Re: [PyMOL] Creating PDB files from Primary Sequence
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 Associatephone: 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
Re: [PyMOL] Creating PDB files from Primary Sequence
Hi pymolers is it possible to generate a template nucleic acid structures from sequence in pymol? Blanton Tolbert PhD Candidate University of Rochester Biophysics and Structural Biology 575 Elmwood Ave Rochester, NY 14642 Blanton Tolbert PhD Candidate University of Rochester Biophysics and Structural Biology 575 Elmwood Ave Rochester, NY 14642
Re: [PyMOL] Creating PDB files from Primary Sequence
Hi, I just felt like making a correction to the language I used. It seems a few words went missing! * Robert Campbell r...@post.queensu.ca [2005-08-11 11:28] wrote: 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 I meant to say that I had already written a script to do this, but had not put it on my web site. It is there now. It does the same sort of operation, but makes it easier to specify the exact phi/psi angles to use. Brain is now re-engaged, before typing commences. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 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
Re: [PyMOL] Creating PDB files from Primary Sequence
Hi Blanton, * Blanton Tolbert blanton_tolb...@urmc.rochester.edu [2005-08-11 11:53] wrote: Hi pymolers is it possible to generate a template nucleic acid structures from sequence in pymol? Not as far as I've found. There are other programs that can do this: B (aka Biomer) (http://www.scripps.edu/mb/case/Biomer/) NAMOT (http://namot.lanl.gov/) 3DNA (http://rutchem.rutgers.edu/~olson/3DNA/) Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 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
