Mcsalign: Difference between revisions

	Included in psico; This command or function is available from psico, which is a PyMOL extension.
Module	psico.mcsalign

Latest revision as of 09:43, 27 May 2020

mcsalign aligns two small-molecule selections based on Maximum-Common-Substructure.

mcsalign is available from the psico package and requires rdkit and csb.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c rdkit rdkit
conda install -c speleo3 csb

mcsalign mobile, target [, mobile_state [, target_state
    [, cycles [, timeout [, method ]]]]]

mobile = str: atom selection of mobile object
target = str: atom selection of target object
mobile_state = int: object state of mobile selection {default: -1 = current state}
target_state = int: object state of target selection {default: -1 = current state}
cycles = int: number of weight-refinement iterations for weighted RMS fitting {default: 5}
timeout = int: MCS search timeout in seconds {default: 10}
method = indigo or rdkit {default: check availability}

Align Cytochrome C and Hemoglobin based on their Heme moieties:

fetch 3zcf 4n8t, async=0
zoom /4n8t//A/HEM, animate=2, buffer=3

import psico.mcsalign
mcsalign /3zcf//A/HEC, /4n8t//A/HEM

Align a set of small molecules to a reference

fetch ala ile arg trp met
extra_fit *, ala, method=mcsalign

@@ Line 14: / Line 14: @@
   conda install -c schrodinger pymol-psico
   conda install -c rdkit rdkit
-  conda install -c bioconda csb
+  conda install -c speleo3 csb
-On Windows, replace the last line with:
+== Usage ==
-  pip install -i https://pypi.anaconda.org/pypi/simple csb
+  mcsalign mobile, target [, mobile_state [, target_state
+     [, cycles [, timeout [, method ]]]]]
+== Arguments ==
+* '''mobile''' = str: atom selection of mobile object
+* '''target''' = str: atom selection of target object
+* '''mobile_state''' = int: object state of mobile selection {default: -1 = current state}
+* '''target_state''' = int: object state of target selection {default: -1 = current state}
+* '''cycles''' = int: number of weight-refinement iterations for weighted RMS fitting {default: 5}
+* '''timeout''' = int: MCS search timeout in seconds {default: 10}
+* '''method''' = indigo or rdkit {default: check availability}
 == Example ==
@@ Line 29: / Line 40: @@
   import psico.mcsalign
   mcsalign /3zcf//A/HEC, /4n8t//A/HEM
+Align a set of small molecules to a reference
+ fetch ala ile arg trp met
+ extra_fit *, ala, method=mcsalign
 == See Also ==
@@ Line 34: / Line 50: @@
 * [[align]]
 * [[pair_fit]]
+* [[LigAlign]]
 [[Category:Script Library]]
 [[Category:Structural_Biology_Scripts]]