[PyMOL] unable to export obj

l versions 1.7.4 and 1.6.0. Saving into an obj file works well when surface_type is set to 0, or 1. Any help? Best, Albert -- ----- Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy,

[PyMOL] RMS over a MD trajectory.

RMS along the trajectory if I simply: align trj, pdb1 as it is told in: http://www.pymolwiki.org/index.php/Align However, I am unable to get the list of RMS values printed out. How could I do that? Thanks, Albert -- ----- Dr Albert Solernou EPSRC Resea

Re: [PyMOL] RMS over a MD trajectory.

The first value in the tuple i.e. rms[0] should be the RMS value. > > HTH > > Carsten > > -Original Message- > From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] > Sent: Wednesday, May 06, 2015 8:32 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMS ove

Re: [PyMOL] RMS over a MD trajectory.

-atom RMSD and RMSD after > outlier rejection. > http://pymolwiki.org/index.php/Align#RMSD > > If your "trj" and "pdb1" have identical topology and matching atom > identifiers, then you can also use cmd.rms(). > http://pymolwiki.org/index.php/Rms > > Ch

Re: [PyMOL] RMS over a MD trajectory.

. The colorbyrmsd.py > (http://pymolwiki.org/index.php/ColorByRMSD) script gives a nice illustration > on how to approach this this. > > Carsten > > -Original Message- > From: Albert Solernou [mailto:a.soler...@leeds.ac.uk] > Sent: Friday, May 08, 2015 10:04 AM &g

[PyMOL] rms_cur, rms, fit - No atoms selected

I'm new at pymol, and I'm trying to use the commands rms and rms_cur. I have two pdb files, with two proteins in each. First, I load the files > load 1acb_321000.pdb, c321 > load 1acb_dock.pdb, dock then I select the backbone of the B chain of each complex, > select lc, /c321//b//ca+c+n+o > sele

Re: [PyMOL] rms_cur, rms, fit - No atoms selected

he > "alter" command to set the identifiers to matching values before issuing such > commands: > > alter all, segi='' > > alter c321 and chain E, chain='A' > > alter c321 and chain I, chain='B' > > etc. > > Cheer

[PyMOL] selecting faces and vertices in CGOs

-- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Transform Data into Opportunity. Accelerate data analysis in your

Re: [PyMOL] selecting faces and vertices in CGOs

t; > Cheers, > Thomas > > On 30 Mar 2016, at 10:40, Albert Solernou wrote: > >> Dear All, >> I was wondering if there is a way to select faces, vertices and/or edges >> from a CGO either using the mouse or the command line. How difficult >> would be to add

[PyMOL] loading StringIO

-- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- The Command Line: Reinvented for Modern Developers Did the

Re: [PyMOL] loading StringIO

>def load_object(type,object,name,state=0,finish=1,discrete=0, > quiet=1,zoom=-1,_self=cmd): > ''' > DESCRIPTION > > "load_object" is a general developer function for loading Python objects > into PyMOL

Re: [PyMOL] loading StringIO

That's lovely, David. Thanks, Albert On 10/26/2016 11:56 AM, David Hall wrote: > https://pymolwiki.org/index.php/Read_Pdbstr > > -David > > On Oct 26, 2016, at 3:55 AM, Albert Solernou <mailto:a.soler...@leeds.ac.uk>> wrote: > >> Dear All, >> I wa

[PyMOL] sources for PyMOL 2

-- - Dr Albert Solernou EPSRC Research Fellow, Department of Physics and Astronomy, University of Leeds Tel: +44 (0)1133 431451 -- Check out the vibrant tech community on one of the world&#

Re: [PyMOL] sources for PyMOL 2

OK, I found the answer myself, googling in this email list. Sources will be released early next year, I understood. I'll wait patiently :) Cheers, Albert On 22/11/17 11:49, Albert Solernou wrote: Dear All, we have been writing a plugin for PyMOL during the last years, released as G