[PyMOL] Fedora 3 problem

I recently upgraded to Fedora Core 3 and have been having some strange problems with PyMOL. Molecules look fine when rendered as lines, sticks or mesh, but spheres, surfaces, and sometimes cartoons only appear for half the molecule. See the following page for examples of this. I've also posted v

[PyMOL] Connectivity Problem for Visualizing Pseudo-structure

I am using Pymol to visualize a "pseudo polymer" generated by some brownian dynamics code. We take the coordinate files generated by our simulation and convert them into a PDB file using the hetatm representation and having explicit connections defined with conect. For example: HETATM

RE: [PyMOL] orient the molecule

This is tricky because the view matrix isn't quite the same format as the coordinates translation matrix. Here's some code that will do what you want: # transform selection coordinates by the camera view cv=list(cmd.get_view()) cmd.transform_selection("all", \ cv[0:3]+[0.0]+ \ cv[3:6]+[0.0]

Re: [PyMOL] orient the molecule

Thanks! But translate[x,y,z] only translate the molecule. What I want is to put longest length of molecule in the X axes, the second Y axes, the third z axes. Just like what orient command does which change the view of camera but not the coordinates. Now I want the coordinates also change afte

Re: [PyMOL] atom number labels?

Hi Xavier, * Xavier Deupi [2005-04-20 10:49] wrote: > > I'm a new user, so my question is *extremely* basic... > > I want to display atom numbers as labels, but this property does not > appear in the list of properties that can be displayed using the command > 'label'. > > How can I do it?

Re: [PyMOL] orient the molecule

Hi, I think that you should use translate[x,y,z] to change the coordinates of your molecule bye andrea 2005/4/21, Bingding Huang : > Hi, > When I try "orient" command to orient the molecule, the camera changes > but the coodinates don't change. > I wonder whether it is possible that when I orie

[PyMOL] orient the molecule

Hi, When I try "orient" command to orient the molecule, the camera changes but the coodinates don't change. I wonder whether it is possible that when I orient the molecule the coodinates also change. Thanks Bingding

Re: [PyMOL] BEWARE: recent nVidia drivers

Yes, I've also downgraded from the 7174 driver to the 6629 driver because of huge performance problems with another open source density fitting program. We are using Scientific Linux, another RedHat Enterprise Clone, as operating system. Cheers, Dirk. Warren DeLano wrote: Folks, You may h