Re: [PyMOL] problem installing

Hi again, I tried installing from the renamed directory and I got the same error message. Thanks again -Greg From: "Warren DeLano" To: Subject: Re: [PyMOL] problem installing Date: Tue, 20 Jun 2006 15:48:36 -0700 > Hi all, > > I recently got a new machine and for whatever reason I am > u

[PyMOL] problem installing

Hi all, I recently got a new machine and for whatever reason I am unable to install any of the versions of PyMol (0.99rc6, rc3, 0.98) on this new machine. I am running Windows XP Professional. Upon unzipping the file, i run the setup.exe and get the following error message: C:\pymol1\pymol

[PyMOL] Surface representations

Hi Pymolers, I am looking at a protein molecule in surface representation. Is there a way to have the surface be "closer" to the atoms/sidechains, i.e. not as bulky? This is just for illustration sake. Thanks! -Greg

[PyMOL] residue replacements / modified amino acids

Hi everyone, Two part'er here: 1. Is there a simple way in pymol to replace an amino acid in a given structure?  If so, how can you then check (other than visibly) if there are any glaring steric/electrostatic clashes? 2. Is there a way of incorporating non-native or modified amino acids into the p

RE: [PyMOL] saving images

already doing it, you should >raytrace your scene by hitting the "ray" button before you write out >your image file. >Scott > >On Sep 13, 2004, at 8:03 AM, Greg C wrote: > >>Hello all, >> >>I'm having a problem saving the pymol output as an image. 

[PyMOL] saving images

Hello all, I'm having a problem saving the pymol output as an image.  I'm working with asingle alpha helix (~25 residues) with the residues displayed as lines, the backbone as a ribbon, and one or more of the residues as spheres.  When i go to save the image, the lines are no longer present in the

[PyMOL] Coloring Amino acids

Hi all, I was wondering if there is a way to color all of a specific type of amino acid the same color in a pdb file (i.e. all the Leucines colored green, all the lysines blue, etc).  Thanks -Greg   Greg Caputo Ph.D. Postdoctoral Research Associate Department of Medical Biochemistry & Genetics

[PyMOL] hiding one chain in pymol

I am having difficulty in displaying only one of 2 chains in a PDB file.  The file is basically a homodimer, but I want to only display one of the monomers.  I can hide one of the two chains by selecting it and then hiding it, but the problem is that I am left with one chain and a collection of pin