Re: [PyMOL] surfaces involving more than one object

Hi Bob, This is probably not the slickest way to do this but generally I think it is one surface one object, so in a simple case of a peptide bound to a protein, I would select the peptide chain (right click in the viewer) and extract that selection to a new object and then you can generate tw

Re: [PyMOL] PyMOL measurements

But as far as I can tell, in the session file, the coordinates are just numbers -- no reference to atoms. What am I missing? On Fri, May 31, 2013 at 8:57 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Bob, > > We added this a year or two ago: > > set dynamic_measures, 1 > > In

[PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

Dear all, I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu 12.10. I have compiled pymol from source ( http://www.pymolwiki.org/index.php/Linux_Install). When running the plugin, I can set the grid, but after clicking on Run APBS, I get the following error: Unexpected error

Re: [PyMOL] PyMOL measurements

Hi Bob, We added this a year or two ago: set dynamic_measures, 1 In newer versions of PyMOL this is enabled by default. Cheers, -- Jason On Fri, May 31, 2013 at 8:27 AM, Robert Hanson wrote: > Is there a way to tie measurement ends to specific atoms, so that when the > structure is tweaked

[PyMOL] PyMOL measurements

Is there a way to tie measurement ends to specific atoms, so that when the structure is tweaked, those measurements update automatically? -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr I

[PyMOL] surfaces involving more than one object

PyMOL questions about surfaces: Simple enough to create a surface for one object. What about for only a portion of the object? How to do each of these? -- closed surface ignoring a selected set of atoms -- open surface not ignoring any atoms, but also not displaying their part Is the rule, "

[PyMOL] PyMOL session file reader for Jmol

Hello, PyMOL users, The driving force behind these last four months of Jmol/JSmol development has been e-publication. The goal has been to produce a means of e-publishing working interactive biomolecular models that are ubiquitously accessible (i.e. no Java, no WebGL). We achieved that goal for J