Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

Hi all I've been trying to install apbs to use this new plugin, as I imagine a lot of people will want to. I run into a problem in the compilation which I wonder if anyone can help with. [I know this is not strictly a Pymol question but given the general interest perhaps I can be excused. There

Re: [PyMOL] PyMOL + APBS for easy, accurate electrostatics calculations

On Thursday 15 July 2004 13:30, Daniel Rigden wrote: -- begin configuring for MALOC linkage checking for FETK_INCLUDE... yes checking for FETK_LIBRARY... yes checking maloc/maloc.h usability... yes checking maloc/maloc.h presence... yes checking for maloc/maloc.h... yes

[PyMOL] sequence visualisation bug ?

Hi all When I visualise sequences, all Glu residues (as well as all Asp residues) are shown as D! Has anyone else seen this? Daniel -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences

Re: [PyMOL] sequence visualisation bug ?

Yes, I've got the same problem. Jules Daniel Rigden wrote: Hi all When I visualise sequences, all Glu residues (as well as all Asp residues) are shown as D! Has anyone else seen this? Daniel

[PyMOL] selection of residues with negative numbers

Hi All- I cannot make PyMOL make selections of residues with negative (sequence) numbers. Any quick way around this? ex. that works: PyMOLshow sticks, //mod1//10/ ex. that fails: PyMOLshow sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 i; :4 )-- I found this post on the

RE: [PyMOL] selection of residues with negative numbers

Douglas, I don't think PyMOL can handle negative selections yet. Just make them positive: alter all, resi=int(resi)+100 etc. Cheers, Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020

[PyMOL] Problem in sequence viewer for GLU

Hi, I found a little bug in the sequence viewer in the Pymol version 0.96 for linux: All glutamic acid (E) are identified by the aspartic acid letter (D). But the sequence is readed correctly, because when I color my GLU (color yellow, resn GLU) the D become yellow in the sequence viewer.

[PyMOL] A couple of quick PyMOL + APBS notes

Hi all, I've been getting two questions about APBS from a few people, so I thought I'd send the answers here: 1) Does APBS take a lot of memory? APBS can certainly take a lot of memory. In addition, my plugin sets up a grid that's a little finer than the APBS default (more grid points ==

Re: [PyMOL] A couple of quick PyMOL + APBS notes

The reason it doesn't work is because, I think, APBS was not compiled by the fink g77. More likely it was compiled by a g77 from http://hpc.sourceforge.net/ or other similar places. So you need to install that version of g77 to get APBS running on you mac. If anybody can compiled APBS using

Re: [PyMOL] A couple of quick PyMOL + APBS notes

Verified. I downloaded the g77 available from http://hpc.sourceforge.net, copied the files to the respective directories in /usr/local/, and the binary appears to work now (at least no errors when I run it with no input as before). Thanks! Doug On Jul 15, 2004, at 8:02 PM, Jianghai Zhu