This is a read-only mirror of pymolwiki.org
Difference between revisions of "Peptide Sequence"
Jump to navigation
Jump to search
m (11 revisions) |
|||
| (7 intermediate revisions by 3 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'''. |
| + | |||
| + | 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 02:00, 28 March 2014
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)