
result_log_name = "%s_Results.log"%(Newdir)
*# Reorganized the input order, which means that: molecule=all is default.
result_pka_file_stripped_name = filename.replace(".pdb",".stripped")
if source == "ID":
result_pka_file_name = "%s%s%s.pka"%(Newdir,filename,logtime)
result_pka_input_file_name = "%s%s%s.propka_input"%(Newdir,filename,logtime)
result_log_name = "%s_Results.log"%(Newdir)
result_pka_file_stripped_name = "%s%s%s.stripped"%(Newdir,filename,logtime)
if platform.system() == 'Windows': filepath = "\\"
if platform.system() == 'Linux': filepath = "/"
### Open the files
result_pka_file = open(result_pka_file_name, "w")
result_input_pka_file = open(result_pka_input_file_name, "w")
result_log = open(result_log_name, "a")
result_pka_file_stripped = open(result_pka_file_stripped_name, "w")
return(result_pka_file, result_input_pka_file, result_log, filepath, result_pka_file_name,result_pka_file_stripped)


def ResiRange(resi):
=== Known bugs ===
resi = resi.split('.')
* Bonds can be multiplied from amino acids to Ligands like ZN or ATP. Assume the shortest bond to be correct.
resiList = []
*# ZN: This is caused, since ZN has no ID number and when there are several in the same chain. This can be reproduced for 1HP1, bond: A41ZNCC. Here it shows to bonds, where only the shortes is correct. No fix possible.
for i in resi:
*# ATP: This is caused, since propka sometimes eats the ending of the atom name. In the .pdb file is written O3', which propka represents like O3. Therefore a wildcard "*" is generel inserted, which can cause multiple bonds to the ATP molecule. This can be reproduced for 1HP1, bond: A504ATPSH. Here multiple bonds are made to all the O3*,O2* atoms. No fix possible.
if '-' in i:
* The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
tmp = i.split('-')
*# This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
resiList.extend(range(int(tmp[0]),int(tmp[-1])+1))
* Alternative configurations of a Ligand is at the moment a problem, and will not be shown. For example 1HXB and the ligand ROC.
if '-' not in i:
*: The script extraxt AROC and BROC from pymol, which does match with ROC in the .pka file. Try save the protein with only one configuration of the Ligand.
resiList.append(int(i))
** >In pymol:
return(resiList)
**: fetch 1hxb, async=0
**: create 1hxbA, 1hxb and not alt B
**: save 1hxbA.pdb, 1hxbA
** >Quit pymol
** >Manually replace with text editor in .pdb file "AROC" with " ROC"  Remember the space " "!
** >Then in pymol
**: load 1hxbA.pdb
**: import propka
**: propka verbose=yes


def ResnRange(resn):
resn = resn.split('.')
return(resn)


def ChainRange(chain):
chainstring = chain.replace(".","+").upper()
return(chainstring)
</source>


[[Category:Script_Library]]
[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]
[[Category:Structural_Biology_Scripts]]
[[Category:Biochemical_Scripts]]
[[Category:Pymol-script-repo]]

Latest revision as of 11:06, 15 January 2012

Type Python Script
Download propka.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Acknowledgement

propka.py contact and relies on the result from the propka server

The PROPKA method is developed by the Jensen Research Group , Department of Chemistry, University of Copenhagen.

Introduction

This script can fetch the pka values for a protein from the propka server. The "propka" function downloads the results and processes them.
It also automatically writes a pymol command file and let pymol execute it. This command file make pka atoms, rename them, label them and color them according to the pka value.

If you put the mechanize folder and the propka.py script somewhere in your pymol search path, then getting the pka values is made super easy. By the way, did you know, that you don't have to prepare the .pdb file by adding/removing hydrogens? The propka server uses its own internal hydrogen placement algorithm.

import propka
fetch 4ins, async=0
propka

If there is no web connection, it is possible to process a result file from a previous run or from a downloaded propka webpage result. This can be a handsome feature in a teaching/seminar situation, since it speeds up the pymol result or that an available web connection can be doubtful. Just point to the .pka file: Remember the dot "." which means "current directory".

import propka
load 4ins.pdb
propka pkafile=./Results_propka/4ins"LOGTIME".pka, resi=18.25-30, resn=cys

The last possibility, is just to ask for the pka values of a recognized PDB id. This is done with the "getpropka" function.

import propka
getpropka source=ID, PDBID=4ake, logtime=_, showresult=yes

Dependency of python module: mechanize

The script needs mechanize to run. The module is included in the project, Pymol-script-repo.

  • On windows, it is not easy to make additional modules available for pymol. So put in into your working folder.
  • The easy manual way:
  1. Go to: http://wwwsearch.sourceforge.net/mechanize/download.html
  2. Download mechanize-0.2.5.zip. http://pypi.python.org/packages/source/m/mechanize/mechanize-0.2.5.zip
  3. Extract to .\mechanize-0.2.5 then move the in-side folder "mechanize" to your folder with propka.py. The rest of .\mechanize-0.2.5 you don't need.
  • You can also see other places where you could put the "mechanize" folder. Write this in pymol to see the paths where pymol is searching for "mechanize"
  • import sys; print(sys.path)

Examples

Read about the proteins here:
http://www.proteopedia.org/wiki/index.php/4ins
http://www.proteopedia.org/wiki/index.php/1hp1

import propka

fetch 4ins, async=0
propka        OR
propka 4ins   OR
propka 4ins, resi=19.20, resn=ASP.TYR, logtime=_, verbose=yes

import propka
fetch 1hp1, async=0
propka molecule=1hp1, chain=A, resi=305-308.513, resn=CYS, logtime=_

import propka
getpropka source=ID, PDBID=4ins, logtime=_, server_wait=3.0, verbose=yes, showresult=yes

pka atoms are created and renamed for their pka value. That makes it easy to "click" the atom in pymol and instantly see the pka value.

The atoms b value are also altered to the pka value, and the atoms are then spectrum colored from pka=0-14.

The pka value of 99.9 represent a di-sulphide bond, and is colored gold and the sphere size is set a little bigger.

If one wants to see the specified result, the logfile ./Results_propka/_Results.log saves the link to the propka server. Here one can see in an interactive Jmol appp, the interactions to the pka residues.

Use of script

cd /home/tlinnet/test

import propka

### The fastest method is just to write propka. Then the last pymol molecule is assumed and send to server. verbose=yes makes the script gossip mode.
fetch 4ins, async=0
propka

### Larger protein
fetch 1hp1, async=0
propka logtime=_, resi=5-10.20-30, resn=CYS.ATP.TRP, verbose=yes

### Fetch 4ins from web. async make sure, we dont execute script before molecule is loaded. The resi and resn prints the interesting results right to command line.
fetch 4ins, async=0
propka chain=*, resi=5-10.20-30, resn=ASP.CYS, logtime=_

### If there is no web connection, one can process a local .pka file. Either from a previous run or from a downloaded propka webpage result.
### Then run and point to .pka file with: pkafile=./Results_propka/pkafile.pka Remember the dot "." in the start, to make it start in the current directory.
load 4ins.pdb
propka pkafile=./Results_propka/4ins_.pka, resi=18.25-30, resn=cys,

### Some more examples. This molecule has 550 residues, so takes a longer time. We select to run the last molecule, by writing: molecule=1hp1
fetch 4ins, async=0
fetch 1hp1, async=0
propka molecule=1hp1, chain=A, resi=300-308.513, resn=CYS.ATP.TRP, logtime=_, verbose=no, showresult=no
propka molecule=1hp1, pkafile=./Results_propka/1hp1_.pka, verbose=yes

Input paramaters

############################################Input parameters: propka############################################
############# The order of input and changable things:
propka(molecule="NIL",chain="*",resi="0",resn="NIL",method="upload",logtime=time.strftime("%m%d",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no",pkafile="NIL")
# method : method=upload is default. This sends .pdb file and request result from propka server.
## method=file will only process a manual .pka file, and write a pymol command file. No use of mechanize.
## If one points to an local .pka file, then method is auto-changed to method=file. This is handsome in off-line environment, ex. teaching or seminar.
# pkafile: Write the path to .pka file. Ex: pkafile=./Results_propka/4ins_.pka
# molecule : name of the molecule. Ending of file is assumed to be .pdb
# chain : which chains are saved to file, before molecule file is send to server. Separate with "." Ex: chain=A.b
# resi : Select by residue number, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." or make ranges with "-". Ex: resi=35.40-50
# resn : Select by residue name, which residues should be printed to screen and saved to the log file: /Results_propka/_Results.log.
## Separate with "." Ex: resn=cys.tyr
# logtime : Each execution give a set of files with the job id=logtime. If logtime is not provided, the current time is used.
## Normal it usefull to set it empty. Ex: logtime=_
# verbose : Verbose is switch, to turn on messages for the mechanize section. This is handsome to see how mechanize works, and for error searching.
# showresult : Switch, to turn on all results in pymol command window. Ex: showresult=yes
# server_wait=10.0 is default. This defines how long time between asking the server for a result. Set no lower than 3 seconds.
# version=v3.1 is default. This is what version of propka which would be used.
## Possible: 'v3.1','v3.0','v2.0'. If a newer version is available than the current v3.1, a error message is raised to make user update the script.
############################################Input parameters: getpropka############################################
############# The order of input and changable things:
getpropka(PDB="NIL",chain="*",resi="0",resn="NIL",source="upload",PDBID="",logtime=time.strftime("%Y%m%d%H%M%S",time.localtime()),server_wait=3.0,version="v3.1",verbose="no",showresult="no")
# PDB: points the path to a .pdb file. This is auto-set from propka function.
# source : source=upload is default and is set at the propka webpage.
# source=ID, PDBID=4ake , one can print to the command line, the pka value for any official pdb ID. No files are displayed in pymol.
# PDBID: is used as the 4 number/letter pdb code, when invoking source=ID.

Examples

Example 1 - Mutagenesis analysis - part 1

This script was developed with the intention of making analysis of possible mutants easier. For example, the reactivity of Cysteines in FRET maleimide labelling is determined by the fraction of the Cysteine residue which is negatively charged (C-). This fraction is related to its pKa value and the pH of the buffer: f(C-)=1/(10(pK-pH)+1). So, one would be interested in having the lowest possible pKa value as possible. Ideally lower than the pH of the buffer. To analyse where to make the best mutant in your protein, you could do the following for several residues. We do the mutagenesis in the command line, since we then could loop over the residues in the protein.
So, in a loop with defined residues, this could look like the following code. Note, now we are quite happy for the result log file, since it collects the pka for the mutants.

Download: examples/propka_1.pml
This code has been put under version control in the project Pymol-script-repo

<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_1.pml" highlight="python" />

Example 2 - Mutagenesis analysis - part 2

To only loop over surface residues, you might want to find these with the script FindSurfaceResidues.

Download: examples/propka_2.pml
This code has been put under version control in the project Pymol-script-repo

<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_2.pml" highlight="python" />

A little warning though. You need to be carefull about the rotamer you're choosing. It can happen that the first rotamer ends up being in physically non-reasonable contact distance to other residues, so atoms become overlayed. Also, the mutagenesis wizard can have the funny habit of sometimes not adding hydrogens to terminal -C or -N after mutating a residue.

Example 3 - Scan a range of proteins

Could be done with this script

Download: examples/propka_3.pml
This code has been put under version control in the project Pymol-script-repo

<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/propka_3.pml" highlight="python" />

ScriptVersion

Current_Version=20111202

Changelog

  • 20111202
    1. This code has been put under version control. In the project, Pymol-script-repo.
  • 20110823
    1. Fixed some issues with selection algebra of Ligands.
    2. Now colors Ligands automatically to purple scheme.
  • 20110822
    1. Made the naming scheme consistent, so one can work with multiple proteins, and the grouping still works.
    2. Bonds to N-terminal and C-terminal did not show up. Fixed.
    3. If one just write "propka", the "last" molecule in the pymol object list is now assumed, instead of the first. This makes mutagenesis analysis easier.
    4. The pka difference from assumed standard values are now also displayed. Standard values are set to: pkadictio = {'ASP':3.9, 'GLU':4.3, 'ARG':12.0, 'LYS':10.5, 'HIS':6.0, 'CYS':8.3, 'TYR':10.1}
    5. The menu size is made bigger, so it can fit the long names for the bonding partners. There's also a slider that you can drag using the mouse
      --it's the tiny tab between the command line and the movie controls. Drag that left or right.
  • 20110821
    1. The resn function was made wrong, only taking the last item of list. Fixed.
    2. resn= can now also be print to screen/log for ligands like ATP. Ex: resn=CYS.ATP.TRP
    3. Ligands are now also written to the "stripped-file". "./Results_propka/PDB.stripped"
    4. Bonds are now also made for Ligands.
  • 20110820
    1. If one points to a result .pka file, then "method" is automatically set to "method=file".
    2. Added the ability for pka values for ligands
    3. Bonds are now generated for the pka atoms.
    4. The color scheme is changed from "rainbow" to "red_white_blue". This is easier to interpret.
    • CC: COULOMBIC INTERACTION. Color is red.
    • SH: SIDECHAIN HYDROGEN BOND. Color is brightorange.
    • BH: BACKBONE HYDROGEN BOND. Color is lightorange.
  • 20110817
    1. If just invoking with "propka", it will select the first molecule. And now it is possible also to write. "propka all".
    2. Removed the "raise UserWarning" if the script is oudated. Only a warning message is printed.
  • 20110816
    1. Made the execution of the pymol command script silent, by only using cmd.API. This will raise a Warning, which can be ignored.
    2. Built-in a Script version control, to inform the user if the propka script is updated on this page
    3. The alternate attribute for the labeling atoms are reset. It was found pymol objected altering names for atoms which had alternate positions/values.
    4. Reorganized the input order, which means that: molecule=all is default.

Known bugs

  • Bonds can be multiplied from amino acids to Ligands like ZN or ATP. Assume the shortest bond to be correct.
    1. ZN: This is caused, since ZN has no ID number and when there are several in the same chain. This can be reproduced for 1HP1, bond: A41ZNCC. Here it shows to bonds, where only the shortes is correct. No fix possible.
    2. ATP: This is caused, since propka sometimes eats the ending of the atom name. In the .pdb file is written O3', which propka represents like O3. Therefore a wildcard "*" is generel inserted, which can cause multiple bonds to the ATP molecule. This can be reproduced for 1HP1, bond: A504ATPSH. Here multiple bonds are made to all the O3*,O2* atoms. No fix possible.
  • The propka server sometimes use another naming scheme for Ligands. These Ligands will not be pka labelled or shown in pymol. The results will still downloaded to "/.Results_propka/file.pka"
    1. This can be reproduced with 1BJ6. Here the propka webpage predicts the pka values for the ligands: AN7,GN1,CN3,CO2,GO2, but the .pdb file names these ligands: DA,DA,DC,DG.
  • Alternative configurations of a Ligand is at the moment a problem, and will not be shown. For example 1HXB and the ligand ROC.
    The script extraxt AROC and BROC from pymol, which does match with ROC in the .pka file. Try save the protein with only one configuration of the Ligand.
    • >In pymol:
      fetch 1hxb, async=0
      create 1hxbA, 1hxb and not alt B
      save 1hxbA.pdb, 1hxbA
    • >Quit pymol
    • >Manually replace with text editor in .pdb file "AROC" with " ROC" Remember the space " "!
    • >Then in pymol
      load 1hxbA.pdb
      import propka
      propka verbose=yes