RE: [PyMOL] modifying atom coordinates

Yes, but what happens when, for example, I take a lysine residue, and connect a glutamine residue? Shouldn't all the atoms have different coordinates from when they are stand alone, based on the forces from nearby atoms? Does pymol account for this as residues are added, or is there a command or wi

RE: [PyMOL] Can't load maps anymore!

Raji, Thanks for sending along the map. PyMOL can still read XPLOR maps just fine -- what's wrong in this situation is that the map doesn't cover the space of the molecule. To see this: load buckleddna.pdb load polya.map, polya, format=xplor zoom enable polya That last command will dra

[PyMOL] Can't load maps anymore!

Hi Everyone, I am trying to load a CNS map around this object "buckleddna". The map doesnt load. I tried to convery it to *.xplor format using Mapman and retry. That doesnt help either. Any suggestions ? Executive: object "buckleddna" created. PyMOL>load polya, polya, 1, xpl

RE: [PyMOL] A couple of movie questions

> First up: Is there any way to tell PyMol *not* to change its view when > loading a > PDB file set auto_zoom,0 > Secondly: Below is an example of a small hack I have written when making > one > particular movie. This one overlays two molecules related by a 2-fold > axis by > doing a simple rota

RE: [PyMOL] negative images

Jules, I think there's a problem with the alpha channel with certain PyMOL images, which means that portions end up being transparent when they shouldn't be. A quick workaround is to put a black rectangle behind the PyMOL image, but I'd like to get a little more information about when the

Re: [PyMOL] energy minimisation in python

On Thu, Sep 18, 2003 at 05:48:56PM +0100, Paulo Martel wrote: > On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote: > > > > And about Ghemical project? > > > > Ghemical is not a Python project, it is a GNU GPL package written in C FWIW, ghemical is written in C++. > using the Gtk to

Re: [PyMOL] energy minimisation in python

On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote: > > And about Ghemical project? > Dear Alan, Ghemical is not a Python project, it is a GNU GPL package written in C using the Gtk toolkit, with the GtkGlarea widget providing OpenGl accelerated graphics in a Gtk window. It provides

Re: [PyMOL] energy minimisation in python

And about Ghemical project? http://www.bioinformatics.org/ghemical/ On Wed, 17 Sep 2003 pymol-users-requ...@lists.sourceforge.net wrote: > On Wed, Sep 10, 2003 at 10:57:59AM +0300, Dr. Daniel James White PhD wrote: > > Warren , > > > > Are you aware of the python MMTK molecular dynamics package?

Re: [PyMOL] A couple of movie questions

Hi Stephen, * Stephen Graham [2003-09-18 21:02] wrote: > First up: Is there any way to tell PyMol *not* to change its view when > loading a > PDB file? For viewing in general, and for movies w/ morphs (etc.) in > particular > it would be nice to not have to re-set the view each time I load a n

[PyMOL] A couple of movie questions

Hi all, I have just a couple of questions with regards to movie making in PyMol. Well, they are more niggling annoyances (holes in my knowledge?) which I can work around if needs be, but would rather not have to. First up: Is there any way to tell PyMol *not* to change its view when loading a PD

[PyMOL] negative images

Hello Pymol types, I have a quick question- has anyone had any trouble printing out images in word using version 0.9 in word XP? The images look fine when viewed on the screen yet when it comes to printing them out they appear as negatives, including the white background which becomes black.