From: Reece H. <re...@in...> - 2004-06-15 01:24:25
|
Amigos- Does anyone know of a way to embed coordinates within a pymol script? I'd like to be able to programmatically generate a self-contained pymol script which loads the embedded coords, defines selections, and highlights selections with colors/rendering. The immediate use for this is to write a CGI which returns a pymol script over http. Thus, the coordinates cannot be expected to exist on the client side (and, in my case, are model coordinates, not a PDB entry). RasMol provides the 'load pdb inline' command which loads a PDB file which appears at the end of the script. I'd like something similar for PyMOL, preferably generalized to multiple structures. An extension to load in which the filename could be '<<TAG' a la sh or perl (gasps heard on the list) would do the trick. Thanks, Reece -- Reece Hart, Ph.D. rk...@ge..., http://www.gene.com/ Genentech, Inc. 650-225-6133 (voice), -5389 (fax) Bioinformatics and Protein Engineering 1 DNA Way, MS-93 http://www.in-machina.com/~reece/ S. San Francisco, CA 94080-4990 re...@in..., GPG: 0x25EC91A0 |
From: Michael G. L. <ml...@um...> - 2004-06-15 02:20:19
|
> Does anyone know of a way to embed coordinates within a pymol script? Have you seen cmd.read_pdbstr() and its companion cmd.get_pdbstr()? -michael > I'd like to be able to programmatically generate a self-contained pymol > script which loads the embedded coords, defines selections, and > highlights selections with colors/rendering. The immediate use for this > is to write a CGI which returns a pymol script over http. Thus, the > coordinates cannot be expected to exist on the client side (and, in my > case, are model coordinates, not a PDB entry). > > RasMol provides the 'load pdb inline' command which loads a PDB file > which appears at the end of the script. I'd like something similar for > PyMOL, preferably generalized to multiple structures. An extension to > load in which the filename could be '<<TAG' a la sh or perl (gasps heard > on the list) would do the trick. > > Thanks, > Reece > -- > Reece Hart, Ph.D. rk...@ge..., http://www.gene.com/ > Genentech, Inc. 650-225-6133 (voice), -5389 (fax) > Bioinformatics and Protein Engineering > 1 DNA Way, MS-93 http://www.in-machina.com/~reece/ > S. San Francisco, CA 94080-4990 re...@in..., GPG: 0x25EC91A0 > > |
From: Reece H. <re...@in...> - 2004-06-15 04:04:58
|
On Mon, 2004-06-14 at 19:20, Michael George Lerner wrote: > Have you seen cmd.read_pdbstr() and its companion cmd.get_pdbstr()? I remembered a discussion about such functionality several months ago (at least), but couldn't remember whether it was a feature request or implemented. Anyway, I got it working. Thanks, Michael. -Reece -- Reece Hart, http://www.in-machina.com/~reece/, GPG:0x25EC91A0 |
From: Reece H. <re...@in...> - 2004-06-16 23:17:33
|
On Mon, 2004-06-14 at 21:04, Reece Hart wrote: > On Mon, 2004-06-14 at 19:20, Michael George Lerner wrote: > > > Have you seen cmd.read_pdbstr() and its companion cmd.get_pdbstr()? I thought I'd post this example, just in case anyone else cares about this: delete all cmd.read_pdbstr("""HEADER CREATED BY CONVERTPROSPECT 27-JAN-02 2tnf \ REMARK 1 \ ATOM 1 N PRO A 9 1.895 67.213 -38.182 1.00 0.00 N \ ATOM 2 CA PRO A 9 1.703 68.680 -38.402 1.00 0.00 C \ ... ATOM 1153 C GLY A 157 6.927 59.108 -38.901 1.00 6.00 C \ ATOM 1154 O GLY A 157 6.700 59.292 -37.676 1.00 6.00 O \ TER 1155 GLY A 157 \ MASTER \ END \ ""","2tnfa") hide all show cartoon color grey ... By the way, one of the troubles I had was the PyMOL requires a .pml suffix for scripts. I was able to coerce this with the following http header: Content-type: application/x-pymol Content-disposition: attachment; filename=2383.pml Cheers, Reece -- Reece Hart, http://www.in-machina.com/~reece/, GPG:0x25EC91A0 |