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?
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
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
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
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
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
(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
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 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
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
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
> --
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
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
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
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
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...
-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
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
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