Re: [PyMOL] pymol

Hi Jason, I removed the fglrx driver, so there is none output of glxgears and glxinfo now. If you want, I can reinstall and test it again. Cause at present the Graphic driver on my laptop is lack. Before I tried twice cause pymol not work so I aborted installation this driver. Last time the inst

Re: [PyMOL] pymol

Hi Zhao, Here's what I had to do when I switched from my normal NVidia card to this test ATI FirePro v8800 on my openSUSE 11.4 machine. First, I uninstalled the nvidia-based kernel and installed the generic openSUSE kernel. Then, I found and installed the fglrx drivers (fglrx64_xpic_SUSE114-8.83

[PyMOL] suface display protein-protein interactions...residues getting bleached.

Hello Pymol users I went to a recent Crystallography workshop and noticed everyone had great pictures of their protein-protein binding interface. One molecule had a surface representation while another did not. The interacting residues were very clear. I have tried to repeat this by making a su

[PyMOL] how to superimpose two maps in pymol

Dear all, In pymol we can superimpose two structures together,and if we want to display the map at the same time, the moving structure will fit the its original map any more, so how to superimpose the maps at the time? Thank you very much! yamei yu

Re: [PyMOL] how to superimpose two maps in pymol

Hi Yamei, You'll need to apply the matrix used in super-positioning one structure over another to the corresponding maps, so that the maps will move with the structure. The command matrix_copy may be used to do this. http://www.pymolwiki.org/index.php/Matrix_Copy --Subhangi On Mon, Apr 18, 201

Re: [PyMOL] suface display protein-protein interactions...residues getting bleached.

Hi Yarrow, Can you please provide a simple script for us to work from? Then we can help modify it to suit your needs. Cheers, -- Jason On Mon, Apr 18, 2011 at 1:57 PM, Yarrow Madrona wrote: > Hello Pymol users > > I went to a recent Crystallography workshop and noticed everyone had great > pi

Re: [PyMOL] PyMOL Project Updates & Open Source PyMOL v1.4b1

Hi, On Fri, Apr 01, 2011 at 05:34:47PM -0400, Jason Vertrees wrote: > I got back from my trip last night and immediately started putting the > new features into the open source branch as promised. I've finished > the merge, pushed the changes to SourceForge (revision 3938), and > uploaded a tar f

[PyMOL] Visualizing protein-ligand complexes of metalloproteins

Hello I am trying to visualize a protein-ligand complex of a metalloprotein using Pymol. The ligand and certain amino acids are coordinated with the metal ions in the binding site.The binding site also have some water molecules which are also making interactions with amino acids and the metal ions.

Re: [PyMOL] Visualizing protein-ligand complexes of metalloproteins

Hi Prija, PyMOL does have trouble with heteroatoms every now and then. Is the structure public--if so, can we please have the PDB ID? It'll be easier for us to hunt for a solution if we have the data. Cheers, -- Jason On Mon, Apr 18, 2011 at 5:45 PM, Prija Ponnan wrote: > Hello > I am trying

Re: [PyMOL] Visualizing protein-ligand complexes of metalloproteins

Visualizing the coordinated bonds are easy, e.g., select zn, resn zn (this would select the metal) show sticks, zn (this will show bonds to any atoms withing bonding distance of zn that are also shown as sticks) Additional bonds to heteroatoms may have to be manually added using the bond command.