[PyMOL] RE: Angstrom-squared values for solvent/protein contact surface per residue

Just to throw my 2 cents in following Warren's invitation, I think Mark Gerstein's programs work well for this (calcsurf.exe or something...they're on his web site) ccp4's areaimol does something similar, though I can't recall whether its output was atom by atom. In either case, you may have to add

Re: [PyMOL] B & W Molscript & David Goodsell look-alike modes

Hi Michael, Try set ray_trace_mode = 0/1/2/3 Check out the wiki for more info and some examples http://www.pymolwiki.org/index.php/Ray#Ray-Tracing_modes Jacob Michael Sawaya wrote: Dear Pymol Users, Can you tell me how to access the B & W Molscript & David Goodsell look-alike modes in PyMOL Re

[PyMOL] RE: making a movie from saved scenes

Hi Sun, Warren (and others?) has posted some text before about this. A simple template for it is as follows with the key being that mview interpolate command at the end. This works, but I haven't been through it recently to remind myself of the nuances of the animate=0 options and the view=0 optio

[PyMOL] B & W Molscript & David Goodsell look-alike modes

Dear Pymol Users, Can you tell me how to access the B & W Molscript & David Goodsell look-alike modes in PyMOL Release 0.99? The "CHANGES" file suggests that these new modes are now offered by version 0.99, but I can find no documentation on how to use them. Thanks for your help, Mike Sawaya

[PyMOL] CVS to Subversion Migration

NOTE: If you are not in the habit of compiling PyMOL straight from the CVS archive, then you can ignore this message. Developers, SourceForge experienced a major system failure last week that has halted development on all CVS-based SourceForge projects, with no resolution in sight. Fortunately

[PyMOL] making a movie from saved scenes

Hi I'm wondering whether you can make a movie that smoothly connects between the saved scenes. For example, a smooth change from scene 1 to scene 2 to ...etc. I'll appreciate any help. Thanks Sun

Re: [PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

Hi Melanie, In the past I have used AREAIMOL, which is part of ccp4, to do something similar. Check out the documentation here http://www.ccp4.ac.uk/html/areaimol.html However, you may also want to look at SURFACE, which is also part of ccp4 and has some nice features, but is no longer being d

RE: [PyMOL] Atom type selection with the *

Matt, There isn't an escape sequence, but PyMOL will automatically disable the asterisk as a wildcard for atom names if any PDB file loaded contains an asterisk in that field. To manually choose another wildcard for that field, issue something like set atom_name_wildcard, % As for coloring at

RE: [PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

Melanie, At present, PyMOL isn't the right tool for this, but perhaps someone on the mailing list will know what is... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francis

Re: [PyMOL] Atom type selection with the *

pymol-users-ad...@lists.sourceforge.net wrote on 04/03/2006 09:49:51 AM: > Hi Pymol users, > > I'm experiencing some trouble with the selection of atom type using the > "*". Sometimes it works and sometimes it doesn't... > I used for example: > color red, objecto* > 'color red, name o*' give t

Re: [PyMOL] resize viewing window

pymol-users-ad...@lists.sourceforge.net wrote on 04/02/2006 06:00:42 PM: > Is there a way to adjust the viewing window without dragging the mouse > on a corner to do so? I need to resize the window for several files and > want to make sure they are all the same. > > Thanks, > James > > Hi James -

[PyMOL] Atom type selection with the *

Hi Pymol users, I'm experiencing some trouble with the selection of atom type using the "*". Sometimes it works and sometimes it doesn't... I used for example: color red, objecto* 'color red, name o*' give the same result. Any idea why it's happening and more interesting what should I do to fi

[PyMOL] Angstrom-squared values for solvent/protein contact surface per residue

Dear Pymol Users, Is it possible to extract numerical values, (i.e. Angstrom-squared per residue) for the solvent/protein contact surface for individual residues in a crystal structure using Pymol? Thank you, Melanie Rogers University of Leeds