Re: [PyMOL] Re: PyMOL-APBS os x

The previous suggestion about downloading g77 and installing it from hpc.sourceforge.net worked for me - at least I didn't get an error when I ran APBS On Jul 15, 2004, at 10:54 PM, Jianghai Zhu wrote: I still can't compile it with scott's method. Do you mind share your binary with us?

Re: [PyMOL] Re: PyMOL-APBS os x

I still can't compile it with scott's method. Do you mind share your binary with us? Jianghai == Jianghai Zhu Molecular Biology & Biochemistry Purdue University == On Jul 15, 2004, at 7:47 PM, William Scott wrote: The best way to overcome this is

[PyMOL] Re: PyMOL-APBS os x

The best way to overcome this is to compile it, so that you don't have to depend on someone's dynamic library. Fink doesn't build the g77 dynamic library, which allows you to avoid this problem. If you use g77 3.4.1 (which is what is currently in fink) with gcc 3.3 you will have some linkin

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 wrot

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

I get this tooall very depressing..enough to put one off Unix for good..just joking. J Dr. James Stevens Senior Research Associate Department of Molecular Biology - BCC206 The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA

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 fi

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

(this might be better suited on an APBS list, but i figured i'd give it a shot here) I downloaded the Mac APBS binary, but I'm seeing this error when trying to run it: % ./apbs-0.3.1-g4 dyld: ./apbs-0.3.1-g4 can't open library: /usr/local/lib/libg2c.0.dylib (No such file or directory, errno

[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 == better

[PyMOL] PyMOL 0.97 Released

PyMOL Version 0.97 has been released to correct an embarassing bug in the sequence viewer. If you've already downloaded 0.96, then please upgrade to 0.97 since 0.96 will not show the correct sequence code for glutamate residues... Also included in 0.97 are the exciting new plugins from Charles

[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. Chee

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] 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: PyMOL>show sticks, //mod1//10/ ex. that fails: PyMOL>show sticks, //mod1//-4/ Selector-Error: Invalid Range. ( s; mod1 & i; :4 )<-- I found this post on the m

RE: [PyMOL] sequence visualisation bug ?

Uhh, oops. Drat! Somehow this slipped by both myself and the beta testers... It looks like we'll need a 0.97 release ASAP! - Warren -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -Original Mes

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] 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 Buildi

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...

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

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 | Hi all, | | APBS (http://agave.wustl.edu/apbs/) is a package that allows you to | perform very fast, accurate electrostatics calculations. I've written a | PyMOL plugin that allows you to run APBS and visualize the results very | easily from within

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