I'll appreciate some help with APBS plugin.
In both Win or Lin the same error appears:
ObjectMapLoadDXFile-Error: Unable to open file!
After googling with this error message I've checked all of the
possibilities:
Map file is loaded OK, folders with apbs.exe and psize.py files do not
contain
Hi,
Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)? It fixes some problems and gives better error
messages on others.
Caltabiano
Lab of Computational Medicine,
BioStatistic Dept.
UAB, Universitat Autonoma de Barcelona
Spain
- Messaggio originale -
Da: Mike Summers summ...@hhmi.umbc.edu
A: Gianluigi Caltabiano chimic...@yahoo.it
Inviato: Martedì 27 marzo 2007, 20:14:37
Oggetto: Re: [PyMOL] APBS
, Universitat Autonoma de Barcelona
Spain
- Messaggio originale -
Da: Mike Summers summ...@hhmi.umbc.edu
A: Gianluigi Caltabiano chimic...@yahoo.it
Inviato: Martedì 27 marzo 2007, 20:14:37
Oggetto: Re: [PyMOL] APBS surface
You need to create individual proteins and then create maps
: Michael Lerner mgler...@gmail.com
A: Gianluigi Caltabiano chimic...@yahoo.it
Cc: pymol-users@lists.sourceforge.net
Inviato: Lunedì 2 aprile 2007, 15:40:24
Oggetto: Re: [PyMOL] APBS surface
PyMOL doesn't know where the electrostatic potential map comes from.
If you load up a map and a structure
Hi everyone,
I am working with a protein-protein complex and I have calculated for each
protein, let's say A and B, apbs electrostatic surfaces.
Everything works fine.
My question is:
I have uploaded the structure of protein A and the surface of protein B.
What it shows to me is a blank surface
Hi Georgios --
I am a newcomer in this field and the use of APBS. I am trying to
produce
an electrostatic potential map for a protein surface and I am using
Windows XP. Although I have installed succesfully Pymol v0.99, APBS
v0.4.0
and the M.Lerner's plug-in,following Lerner's
Hi Anastassis,
I got the same error with a few pdb files.
The problem is the following. The B-factor in the pymol-generated pdb
file is somtimes set to values larger than 100 (119.63 in your case)
thus occupying all its columns of the lovely PDB-format and not leaving
any space to the
Hi,
parseInput
self.parseLines(file.readlines())
File /usr/local/apbs-0.4.0/tools/manip/psize.py, line 116, in
parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00119.63
Any clues ?
It looks like it's reading from a pdb file when it's
Hi -
I installed apbs and tools (0.4.0) in a Linux box.
I then specified the location of psize.py and apbs executable.
when i load a protein and click on 'set grid' according to
instructions I get on a new window a rather cryptic response:
Error: 6
ValueError Exception in Tk callback
Florian,
I had the same problem and I couldnt get everything to work internally
in pymol. I never got pymol to write the *.pqr files. I couldn't
figure it out. However, you can give your pdb to the PDB2PQR server:
http://agave.wustl.edu/pdb2pqr/server.html
Strip the waters/ligands and load in
Hi,
at this purpose, what kind of range (positive - negative) should be
used in order to visualize correctly the potential surface on a
protein? Normally I used -10 to +10 but I am wondering how you behaves
with this issue too.
Thanks in advance
andrea
2006/11/23, D. Eric Dollins
I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
Professional. I've successfully installed maloc, but the apbs install
gives:
error: Failed dependencies
libreadline.so.4 is needed by apbs-0.4.0-1
What to do?
Thanks,
Joe Becker
Merck Research Labs
This is using the binary distributions of APBS?
Becker, Joseph W wrote:
I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
Professional. I've successfully installed maloc, but the apbs install
gives:
error: Failed dependencies
libreadline.so.4 is needed by
HI everyone
I have been able to show electrostatics from APBS by loading the .dx map
using a pml script. However, I would really like to display it on the
surface similar to the apbs plugin option which says color by potential
on solvent accessible surface in the visualization menu. Does anyone
Hi, all
Recently, I obtained APBS windows version and than installed. It works well.
Is it possible use in Pymol windows version?
I found one error message
ObjectMapLoadDXFile-Error: Unable to open file!
Sincerely yours,
Kim, Mun-kyoung
Protein Structure and Function Laboratory
On Wed, 21 Dec 2005, William Scott wrote:
Dear Michael:
Thanks.
It works great. Sorry that I stupidly didn't think to check it.
No problem. I'm glad it works. Almost everything should be the same.
APBS has a new required parameter, sdens (Vacc sphere density) that I've
added to the
I'm not getting very far...
parsePBE: Warning -- parsed deprecated calcforce 0 statement.
parsePBE: Please use calcforce no instead.
PBEparm_check: SDENS not set!
NOsh: MG parameters not set correctly!
Error while parsing input file.
There's a new version on my website
(http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out
and let me know if it works. I've tested it on a few systems that I work
with, and it seems fine. One person has reported some difficulties, but
these may not be related to my plugin.
Hi everyone,
I am trying to run apbs from pymol (0.98) on window and always end up
getting following error message.
objectMap load DX file-error: unable to open file!
Even after using improved plugin apbs tools.py , same error message.I
also tried using externally generated .PQR file as an
I have the same problem on a mac G5 dual processor with newly compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
Interestingly, the programs work fine together on my mac G4 laptop, with
single
I have the same problem on a mac G5 dual processor with newly
compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
Interestingly, the programs work fine together on my mac G4 laptop,
with
Dear Users,
I was wondering does anyone know how to get nice APBS generated
electrostatic surfaces in MacPyMOL. I know the APBS plugin can't/
won't work in MacPyMOL so I guess it's a question of what do I do
with the output from APBS (I assume it's the dx file) to get a
surface in
Hi,
I am trying to run APBS. I have compiled the software
and it is working.. But after few second later i am
getting following error message. I guess there is some
problem with map file. Any solution or help?
Thanks in advance
sn
==
This
I've been trying to generate an electrostatic potential map of the surface of
a protein using Pymol but haven't been successful. I'm working with the latest
version of pymol (0.98, windows version), which brings the APBS plugin (I have
as well installed the APBS plugin apbs_tools.py) that is
Hi,
I just checked the apbs download page and I couldn't find apbs binaries
available for windows. The only way I've seen (through previous mailing
lists posts) is to compile it using cygwin, but the performance is less
than optimal.
So if you or someone else has compiled apbs for windows, the
Hi, I just want to use pymol+apbs and do some calculation on protein
(PDB 1cse ).
Unfortunately, I got the error msg in the following.
This PyMOL(TM) Incentive Product is Copyright (C) 2005 DeLano
Scientific LLC.
A current PyMOL Maintenance and/or Support Subscription may
atoms|All surfaces
...and those generated with the same pdb in Pymol/APBS-tools?
The results I see from this differs from Pymol/APBS-tools as follows...
1) The pqr generated by pymol or the web pdb2pqr web site has -15
net charge whereas GRASP's amber.crg only creates a -11 net charge.
2) The GRASP
I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map
Hi Jack,
In all of the examples distributed with APBS, the pdie (solute dielectric)
The pdie must be the protein dielectric constant though the comment for
pdie in the pymol generated .in-file reads # Solute dielectric ...
that is probably a mistake. The APBS-plugin says Protein Dielectric.
The
Richard,
Actually I don't have a copy of Delphi available (hence the use
of APBS). I did notice that I see more positive surface area on a
molecule with a -13 net charge when the run is done with pdie of 2.0
compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also
noticed an oddity
Douglas Kojetin asked the following question on February 9, 2005:
For example, the molecular surface numbers default to
-1, 0 and 1. If they are changed to -5, 0 and 5, the displayed surface
looks less charged than that displayed with the default numbers.
What do the numbers mean?
I'm not an
Hi,
I've been meaning to update APBS tools so that some of the warnings are
larger and better explained.
WARNING: 53 atoms did not have properties assigned
means that PyMOL couldn't automatically assign properties for 53 atoms in
yoru molecule. This is usually because you have
Hi,
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Mr. Lerner,
Thanks for letting me know about the PDB2PQR server. I was able to generate a
pqr from the NBCR website that then works with APBS to generate the dx map.
I'm not sure how to get the same electrostatic gradient effect on the
Hi,
I have a problem with apbs in pymol. I got it to work fine, if I cutted a
100 aminoacid stretch from my molecule and followed the instructions.
However my protein is a bit bigger, ~800aa, and I cannot get the apbs map
to cover my molecule. I get the whole surface, but only half of it is
Hi all
When trying to install apbs via Bill Scott's suggestions and scripts
for maloc.info and apbs.info, I receive the following message
curl: (22) The requested file was not found
### execution of curl failed, exit code 22
Downloading the file maloc-0.1-2.tar.gz failed.
My question is
Hi
I am attempting to install APBS on a powerbook G4 running 10.3.5. I
would like to use Bill Scott's instructions for the install via fink.
The problem I have is that I do not have a /sw/fink/dists/local
directory. I do have /sw/fink/dists directory. Therefore I cannot
place the
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
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
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 ==
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
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
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