Re: [PyMOL] PyMOL + APBS plugin

Dear Thomas, thank you for these short and perfect answers. 1. All fine now. 2. Updated the plugin and the GUI bug is gone. One more thing though. Whenever I click the button to either set temporary file locations or to set program locations in APBS GUI window I immediately get a Segmenta

[PyMOL] Issue visualizing Delphi electrostatic potential map

I am having trouble visualizing Delphi generated maps in pymol. I've followed a number of tutorials online but they are all quite outdated so that may be a factor. I'm using the newest version of Delphi (v6.2) and PyMol v1.7. I am able to generate the electrostatic potential map in Delphi, howev

Re: [PyMOL] PyMOL + APBS plugin

Hi Matic, 1. If you have conflicting (non-unique) file names, you have two options: a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map) b) Set the "auto_rename_duplicate_objects" setting 2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days a

[PyMOL] PyMOL + APBS plugin

Dear all, I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0. 1. First I tried to perform a couple of APBS calculations through the APBS plugin window and all went great. Then I did a

Re: [PyMOL] show the long helix filament

For such cases I generate the symmetry partners using either the symexp command or the supercell script. Both scripts result in lots of extra objects, which you then have to winnow down to a single helix. Supercell c

Re: [PyMOL] show the long helix filament

Hi Yeping, What is the PDB id you are working with? Perhaps you have to download the biological assembly rather than asymmetric unit. I’d suggest you to go to the PDBe entry (pdbe.org/PDBID) and from the quick links select download ‘Assembly composition XML’. Take a look which assembly id ha

[PyMOL] show the long helix filament

Dear all,I am studying a published protein molecule which was claimed to be helical symmetric. The pdb file contain 3 copies of this molecule arranged in head-to-tail patern. The author claims that this interation is repeated in a  directional manner along the P31 screw axis. Does anyone know how