[PyMOL] selecting residues

Hi, I ran into a problem selecting nearby residues of one molecule regarding the binding partner. The "byres" command seems to work only with one single residue. It does not select the whole residue when using the molecule as reference. creat 4a, byres mol around 4 --- gives incomplete residue

[PyMOL] Re:labeling atoms in GUI

Warren, I want to be able to use those useful definations every time I load pymol. I wonder how to edit the general startup script pymol in order to do that? By the way, I also want pymol to show distance when I click two atoms. Thank you. Eric > Quoting "Warren L. DeLano" > : > > > Richard, >

[PyMOL] make a bond from two different molecule

Hi, I am using the newest pymol windows version. I need to make a bond between the protein and ligand since they form a covalent complex. When I use 'bond' command, pymol requires that two bonded atoms are in the same molecule. I have to load two molecules seperately in order to identify the intera

[PyMOL] question about water molecules

Hi, I am trying to make a movie out of 50 pdb snapshots. I want to show the surrounding residues and water 4 angstroms away from the substrate. If I only work on one snapshot it seems fine--there are three or four water molecules. When I load all 50 snapshots at the same time as different mov state

[PyMOL] select residues 4 angstrom away from the center atom or residue

Hi, I wonder if pymol can do this kind of selection. Thanks. Eric __ Do you Yahoo!? Yahoo! Web Hosting - establish your business online http://webhosting.yahoo.com

[PyMOL] xyz file

Hi, I wonder if pymol can read xyz coordinates. Is xyz movie readable too? Thanks. Eric __ Do you Yahoo!? Yahoo! Shopping - Send Flowers for Valentine's Day http://shopping.yahoo.com

[PyMOL] label is not displayed after raying

Hi, I wonder if anyone has had the similar problem. I can see both the label and dash at normal window. After raytracing there is only a yellow dotted line between two atoms without the distance. How can I make the distance shown on the raytracing picture? Thanks! Happy new year! Eric __

[PyMOL] how to show both ligand and surface

Hi, I am kinda new to pymol. I wonder if I can show both ligand and the surface around it. In other word, can I increase the transparency of the surface so that I can still see the ligand in line representation. Thanks! Eric __ Do you Yahoo!? Yahoo!

[PyMOL] pai-pai stacking

Is there anyway to indicate a pai-pai stacking similar like hydrogen bond? Eric __ Do you Yahoo!? Yahoo! Mail Plus - Powerful. Affordable. Sign up now. http://mailplus.yahoo.com