Re: [PyMOL] Convert PyMOL isomesh or isosurface to cgo?

2012-01-10 Thread James Davidson
Thanks Takanori - that's just what I needed - works brilliantly! : ) I did find that my cgo_line_width setting (1.0) was causing the resultant cgo 'mesh' to appear / draw / raytrace differently to the isomesh counterpart; but I seemed to solve this by setting to -1. The only slight problem I st

Re: [PyMOL] Mutagenesis and states

2012-01-10 Thread Thomas Holder
Hi Justin, could you fetch just the monomer, mutate it and then construct the assembly with http://pymolwiki.org/index.php/BiologicalUnit/Quat ? Cheers, Thomas On 01/10/2012 08:43 AM, Justin Bailey wrote: > Hello > > I have been working with the pdb file 2C0W. It is a filamentous phage > po

Re: [PyMOL] Editing of the pdb structure

2012-01-10 Thread James Starlight
Deal all! I'm intresting about representation of the polarr contacts between ligand and protein 1) Usually I'm ussing Present-> Ligand sites option for that purposes but in my current case I'm working with GFP where tree residues form chromofore group of that protein. So I want to assign that th

Re: [PyMOL] Editing of the pdb structure

2012-01-10 Thread lina
On Tuesday 10,January,2012 09:43 PM, James Starlight wrote: > Deal all! > > I'm intresting about representation of the polarr contacts between > ligand and protein > > 1) Usually I'm ussing Present-> Ligand sites option for that purposes > but in my current case I'm working with GFP where tree resi

Re: [PyMOL] Having problems using clean function

2012-01-10 Thread QT
Hi, I have the same problem. But instead of "Unable to validate freemol.mengine" it's "Unable to import freemol.mengine module" followed by "This pymol build appears to not include full modeling capabilities." The message would take a long time to appear and pymol seems frozen if it is loaded wi

[PyMOL] PyMol 1.4 not running on Ubuntu Linux 11.10

2012-01-10 Thread John Ladasky
Hi folks, I just upgraded my Ubuntu Linux installation to 11.10.  Of course, this removes obsolete versions of applications.  So I had to reinstall PyMol. The Ubuntu Linux 11.10 manifest states that PyMol 1.4.1 is the supported version, and a package file is available.  So, I downloaded and (su