[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

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

[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

[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

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

[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+c,

[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] 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

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 the

[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

[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