Thread: [Apbs-users] ObjectMapLoadDXFile-Error: Unable to open file!
Biomolecular electrostatics software
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From: Rosa G. <ro...@ys...> - 2006-05-06 09:38:23
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Hi all, I use a mac ibook G4 and I have PyMOLX11Hybrid version 0.99rc6 installed. I have installed apbs, maloc and depencies without any problem. When I try to run apbs tools in pymol, after giving the apbs binary location (/sw/src/apbs-0.4.0.tar.gz) and either use 'Use PyMOL generated PQR and PyMOL gene...' or my own PQR file located in a path with no spaces (/Users/ro/Desktop/A.pqr) created with pdb2pqr-1.1.1, although it starts the search it always gives the same error in the console: cs [5, 5, 4] finedim [67.773999214172363, 70.994001388549805, 61.194002151489258] nlev 4 mult_fac 32 finegridpoints [161, 161, 129] Maximum number of grid points exceeded. Old grid dimensions were [161, 161, 129] Fine grid points rounded down from [115, 115, 91] New grid dimensions are [97, 97, 65] APBS Tools: coarse grid: (81,216,86,690,70,030) APBS Tools: fine grid: (67.774,70.994,61.194) APBS Tools: center: (18.031,4.182,36.991) APBS Tools: fine grid points (97,97,65) ObjectMapLoadDXFile-Error: Unable to open file! So, although it seemed to be working, nothing happened! the structure I loaded is exactly as before... no electrostatics surface in sight :-( My pqr file info is as the example shown below: REMARK 1 PQR file generated by PDB2PQR (Version 1.1.1) REMARK 1 REMARK 1 Forcefield Used: amber REMARK 1 REMARK 5 REMARK 6 Total charge on this protein: -7.0000 e REMARK 6 ATOM 1 N MET 1 -4.214 1.267 24.242 0.1592 1.8240 ATOM 2 CA MET 1 -2.770 1.295 24.422 0.0221 1.9080 ... If you have any suggestions or might have spotted what am I doing wrong please let me know. Best regards R. ******************************** Rosa Grenha Structural Biology Laboratory University of York York YO10 5YW |
From: Jinhua Wu <jw...@sa...> - 2006-07-14 22:44:08
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Dear APBS users, Recently I installed pymol and apbs plug-in on my Mac (10.4.6). I tried run apbs in pymol. It failed although the calculation seemed to be fine. I am using the latest apbs_tools.py. Also I looked through the previous posts and tried a few things but no success. Here is the error message - please help me out, thanks! cs [5, 5, 6] finedim [79.357999801635742, 75.404000282287598, 84.568999290466309] nlev 4 mult_fac 32 finegridpoints [161, 161, 193] Maximum number of grid points exceeded. Old grid dimensions were [161, 161, 193 ] Fine grid points rounded down from [101, 101, 119] New grid dimensions are [97, 97, 97] APBS Tools: coarse grid: (100.909,94.187,109.767) APBS Tools: fine grid: (79.358,75.404,84.569) APBS Tools: center: (8.884,-13.040,18.147) APBS Tools: fine grid points (97,97,97) 'import site' failed; use -v for traceback Traceback (most recent call last): File "/Users/jwu/Desktop/Pymol_files/pymol/modules/pmg_tk/startup/apbs_tools.py", line 44, in ? from __future__ import division ImportError: No module named __future__ ObjectMapLoadDXFile-Error: Unable to open file! Jinhua Jinhua Wu Ph.D. Skirball Institute NYU Medical Center 212-263-2306 |
From: Todd D. <to...@cc...> - 2006-07-14 23:00:41
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Hi Jinhua - Although the ObjectMapLoadDXFile error can indicate an issue with getting APBS started, I'm pretty sure this is a PyMOL-centric issue due to the fact that it's a Python error: > from __future__ import division > ImportError: No module named __future__ You might want to try the PyMOL mailing list, or checking to see if your version of Python is up to date (including the __future__ module). Todd On 7/14/06, Jinhua Wu <jw...@sa...> wrote: > Dear APBS users, > > Recently I installed pymol and apbs plug-in on my Mac (10.4.6). > I tried run apbs in pymol. It failed although the calculation seemed to be > fine. I am using the latest apbs_tools.py. Also I looked through the > previous posts and tried a few things but no success. Here is the error > message - please help me out, thanks! > > cs [5, 5, 6] > finedim [79.357999801635742, 75.404000282287598, 84.568999290466309] > nlev 4 > mult_fac 32 > finegridpoints [161, 161, 193] > Maximum number of grid points exceeded. Old grid dimensions were [161, 161, > 193 > ] > Fine grid points rounded down from [101, 101, 119] > New grid dimensions are [97, 97, 97] > APBS Tools: coarse grid: (100.909,94.187,109.767) > APBS Tools: fine grid: (79.358,75.404,84.569) > APBS Tools: center: (8.884,-13.040,18.147) > APBS Tools: fine grid points (97,97,97) > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File > "/Users/jwu/Desktop/Pymol_files/pymol/modules/pmg_tk/startup/apbs_tools.py", > line 44, in ? > from __future__ import division > ImportError: No module named __future__ > ObjectMapLoadDXFile-Error: Unable to open file! > > > Jinhua > > > Jinhua Wu Ph.D. > Skirball Institute > NYU Medical Center > 212-263-2306 > > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |
From: Nathan B. <nat...@wu...> - 2006-07-14 23:38:06
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Yep, that error definitely doesn't look like APBS; I'll see if Warren has any ideas. Thanks! On Jul 14, 2006, at 6:00 PM, Todd Dolinsky wrote: > Hi Jinhua - > > Although the ObjectMapLoadDXFile error can indicate an issue with > getting APBS started, I'm pretty sure this is a PyMOL-centric issue > due to the fact that it's a Python error: > >> from __future__ import division >> ImportError: No module named __future__ > > You might want to try the PyMOL mailing list, or checking to see if > your version of Python is up to date (including the __future__ > module). > > Todd > > > On 7/14/06, Jinhua Wu <jw...@sa...> wrote: >> Dear APBS users, >> >> Recently I installed pymol and apbs plug-in on my Mac (10.4.6). >> I tried run apbs in pymol. It failed although the calculation >> seemed to be >> fine. I am using the latest apbs_tools.py. Also I looked through the >> previous posts and tried a few things but no success. Here is the >> error >> message - please help me out, thanks! >> >> cs [5, 5, 6] >> finedim [79.357999801635742, 75.404000282287598, 84.568999290466309] >> nlev 4 >> mult_fac 32 >> finegridpoints [161, 161, 193] >> Maximum number of grid points exceeded. Old grid dimensions were >> [161, 161, >> 193 >> ] >> Fine grid points rounded down from [101, 101, 119] >> New grid dimensions are [97, 97, 97] >> APBS Tools: coarse grid: (100.909,94.187,109.767) >> APBS Tools: fine grid: (79.358,75.404,84.569) >> APBS Tools: center: (8.884,-13.040,18.147) >> APBS Tools: fine grid points (97,97,97) >> 'import site' failed; use -v for traceback >> Traceback (most recent call last): >> File >> "/Users/jwu/Desktop/Pymol_files/pymol/modules/pmg_tk/startup/ >> apbs_tools.py", >> line 44, in ? >> from __future__ import division >> ImportError: No module named __future__ >> ObjectMapLoadDXFile-Error: Unable to open file! >> >> >> Jinhua >> >> >> Jinhua Wu Ph.D. >> Skirball Institute >> NYU Medical Center >> 212-263-2306 >> >> >> >> >> >> >> --------------------------------------------------------------------- >> ---- >> Using Tomcat but need to do more? Need to support web services, >> security? >> Get stuff done quickly with pre-integrated technology to make your >> job easier >> Download IBM WebSphere Application Server v.1.0.1 based on Apache >> Geronimo >> http://sel.as-us.falkag.net/sel? >> cmd=lnk&kid=120709&bid=263057&dat=121642 >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> > > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: Todd D. <to...@cc...> - 2006-05-09 01:24:43
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Hi Rosa - The ObjectMapLoadDXFile-Error occurs when APBS exits abnormally when run through PyMOL - it essentially doesn't return the DX file, so PyMOL complains about it. We've seen this error a few times on Windows: http://sourceforge.net/mailarchive/message.php?msg_id=3D15327177 Usually the main culprit is a space in either the directory with the APBS file or the directory with the PQR file. Niether one can have spaces. It seems like you were aware of this, so its probably another issue that causes APBS to finish abnormally. With this in mind, if your directories don't have spaces, please try it again with the PyMOL console window open. This window should show you APBS output as well as PyMOL output, and will definitely make it easier to figure out what's going on. Thanks! Todd On 5/6/06, Rosa Grenha <ro...@ys...> wrote: > > Hi all, > > I use a mac ibook G4 and I have PyMOLX11Hybrid version 0.99rc6 installed. > > I have installed apbs, maloc and depencies without any problem. > > When I try to run apbs tools in pymol, after giving the apbs binary locat= ion > (/sw/src/apbs-0.4.0.tar.gz) and either use 'Use PyMOL generated PQR and > PyMOL gene...' or my own PQR file located in a path with no spaces > (/Users/ro/Desktop/A.pqr) created with pdb2pqr-1.1.1, although it starts = the > search it always gives the same error in the console: > > cs [5, 5, 4] > finedim [67.773999214172363, 70.994001388549805, 61.194002151489258] > nlev 4 > mult_fac 32 > finegridpoints [161, 161, 129] > Maximum number of grid points exceeded. Old grid dimensions were [161, 1= 61, > 129] > Fine grid points rounded down from [115, 115, 91] > New grid dimensions are [97, 97, 65] > APBS Tools: coarse grid: (81,216,86,690,70,030) > APBS Tools: fine grid: (67.774,70.994,61.194) > APBS Tools: center: (18.031,4.182,36.991) > APBS Tools: fine grid points (97,97,65)ObjectMapLoadDXFile-Error: Unable = to > open file! > > > > > > So, although it seemed to be working, nothing happened! the structure I > loaded is exactly as before... no electrostatics surface in sight :-( > > > > > > My pqr file info is as the example shown below: > > > REMARK 1 PQR file generated by PDB2PQR (Version 1.1.1) > REMARK 1 > REMARK 1 Forcefield Used: amber > REMARK 1 > REMARK 5 > REMARK 6 Total charge on this protein: -7.0000 e > REMARK 6 > ATOM 1 N MET 1 -4.214 1.267 24.242 0.1592 1.8240 > ATOM 2 CA MET 1 -2.770 1.295 24.422 0.0221 1.9080 > ... > > > > > > > > If you have any suggestions or might have spotted what am I doing wrong > please let me know. > > > Best regards > > R. > > > > > > > > ******************************** > > Rosa Grenha > > Structural Biology Laboratory > > University of York > > York > > YO10 5YW > > |