Peptide Sequence - Revision history

Pyadmin: 11 revisions

2014-03-28T02:00:29Z

11 revisions

Speleo3: mention fab and Builder

2011-08-04T07:47:15Z

mention fab and Builder

Rlc at 15:16, 21 January 2009

2009-01-21T15:16:56Z

Tmwsiy: /* Other Sources */

2005-09-16T13:34:07Z

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2005-09-16T13:33:39Z

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2005-09-16T13:33:04Z

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Tmwsiy: /* Other Sources */

2005-09-16T13:32:48Z

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2005-09-16T13:32:16Z

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2005-09-16T13:31:38Z

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New page

=Building a Peptide Sequence From Hand=
There are more than one method in PyMol for building a peptide sequence from hand. First, you may simply hold down the '''alt''' ('''option''' on Mac) key and type in the one-letter code for the sequence. Secondly, you can write a script like the following
<source lang="python">
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
</source>
which will build the amino acid sequence "DCAHWLGELVWCT".

==Other Sources==
Robert Campbell has notified us of [http://adelie.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) also [[RotamerToggle]] can set the sidechains to different rotamers or specific side-chain angle sets.

@@ Line 7: / Line 7: @@
 ==Other Sources==
-Robert Campbell has notified us of [http://adelie.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'''.
+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)

@@ Line 9: / Line 9: @@
 Robert Campbell has notified us of [http://adelie.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)  (by Dan Kulp)
+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. (by Dan Kulp)
+In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (Dan Kulp)

@@ Line 9: / Line 9: @@
 Robert Campbell has notified us of [http://adelie.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)  (by me, Dan Kulp)
+Also check out [[CreateSecondaryStructure]] , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc)  (by Dan Kulp)
-In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (by me, Dan Kulp)
+In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (by Dan Kulp)

← Older revision		Revision as of 13:33, 16 September 2005
Line 10:		Line 10:

	Also check out [[CreateSecondaryStructure]] , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) (by me, Dan Kulp)		Also check out [[CreateSecondaryStructure]] , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) (by me, Dan Kulp)
		+
	In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (by me, Dan Kulp)		In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (by me, Dan Kulp)

← Older revision	Revision as of 02:00, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
-=Building a Peptide Sequence From Hand=
+== Building a Peptide Sequence From Hand ==
-There are more than one method in PyMol for building a peptide sequence from hand.  First, you may simply hold down the '''alt''' ('''option''' on Mac) key and type in the one-letter code for the sequence.  Secondly, you can write a script like the following
 <source lang="python">
 for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
 </source>
 ==Other Sources==
 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'''.