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

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

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

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)

[PyMOL] Creating PDB files from Primary Sequence

Hello, This may be slightly off-topic, but I was wondering whether PyMol would allow one to enter a peptide sequence (generally short in length) to create a template structure that can then be used for structural refinements (minimizations, etc.) elsewhere. If PyMol cannot do this, is

RE: [PyMOL] Creating PDB files from Primary Sequence

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.

Re: [PyMOL] Creating PDB files from Primary Sequence

Hi James, Sounds like you want a homology model type set up, ie generate coordinates based on a template. Modeller can do this and an easier way is via the swissmodel http://swissmodel.expasy.org//SWISS-MODEL.html If however you want a relatively random structure then pymol _can_ do this.

Re: [PyMOL] Creating PDB files from Primary Sequence

Thanks for the prompt responses, Warren and Joe! Works like a charm! Now, I just wish that my Kensington Expert Mouse could function as a true three button mouse...is there a keystroke that mimics the third mouse button? Thanks again, james