Peptide Sequence: Difference between revisions
Jump to navigation
Jump to search
m (→Other Sources) |
(mention fab and Builder) |
||
| (5 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
=Building a Peptide Sequence From Hand= | == Building a Peptide Sequence From Hand == | ||
There are more than one method in | |||
There are more than one method in PyMOL for building a peptide sequence from hand. | |||
* Simply hold down the '''alt''' ('''option''' on Mac) key and type in the one-letter code for the sequence. | |||
* Use the [[fab]] command | |||
* Use the [[Builder]] in "Protein" mode | |||
* You can write a script like the following which will build the amino acid sequence "DCAHWLGELVWCT". | |||
<source lang="python"> | <source lang="python"> | ||
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa)) | for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa)) | ||
</source> | </source> | ||
==Other Sources== | ==Other Sources== | ||
Robert Campbell has notified us of [http:// | |||
Also check out [[CreateSecondaryStructure]] , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) | Robert Campbell has notified us of [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol his two scripts] to solve the problem. You can apparently specify phi/psi angles, too. Look for '''build_seq.py''' and '''build_seq_phi_psi.py'''. | ||
In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. | |||
Also check out [[CreateSecondaryStructure]] , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) (Dan Kulp) | |||
In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (Dan Kulp) | |||
Latest revision as of 02:47, 4 August 2011
Building a Peptide Sequence From Hand
There are more than one method in PyMOL for building a peptide sequence from hand.
- Simply hold down the alt (option on Mac) key and type in the one-letter code for the sequence.
- Use the fab command
- Use the Builder in "Protein" mode
- You can write a script like the following which will build the amino acid sequence "DCAHWLGELVWCT".
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
Other Sources
Robert Campbell has notified us of his two scripts to solve the problem. You can apparently specify phi/psi angles, too. Look for build_seq.py and build_seq_phi_psi.py.
Also check out CreateSecondaryStructure , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) (Dan Kulp)
In addition, Rotamer Toggle can set the sidechains to different rotamers or specific side-chain angle sets. (Dan Kulp)