RE: [PyMOL] RE: povray image mapping and default pigments

I'm glad you solved your problem, but more importantly when are we going to get to see this picture of an easter bunny on some wood-textured rendition of a half-submerged albumin glowing softly in the warm lights of a double sunset over an infinite lake lapping at the shores of a checkered bea

[PyMOL] RE: povray image mapping and default pigments

To answer my own question...instead of entirely taking out the pigment{blah blah blah} statements from the texture_lists in the povray input as used to work, I found that in this case replacing them with "pigment {}" statements was still a permissible syntax and also allowed a #default pigment decl

[PyMOL] povray image mapping and default pigments

This is for the povray gurus out there... Occasionally I muck around with the time-consuming practice of trying to map pictures onto molecular surfaces with povray. I had this working to some extent, but something has changed (I think with the povray file format produced by pymol & make_pov where

[PyMOL] RE: filter for edit settings window

Hi Michelle, In case no one's mentioned it yet, Zac Panepucci has contributed a grepset.py script which, after being run, allows you to type "grepset x" to see all settings (and their values) associated with whatever x is. It's not directly integrated into the pymol distribution but pretty

Re: [PyMOL] another question about ca trace model.

Hi, Noinaj: Thanks for your suggestion. I feel it is not the assignment problem. I tried using "cartoon tube" to show the 2nd structure and the strand part can showed up. Then I painted the molecule according to the secondary structure by using util.cbss("morphy_01","red","yellow","green") and

Re: [PyMOL] isomesh for electrostatic potential

On Tue, 18 Apr 2006, Chun Tang wrote: Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of

[PyMOL] isomesh for electrostatic potential

Dear PyMoler, In the pymol apbs tool, there is an option to show the negative/positive isosurface (not the molecular surface) upon loading an electrostatic map. My question is if there is a way to show the electrostatic potential surface as mesh instead of solid surface, also if it is possible to

RE: [PyMOL] anybody have experience with the "get_area" command?

Hi Tom, There are some pitfalls with get_area that have led me to recommend against its use until we can prepare some more comprehensive documentation and examples for its use. If you have other tools for measuring areas, then I recommend using them instead. If not, then here is a partial exa

[PyMOL] anybody have experience with the "get_area" command?

Does it work? We're running version 0.99rc6 on both windoze and linux (RHEL,WS4) and the "get_area" command returns nothing (no error, no value). I've tried this with a number of situations, including loading a single object with a single protein chain and issuing "get_area all", "get_area n+

Re: [PyMOL] mutations

Orla, This is simply, for the most part. Here is what I do. Load your *.pdb file. Then under WIZARD in the menu bar, select MUTAGENESIS. Then pretty much, follow directions. In the PyMOL VIEWER window, it will ask you to ' pick a residue.' Once you pick a residue, select the type of resi

[PyMOL] (small) Pymol feature request--filter for edit settings window

While we're discussing ways to make our favorite program a little better, I had an idea I thought I'd throw out there... While making some figures the other day, I found myself scrolling endlessly through the edit settings menu (under Setting --> Edit All) a number of times, mostly to locate a

[PyMOL] mutations

Hi all I'm a newbie to Pymol and so far have been very impressed. However I have tried to mutate some residues in my structure and have hit a brick wall. Has anyone done this with pymol and let me know how to do it? Regards Orla Dr.Orla O'Sullivan Research Officer Biotechnology

Re: [PyMOL] another question about ca trace model.

Tiger, Unfortunately I don't have much experience with this procedure. But one thing came to mind, you can manually assign secondary structure within DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have generated for the morph, but if nothing else works, you could try manua

[PyMOL] another question about ca trace model.

Hi, there: I am trying to make a movie following the intruction at http://ginsberg.med.virginia.edu/~dcoop/Help/morph.html From Lsqman, I got a serial of PDB files morphing between two conformations. These PDB files contain only alpha carbon and non-hydrogen side-chain atoms. Then I used DSSP t