Re: [PyMOL] cylindrical helices

Hi Thomas, Thanks for input - the 'bug' was because the misbehaving PDB had ACs for residues in the helices that were not being drawn correctly. Stripping out the alternative conformations fixed problem, and dss forces cylinder to match dssp header, so I'm good. Mark >Hi Mark, > >cylindri

[PyMOL] morph command questions

I have two questions about the morph command in PyMOL 1.7 1) Is it possible to keep atom label text displayed throughout the morph? I've run a script morphing from mol1 to mol2 with text associated with mol1, but the label disappears at the start of the morph. 2) Is it possible to have the dis

[PyMOL] mac stereo questions

Dear Warren and users, I'm in process of setting up a new G5 with stereographics card and cannot get PyMol (both MacPymol and the hybrid version) to work with quad buffered stereo. When I switch to stereo the display shows two objects in same pane, but there is no stereo effect. I've get seten

[PyMOL] manual update

Dear Warren, I would second Dirk's statement below. The manuals on web are a couple of years out of date now, and while the wiki and bulletin board are very useful sources of information, I too would prefer to have good up to date documentation, rather than more and more improvements with poo

[PyMOL] Manual updates?

Hi, This is really for Warren. A while ago there was discussion of the ± of updates versus new manuals. The current documentation is now several years out of date. Are their plans to update this? Thanks to all who have worked on Wiki and posted scripts on web sites. Mark --

[PyMOL] Sticks and distances with individual transparencies

Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothing changes although the log output suggests the change is be

[PyMOL] Sticks and distances with individual transparencies - repost

Apologies for prior post message font was nearly unreadable Dear All, I'm trying to write a Pymol script with which produces a mixture of both solid and transparent sticks I'm using the current 1.0 incentive release of MacPymol. After drawing all my sticks I issue following commands, but nothi

Re: [PyMOL] Macintel stereo not working

Hi Warren & PyMolers, We just got an 8-core intelmac. Its recognized as such by PyMOL. But hardware stereo does not work. I download the 1.0r1. version and tried running as both MacPymol and X11hybrid. Clues are: 1) the emitter does not light when I switch to stereo mode (quad buffered). 2

Re: [PyMOL] Macintel stereo - fixed

Hi Warren & PyMolers, Elaine Podell suggested having the CRT monitor as the first monitor (systems preferences/displays) and the flat panel monitor as the 2nd. This fixed the problem - thanks. Anyone know how if you can move dock to display 2 (the flat panel)? -- Mark Mayer Ph.D.

[PyMOL] sphere diameter

hello, Can't find anything about this in docs or in settings: Where are sphere diameter settings controlled for individual atomic species: I'm trying to make fig with ions and the sizes don't seem to be right - Cl too small and Na too big. Thanks -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bld

[PyMOL] Transparency in individual molecules/objects?

Hi All,' If I have a PyMol script with multiple molecules loaded, is there a way to set transparency (say for sticks or spheres), on a by molecule, or even better on an object by object case. Used to be able to do this in molscript/raster3d, but for PyMol I've only figured out how to set sphe

Re: [PyMOL] Transparency in individual molecules/objects?

...@lists.sourceforge.net]on Behalf Of Dr. Mark Mayer Sent: Thursday, March 20, 2008 4:46 PM To: PyMOL-users@lists.sourceforge.net Subject: [PyMOL] Transparency in individual molecules/objects? Hi All,' If I have a PyMol script with multiple molecules loaded, is there a way to set transparency

[PyMOL] How to make Transparency in individual molecules/objects

Thanks to Carsten and Mauricio. Following approaches work: 1) set stick_transparency, 0.4, molecule4 Useful if you are drawing multiple selections from Mol4 and want it transparent 2) Individual objects create M223Dser, /mol4//D/MET`223 and !mc show sticks, M223Dser set stick_transparency=0.9

Re: [PyMOL] Quick Updates

Hi Jason, One point of clarification for the Mac community. In addition to acquiring a Quadro card, users will also need a fast CRT for stereo. Drivers do not work with 120 Hz flat panels. Apple has really dropped the ball on this one. Mac users might be interested to know that I have been r

Re: [PyMOL] alter atom coordinates

Hi All, Is there a way to select an individual atom, could be a dummy atom, or an ion I've inserted into a PDB, and then grab and move that atom to a new position? I'm trying to make a Fig showing a vector running through the center of an alpha helix drawn using cylinder cartoon mode, using di