Hello Gilles,
The ObjectMapLoadDXFile-Error you are still having may sound familiar to us.
Could you send us the following screenshots from your PyMOL APBS Tools?
1. A screenshot of the Main tab.
2. A screenshot of the APBS Location tab.
3. A screenshot of the Temporary File Locations tab.
With the above screenshots, we may be able to help you with this issue.
Thanks,
Yong
2008/9/22 Gilles Truan <gilles.tr...@cgm.cnrs-gif.fr>
> 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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>>>>> _______________________________________________
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>>>>> apbs-us...@lists.sourceforge.net
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>>>>>
>>>>>
>>>> --
>>>> Associate Professor, Dept. of Biochemistry and Molecular Biophysics
>>>> Center
>>>> for Computational Biology, Washington University in St. Louis
>>>> 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/
>>
>>
>>
>>
>>
>>
>>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
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>
--
Yong Huang, D.Sc.
Center for Computational Biology
Washington University School of Medicine
