Re: [PyMOL] Embedding pymol

While I've got your attention Is it possible to embed a pymol window into a bigger independent application? I've written a PymolQt C++ class that tries to put pymol inside a QWidget and replaced the glut input functions by Qt stuff. I had to do some changes to pymol to make this work an

[PyMOL] Delete atoms out of unit cell box

Is there an easy way to delete all atoms that fall outside of the unit cell after doing a symexp? I'm doing it by hand which takes too long and is error prone... Thanks in advance.

Re: [PyMOL] Delete atoms out of unit cell box

I have tweaked a script by Tsjerk Wassenaar that can remove atoms out of a unit cell. I have encountered 2 problems. First is even though i knew the Atom i wanted to remove from the model i had no easy way to do it because i didn't found any unique identifier for an Atom in the atom class. So w

[PyMOL] Problem with Save Session

If you open a session, then open another session and do "Save Session" it will overwrite the file of the first session with the second session and it won't even issue a warning, which was really not what was i expected to when i did the Save Session. I think something like a variable that indica

Re: [PyMOL] code for calculating surface area

On Mon, 19 Jul 2004 18:27:18 +0930, Michael Sorich wrote: Hi, Could someone point me to the code used to calculate surface area (i.e. code to calculate surface dots and the code to find the area of the dots)? I presume that it is somewhere in the PyMOL\modules\pymol or PyMOL\modules\chempy m

Re: [PyMOL] Pymol segmentation fault - fedora core 1

On Mon, 26 Jul 2004 10:40:47 +0100, Roger Dodd wrote: Hi everyone, I've recently updated to the 0.97 release of pymol and although it ran fine to start with, it's now generating a segmentation fault. I installed from the * pymol-0_97-bin-linux-libc6-i386.tgz*

Re: [PyMOL] electron density maps

On Sun, 08 Aug 2004 17:57:00 -0400, christopher faehnle wrote: I am a new pymol user and am trying to load an electron density map (ccp4 format). When I do this nothing happens. Any suggestions, tips, etc would be appreciated. The map probably loads just fine (there should be a new obj

[PyMOL] Hidden files in file browser

I think it would be nice if pymol didn't show the hidden files in the file browser, as there are usually quite a lot of those in a user home. -- All generalizations are false, including this one. -- Mark Twain

Re: [PyMOL] Swissprot

Is there a PDB parser class somewhere for reading in the PDB files? layer2/ObjectMolecule2.c:ObjectMoleculePDBStr2CoordSet() is probably a good place to start. -- All generalizations are false, including this one. -- Mark Twain

Re: [PyMOL] List participation commentary......

On Wed, 17 Nov 2004 10:48:49 -0800 (PST), Thomas Stout wrote: Hi All -- Recently I've noticed a growing number of questions being posed to the PyMOL mailing list that never seem to get responses. I infer from this that one or both of two things are happening: either 1) list members that kn

Re: [PyMOL] rendering pictures to publish

For OpenGL-based images, you're limited by the maximum dimensions of your display. Hopefully that restriction will be eliminated before too much longer... Actually the restriction is how big a window your window manager supports, which can be bigger than your display. The png commands still ca

Re: [PyMOL] question abut loading xplor map

On Fri, 14 Jan 2005 11:53:00 -0500, Qun Wan wrote: Hi, everyone: I have a simple question about loading the electron density map. I have generated x-plor format map and try to load it into pymol. However, pymol only shows me the unit cell, not the map. Does anyone know how can I "see" the map,