Dear all,
Sorry for the late answer but I finally managed to find what the error is...
First thing, I work on a Windows XP environment (nobody's perfect!!),
and some of the problems were related to that.
When I tried running everything from the command line (ie pdb2pqr and
apbs) I did get the files 1CJC.pqr and the corresponding map pot.dx. I
was able to read them with pymol and everything works. The problem
arises only with the APBS pymol plugin. In the CJC file, residues with
the alternate configuration A (and frankly I do not see the reason for
that as the alt B is not present....) existed and the handling of these
alt conformations is different if pymol or pdb2pqr do the charge
calculation. When the pdb file is transformed by pdb2pqr (command line
version 1.3.0), the alternate sidechains conformations disappear. When
Pymol transforms the file into a pqr one the alt field is still present
and apbs does not understand the atom that looks something like
"NH1AARG". If I use the file generated by pdb2pqr (with the --apbs-input
option) it works, apbs reads and does the calculation. The trick is the
to remove alternate configurations (specially when no alt B exists!!!).
I have done it on the CJC file and everything works perfectly from the
apbs plugin and without the need to generate the pdb2pqr file.
I was not able to pinpoint the problem with the pymol output when
running APBS. I noticed that the error messages differ a bit if I run
Pymol from a link (ie without a shell window) or from the pymol command
in a DOS shell. In the Pymol command window the error message is :
* APBS Tools: coarse grid: (301.633,318.546,307.146)
APBS Tools: fine grid: (197.431,207.380,200.674)
APBS Tools: center: (11.993,-11.506,14.548)
APBS Tools: fine grid points (97,97,97)
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
*
while in the cmd window the message is
*Reading PQR-format atom data from pymol-generated.pqr.
Valist_readPQR: Error parsing atom 3526!
Error reading molecules!
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?*
which of course is much more informative because it points directly to
the error in the pqr file that I had not been able to find because the
pqr looked ok to me (Unfortunately I did not jump to the 3526th atom
that has the alt A conformation!!).
Now the last problem: running the APBS plugin in WinXP generate path
errors because of the spaces in the paths.
*Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from **D:\Documents.
VASSERT: ASSERTION FAILURE! filename vmem.c, line 241, ((num > 0) &&
(size > 0))
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information.
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?*
So the path is not complete (D:\Documents and Settings\Gilles\Mes
Documents\blahblahblah\ is missing). Again, the error message in the
pymol console was not complete:
* APBS Tools: coarse grid: (103.210,121.009,109.487)
APBS Tools: fine grid: (80.712,91.182,84.404)
APBS Tools: center: (17.315,-2.473,13.671)
APBS Tools: fine grid points (97,97,97)
ObjectMapLoadDXFile-Error: Unable to open file!
*
Unfortunately I thought I had the same error while trying to run APBS
with the 1CJC file and using the pymol generated pqr (error with alt
conformations) or using the pqr file generated independantly (PATH error
with spaces in path names). It is all sorted out now. I can use the
pdb2pqr web site to generate the pqr and apbs input files or directly
pymol APBS plugin with the b factor and alternate conformation "blanked
out" before use!!!
I finally looked at the apbs.py file to see where the pqr calculation
was and added a few commands after line 1491: here they are:
pymol.cmd.remove('%s and alt b' %sel)
pymol.cmd.alter ('%s' %sel,'b=0')
pymol.cmd.alter ('%s' %sel,'alt=""')
pymol.cmd.sort('%s' %sel)
I tried the APBS script on the 1CJC file and it works. I am not 100%
sure it will work for every file as I only deleted the "b" conformation
(do PDB files with more than 2 alt conformations exist?). And BTW it is
a bit crude to decide to switch to the "a" conformation instead of
letting the user choose his preferred one!!
Anyway, I think the problem is solved for me, except for this PATH
problem in APBS trying to read an external pqr file. But so far, I think
I will definitely manage with the different workarounds.
Gilles
Nathan Baker a écrit :
Hi Gilles --
I installed APBS 0.4.0 and my pymol version is the latest build for
windows, ie 1.1 r0, the apbs plugin is the latest also I believe.
That's a very old version of APBS (2005); the latest is 1.0.0 and can
be downloaded from http://apbs.sourceforge.net/#download
The b factor error is only visible when calculating the grid. I
already use the b factor change (alter 1cjc, b=0), and the workaround
works perfectly when the error message complains about strange
numbers in the file (ValueError: invalid literal for float():
1.00101.34). I also tried to do a pdb2pqr (via the web interface)
before doing apbs, but I have never been able to read the pqr file
through the APBS interface.
What sorts of errors do you receive? Almost all of my PyMOL
calculations are performed with pre-generated PQR files from PDB2PQR
without problem.
In my hands, the pymol pdb to pqr conversion works quite well. My
second problem is apparently not related to the b factor or the pqr
file: it seems that for some pdb files, APBS cannot (or does not) see
(or write) the pymol-generated.dx file...
If I fetch 1EHB pdb file, I can calculate an APBS map (removing water
and hem molecules). If I fetch 1CJC pdb file, I cannot (again
removing water and fad molecules)!! If I fetch again 1EHB and redo
the calculation, everything goes fine. Here is the output of the
commands...
This is generally due to an APBS error; although the error messages
often get obscured through the "APBS Tools" interface (Warren, is
there some way to make these errors more transparent?). If you visit
your working directory for the APBS calculation, you should find the
input and PQR files used with the calculation. Can you send those to us?
Thanks,
Nathan
PyMOL>fetch 1ehb
PyMOL>remove resn hoh+hem
APBS Tools: coarse grid: (61.146,53.431,62.444)
APBS Tools: fine grid: (55.968,51.430,56.732)
APBS Tools: center: (16.504,0.863,7.287)
APBS Tools: fine grid points (97,97,97)
DXStrToMap: Dimensions: 97 97 97
DXStrToMap: Origin -11.480 -24.852 -21.079
DXStrToMap: Grid 0.583 0.536 0.591
DXStrToMap: 912673 data points.
PyMOL>delete all
PyMOL>fetch 1cjc
PyMOL>remove resn hoh+fad
Maximum number of grid points exceeded. Old grid dimensions were
[129, 161, 161]
Fine grid points rounded down from [91, 115, 115]
New grid dimensions are [65, 97, 97]
APBS Tools: coarse grid: (100.841,119.466,106.848)
APBS Tools: fine grid: (79.318,90.274,82.852)
APBS Tools: center: (17.545,-2.019,13.919)
APBS Tools: fine grid points (65,97,97)
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
PyMOL>delete all
PyMOL>fetch 1ehb
PyMOL>remove resn hoh+hem
APBS Tools: coarse grid: (61.146,53.431,62.444)
APBS Tools: fine grid: (55.968,51.430,56.732)
APBS Tools: center: (16.504,0.863,7.287)
APBS Tools: fine grid points (97,97,97)
DXStrToMap: Dimensions: 97 97 97
DXStrToMap: Origin -11.480 -24.852 -21.079
DXStrToMap: Grid 0.583 0.536 0.591
DXStrToMap: 912673 data points.
DeLano Scientific a écrit :
Nathan,
Strictly speaking, the issue may be with PDB2PQR itself, not APBS.
Furthermore, we don't yet know whether a combined development
version of all
three packages would still reproduce the problem.
As an aside, a good reason for PyMOL to see PQR files is for diagnostic
visualization: to enable the user to inspect and modify or
manipulate what
is being fed directly into APBS.
PyMOL can read & write PQR directly, though we may have issues reading
non-PDB-like PQR files. I would generally agree that use of PDB2PQR to
convert PDBs to PQRs is the preferred route, since PyMOL doesn't do any
checking or optimization.
Anyway, based on reported symptoms alone, the problem appears to be
that
some component in the PyMOL->APBS pipeline assumes that the input
PDBs are
space-delimited rather than column-delimited. This guess is based
on the
observation that a B-factor of 100 or greater eliminates the space
between
the occupany and the B factor in spec-compliant PDB files, and the
calculation fails.
As a starting point for troubleshooting, I just pulled current pdb2pqr
source from trunk and CANNOT reproduce the problem, so either this is
already a solved problem with current code, or something else is
going on.
Gilles, what versions of PyMOL and APBS are you using?
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-----Original Message-----
From: Nathan Baker [mailto:nathanaba...@mac.com] Sent: Wednesday,
September 17, 2008 6:28 PM
To: DeLano Scientific
Cc: gilles.tr...@cgm.cnrs-gif.fr; pymol-users@lists.sourceforge.net;
apbs-us...@lists.sourceforge.net
Subject: Re: [Apbs-users] [PyMOL] Strange behaviour with APBS
Hi Warren --
The PQR format (which doesn't really have a standard) is basically just
whitespace delimited. I'm curious, though -- why would a PyMOL APBS
invocation ever see the PDB file? Wouldn't a user first convert it
to PQR
with PDB2PQR (ideally) or with PyMOL's built-in functionality?
Thanks,
Nathan
On Sep 17, 2008, at 2:21 PM, DeLano Scientific wrote:
Gilles,
The PyMOL and APBS programs have differing views as to whether PDB
& PQR files are column-based or space-delimited, respectively. We
must eventually sort this out, because it causes continued grief
for our users in common.
For now, however, the workaround is to make sure no B-factors
exceed 100.
alter all, b=min(b,99.9)
should about do it.
Cheers,
Warren
-----Original Message-----
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of
Gilles Truan
Sent: Wednesday, September 17, 2008 1:09 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Strange behaviour with APBS
I have noticed a strange behaviour of the APBS module. I used it a
lot recently and it works perfectly for 95% of the structures I
analyzed. I usually fetch the pdb code, then remove waters,
heteroatoms and so on. I also noticed that in some cases, when the
b factor is quite big (over
100) APBS cannot work the pdb file because it mixes up the b factor
and the number which is just before (occupancy). But I managed with
that, I usually erase the b factor to 0 before doing the APBS
calculation and everything works fine then.
The other strange behavious is related to nothing I can pinpoint
unfortunately. For some files (I always fetch them with the fetch
command from Pymol), I can set the grid OK and when I launch APBS,
I can see the file being processed (I see the select and hydrogens
go on!) and then it stops with the following error message:
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?
All the paths for APBS are correctly setup, the temp files are
setup as well.
If I then fetch a new file, APBS works, even for several files (one
after
another) and if I come back to the file I wanted to do first, it
gives me the same error message (BTW, the pdb file is 1CJC).
Any help would be greatly appreciated!!!
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Center
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Web: http://cholla.wustl.edu/
<gilles_truan.vcf>
--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/
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