Re: [PyMOL] image resolution

cmd.get_povray. I am assuming that python doesn't understand get_povray without being told to? So how do I tell it to? Or whatever. Bronwyn Carlisle Biochemistry Department University of Otago Dunedin New Zealand Tel 64 3 479 7704 ::end B. Carlisle quote:: -- Jacob Corn Gladstone Institute

[PyMOL] Separate surfaces

Hi all, It's possible that I've run into a bug/undocumented feature, but I'd like to see if anyone has a solution to the following problem. I'm working on a movie script that will (in part) make two separate surfaces for each subunit in a dimer (excluding a drug bound between the subunits),

[PyMOL] v0.95 breaking pymolrc

I started PyMOL from). However, after updating to v.095 the parser can no longer find these files. I've tried calling the files as C:\thing\thing\thing.py and so on, but so far, no luck. Is this a bona-fide bug or have others run into this problem and found a solution? Jacob -- Jacob Corn UC

Re: [PyMOL] showing sequence conservation on the surface

with the B-factor column replaced with relative conservation. If you open this PDB and run the color_b script (http://adelie.biochem.queensu.ca/~rlc/work/pymol/) with a two-color ramped gradient (eg - white-green) you'll have a very intuitive view of potential hot spots. Enjoy! -- Jacob Corn UC Berkeley

Re: [PyMOL] rtools from .pml scripts

[...] pymol launches as usual after that, and I also can use rtools commands without problems within it. ideas? thanks, christian -- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-8893 Fax: 510-643-9290 jc...@uclink.berkeley.edu

Re: [PyMOL] rtools from .pml scripts

-- Jacob Corn UC Berkeley - Berger Lab Lab: 510-643-8893 Fax: 510-643-9290 jc...@uclink.berkeley.edu

[PyMOL] Plugins segfaults

Debian boxes set up identically to the working Debian box. Since this is clearly not the case, we're looking for clues about how PyMOL interfaces with the plugin scripts. That is, where should we start looking for broken things on one Debian box versus another? Jacob -- Jacob Corn UC Berkeley

Re: [PyMOL] Problem with pml script and png command

Hi Gregori, If you are just saving an image without rendering it (eg - png without ray) then the raw OpenGL output is sent to the file. Meaning, if you have the command line/menu window open in front of the graphics window, your images will be cut off where they overlap. This might or might

[PyMOL] Creating one object from two

just the two objects I want and try create objectx, (all) the problem still occurs. Since this has happened with two independent pdbs, I'm wondering if any one else has run into the problem. If so, is there a workaround? Jacob -- Jacob Corn UC Berkeley - 315 Hildebrand Hall jc

Re: [PyMOL] Creating one object from two

and collating them. I don't know about anyone else, but I think that task would be nice to do in PyMOL. Would it be hard to alter the create command so that it makes sure there are no clashes between atom/chain/etc. naming? Jacob Robert Campbell wrote: Jacob, * Jacob Corn jc

Re: [PyMOL] SHARP map not opening in PyMOL

format), but it does not open the map. According to the pymol users manual, it should open ccp4 format maps. Has anyone had this problem before, and what can I do to get around it? Thanks! Sivaram Mylavarapu. -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc

Re: [PyMOL] B W Molscript David Goodsell look-alike modes

mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Jacob Corn The Berger Lab UC Berkeley - Molecular and Cell Biology jc...@uclink.berkeley.edu phone: 510-643-8893 fax: 510-643-9290

Re: [PyMOL] symmetry and density maps

Hi Richard, Unfortunately, PyMOL will not do symmetry expansion. You could use ccp4s mapmask to extend an existing map around a molecule. An example script is below (BORDER is the number of angstroms around the input model to calculate the new map) mapmask \ XYZIN model.pdb \ MAPIN

[PyMOL] problems using selection wildcards?

gets backbone amides. color nitrogen, name NH+ (or NH*) does nothing. This seemed to work reliably in the last release. For the nonce I'm using the symbol selector, but I found atom selection wildcards oh-so-convenient... Am I doing something wrong? Jacob -- Jacob Corn The Berger Lab UC

[PyMOL] select/deselecting objects via script?

I'd like to write a jiffy that binds the up and down arrow keys to move up/down the list in the object/selection pane. I'd like (for example) pressing the down arrow to equate to clicking the currently active object (thus hiding its representation) and clicking the next object down (thus

Re: [PyMOL] select/deselecting objects via script?

OK, I'm feeling a little silly now... I found enable/disable (sorry for not rtfm'ing closely). But is there a way to get whether an object is currently dis/enabled? Jacob On Apr 22, 2009, at 9:04 AM, Jacob Corn wrote: I'd like to write a jiffy that binds the up and down arrow keys