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.
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. 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...
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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