Hi folks, * Warren DeLano <war...@delsci.com> [2005-08-10 16:41] wrote: > James, > > > PyMol would allow one to enter a peptide sequence (generally short in > > length) to create a template structure that can then be used > > Just hold down ALT/OPTION and type in the peptide sequence. The > numbering will be arbitrary, but at least you'll have something to work > with. > > >From a script, you can hack this as follows: > > for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
I had already written a script to do this, but making it easier to specify the exact phi/psi angles to use. I borrowed bits of the editor.py file already within PyMOL and created a new front end to it. There are two versions. build_seq.py builds a stretch of residues with the same phi/psi angles: build_seq QGAADLESLGQYF, ss=helix or build_seq QGAADLESLGQYF, phi=-75, psi=-35 while build_seq_phi_psi.py reads a file containing the sequence and phi/psi angles to use for each residue: build_seq_phi_psi filename where filename contains lines like: Q 30. 50. G -57. 60. A 120. 30. A -50. 60. D -57. 60. L -119. 113. E -119. 113. For both scripts a new object named for the first residue is created (gln in this case), unless you've picked an atom to build from, thus creating a pk1 selection. Then the sequence is added onto that atom. Both scripts are downloadable from my PyMOL scripts site (under the section called "modelling"). http://adelie.biochem.queensu.ca/~rlc/work/pymol Cheers, Rob -- Robert L. Campbell, Ph.D. <r...@post.queensu.ca> Senior Research Associate phone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
