Re: [PyMOL] APBS problem

[Andreas Forster]

Hi Albert,

I apologize that I take your email for a grumpy old man's rant, but I feel
this mailing list is getting washed out with poorly formulated questions.

What happened to specifying what OS you use, what version of PyMOL, what
version of the apbs plugin.  Also, to give answers, it would help to know
what settings you chose for the calculation of the electrostatic
potential.  There's a bunch of buttons to click.  Which ones did you
choose?  What step have you already taken to overcome the problem?

Basically, I'm asking new users to spend a leisurely coffee break reading
http://www.catb.org/~esr/faqs/smart-questions.html and then ask better
question.

The answer to your problem:  /tmp/1-PE0.dx needs to be generated.  That's
all I can infer from the information you gave.

All best.


Andreas


On Thu, Oct 8, 2015 at 4:30 PM, Albert  wrote:

> Hello:
>
> I am trying to calculate the protein surface electstatic properities by
> APBS plugin in pymol. But it always failed with messages:
>
> Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
> ObjectMapLoadDXFile-Error: Unable to open file!
> ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?
>
> Does anybody has any idea how to solve this problem?
>
> thx a lot
>
>
>
>
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[PyMOL] APBS problem

[Albert]

Hello:

I am trying to calculate the protein surface electstatic properities by 
APBS plugin in pymol. But it always failed with messages:

Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?

Does anybody has any idea how to solve this problem?

thx a lot



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Re: [PyMOL] APBS problem

[Albert]

thanks a lot for reply.

Problem solved after I specify the maloc library path explicitly in my 
tcsh environment.


setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib



On 10/08/2015 05:02 PM, Andreas Forster wrote:

Hi Albert,

I apologize that I take your email for a grumpy old man's rant, but I 
feel this mailing list is getting washed out with poorly formulated 
questions.


What happened to specifying what OS you use, what version of PyMOL, 
what version of the apbs plugin.  Also, to give answers, it would help 
to know what settings you chose for the calculation of the 
electrostatic potential.  There's a bunch of buttons to click.  Which 
ones did you choose?  What step have you already taken to overcome the 
problem?


Basically, I'm asking new users to spend a leisurely coffee break 
reading http://www.catb.org/~esr/faqs/smart-questions.html 
 and then ask 
better question.


The answer to your problem: /tmp/1-PE0.dx needs to be generated.  
That's all I can infer from the information you gave.


All best.


Andreas


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[PyMOL] APBS problem on showing the molecular surface

[Yoshitaka MORIWAKI]

Dear PyMOL users,

I'm in trouble in using APBS plugin to display the molecular surface.

The calculations of set Grid and Run APBS were successfully finished,
but showing the surface by the button of show in the Visualization (1) tab 
fails with the following message

 ObjectMapLoadDXFile: Loading from 
'/Users/yoshitaka/Desktop/pymol-generated.dx'.
 DXStrToMap: Dimensions: 97 129 129
 DXStrToMap: Origin  -31.288  -19.104  -13.876
 DXStrToMap: Grid0.4840.4970.462
 DXStrToMap: 1614177 data points.
type 'exceptions.ValueError' Exception in Tk callback
  Function: bound method VisualizationGroup.showMolSurface of 
pmg_tk.startup.apbsplugin.VisualizationGroup instance at 0x1077ca3f8 (type: 
type 'instancemethod')
  Args: ()
Traceback (innermost last):
  File /usr/local/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, 
line 1747, in __call__
return apply(self.func, args)
  File 
/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py,
 line 2433, in showMolSurface
self.updateMolSurface()
  File 
/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py,
 line 2471, in updateMolSurface
self.updateRamp()
  File 
/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py,
 line 2458, in updateRamp
ramp_name = self.getRampName()
  File 
/usr/local/Cellar/pymol/1.7.1.3/lib/python2.7/site-packages/pmg_tk/startup/apbsplugin.py,
 line 2440, in getRampName
idx = [i for i in pymol.cmd.get_names() if pymol.cmd.get_type(i) == 
'object:molecule'].index(self.molecule.getvalue())
type 'exceptions.ValueError': '' is not in list


Please tell me how to solve this plobrem.
I describe my settings as follows:

machine: Mac OS X 10.9.4, Intel Core i7, 16GB.
Xquartz is installed. The versions of gcc and g++ compilers are 4.8.1.

I installed tcl/tk (ver. 8.5.15), python (ver. 2.7.8), pmw (ver. 1.3.3), and 
PyMOL (ver. 1.7.1.3) by using Homebrew.
  brew uninstall python tcl-tk pmw pymol
  brew tap homebrew/dupes
  brew tap homebrew/science
  brew install homebrew/dupes/tcl-tk --enable-threads --with-x11
  brew install python --with-brewed-tk
  brew install pymol

Next, I installed openmpi 1.8.1 in this way:
  brew install openmpi
  cd /usr/lib/
  sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libmpi.1.dylib libmpi.0.dylib
  sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-rte.7.dylib 
libopen-rte.0.dylib
  sudo ln -s /usr/local/Cellar/open-mpi/1.8.1/lib/libopen-pal.6.dylib 
libopen-pal.0.dylib

APBS and PDB2PQR binaries were employed from APBS-1.4-osx.tar.gz and 
pdb2pqr-osx-bin-1.9.0.tar.gz, respectively.

The plugin apbsplugin.py was downloaded from 
http://www.pymolwiki.org/index.php/Apbsplugin;.

The environment variable DYLD_FALLBACK_LIBRARY_PATH was set as 
/usr/local/Cellar/open-mpi/1.8.1/lib:/Users/yoshitaka/apps/APBS-1.4-osx/lib:$DYLD_FALLBACK_LIBRARY_PATH
for the calculation.

Thank you for your help.

Yoshitaka


**
Yoshitaka Moriwaki
Dept. of Biotechnology, Grad. Sch. of Agri. and Life Sci.,
The Univ. of Tokyo
**

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Re: [PyMOL] APBS problem

[Thomas Holder]

Hi Warren,

run pdb2pqr with the --whitespace argument to make sure the columns
are separated with whitespace.

If you still want to adjust the coordinates, you can use the
alter_state command in PyMOL.

alter_state 1, all, (x,y,z)=(x+100,y+100,z+100)

http://www.pymolwiki.org/index.php/Alter_State

Cheers,
   Thomas

Warren Gallin wrote, On 08/30/12 06:54:
 Hi,
 
 I am having trouble running APBS on a structure, and it appears to be
 because some of the coordinates are -100 or more negative.  This
 leads to APBS reading numbers from adjacent columns as concatenated
 strings because there is no space between the columns.
 
 This is happening either if I use the plugin or run PDB2PQR and APBS
 as stand-alone applications.
 
 If I can adjust the co-ordinates such that the relative positions of
 the atoms do not change but the coordinates stay greater than -100 I
 think that the problem would be solved.
 
 Has anyone ever encountered this problem, and is there a simple
 solution in PyMol to adjust the coordinates and then save a simple
 PDB file with the corrected values?
 
 Thanks,
 
 Warren Gallin

-- 
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MPI for Developmental Biology
Spemannstr. 35
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[PyMOL] APBS problem

[Warren Gallin]

Hi,

I am having trouble running APBS on a structure, and it appears to be 
because some of the coordinates are -100 or more negative.  This leads to APBS 
reading numbers from adjacent columns as concatenated strings because there is 
no space between the columns.

This is happening either if I use the plugin or run PDB2PQR and APBS as 
stand-alone applications.

If I can adjust the co-ordinates such that the relative positions of 
the atoms do not change but the coordinates stay greater than -100 I think that 
the problem would be solved.

Has anyone ever encountered this problem, and is there a simple 
solution in PyMol to adjust the coordinates and then save a simple PDB file 
with the corrected values?

Thanks,

Warren Gallin
--
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Exclusive live event will cover all the ways today's security and 
threat landscape has changed and how IT managers can respond. Discussions 
will include endpoint security, mobile security and the latest in malware 
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[PyMOL] Pymol apbs problem

[Evan Kantrowitz]

With a certain file 1za1 from pdb when I try to run apbs I get the  
errors below.  Other files are OK.  Any suggestions?


error: 1
ValueError Exception in Tk callback
  Function: function lambda at 0x182892b0 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ 
Pmw_1_2/lib/PmwBase.py, line 1747, in __call__

return apply(self.func, args)
  File /Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ 
Pmw_1_2/lib/PmwDialog.py, line 153, in lambda

command=lambda self=self, name=name: self._doCommand(name))
  File /Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/ 
Pmw_1_2/lib/PmwDialog.py, line 132, in _doCommand

return command(name)
  File /Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/ 
pmg_tk/startup/apbs_tools.py, line , in execute

self.runPsize()
  File /Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/ 
pmg_tk/startup/apbs_tools.py, line 1155, in runPsize

size.runPsize(pdb_filename)
  File /sw/share/xtal/bin/psize.py, line 267, in runPsize
self.parseInput(filename)
  File /sw/share/xtal/bin/psize.py, line 102, in parseInput
self.parseLines(file.readlines())
  File /sw/share/xtal/bin/psize.py, line 116, in parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00101.59



---
Evan R. Kantrowitz,  
Ph.D   
evan.kantrow...@bc.edu
Boston  
College  
  Tel. 617-552-4558
Department of  
Chemistry
   FAX 617-552-2705
Merkert Chemistry Center, Rm  
239  www2.bc.edu/ 
~kantrow

Chestnut Hill, MA 02467
---

Re: [PyMOL] Pymol apbs problem

[DeLano Scientific]

 Evan,
 
This appears to be a problem with file format incompatibility between PyMOL
and the psize.py script.  I suspect that rounding off the atom coordinates
will eliminate it:
 
alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
int(z*1000)/1000.0)
 
Cheers,
Warren
  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September 21, 2007 7:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Pymol apbs problem



With a certain file 1za1 from pdb when I try to run apbs I get the errors
below. Other files are OK. Any suggestions? 

error: 1
ValueError Exception in Tk callback
Function: function lambda at 0x182892b0 (type: type 'function')
Args: ()
Traceback (innermost last):
File
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Base.py, line 1747, in __call__
return apply(self.func, args)
File
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Dialog.py, line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
File
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
Dialog.py, line 132, in _doCommand
return command(name)
File
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
_tools.py, line , in execute
self.runPsize()
File
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
_tools.py, line 1155, in runPsize
size.runPsize(pdb_filename)
File /sw/share/xtal/bin/psize.py, line 267, in runPsize
self.parseInput(filename)
File /sw/share/xtal/bin/psize.py, line 102, in parseInput
self.parseLines(file.readlines())
File /sw/share/xtal/bin/psize.py, line 116, in parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00101.59




---
Evan R. Kantrowitz, Ph.D evan.kantrow...@bc.edu
Boston College Tel. 617-552-4558
Department of Chemistry FAX 617-552-2705 
Merkert Chemistry Center, Rm 239 www2.bc.edu/~kantrow
Chestnut Hill, MA 02467
---

Re: [PyMOL] Pymol apbs problem

[wgscott]

Hi Evan:

I ran pdb2pqr by hand and I think the Zn and CTP is problematic:

REMARK   5 WARNING: PDB2PQR was unable to assign charges
REMARK   5  to the following atoms (omitted below):
REMARK   5  7220 ZN in ZN 154
REMARK   5  7221 ZN in ZN 154
REMARK   5  7222 N1 in CTP 901
REMARK   5  7223 C2 in CTP 901
REMARK   5  7224 N3 in CTP 901
REMARK   5  7225 C4 in CTP 901
REMARK   5  7226 C5 in CTP 901
REMARK   5  7227 C6 in CTP 901
REMARK   5  7228 O2 in CTP 901
REMARK   5  7229 N4 in CTP 901
REMARK   5  7230 C1' in CTP 901
REMARK   5  7231 C2' in CTP 901
REMARK   5  7232 O2' in CTP 901
REMARK   5  7233 C3' in CTP 901
REMARK   5  7234 C4' in CTP 901
REMARK   5  7235 O4' in CTP 901
REMARK   5  7236 O3' in CTP 901
REMARK   5  7237 C5' in CTP 901
REMARK   5  7238 O5' in CTP 901
REMARK   5  7239 PA in CTP 901
REMARK   5  7240 O1A in CTP 901
REMARK   5  7241 O2A in CTP 901
REMARK   5  7242 O3A in CTP 901
REMARK   5  7243 PB in CTP 901
REMARK   5  7244 O1B in CTP 901
REMARK   5  7245 O2B in CTP 901
REMARK   5  7246 O3B in CTP 901
REMARK   5  7247 PG in CTP 901
REMARK   5  7248 O1G in CTP 901
REMARK   5  7249 O2G in CTP 901
REMARK   5  7250 O3G in CTP 901
REMARK   5  7251 N1 in CTP 902
REMARK   5  7252 C2 in CTP 902
REMARK   5  7253 N3 in CTP 902
REMARK   5  7254 C4 in CTP 902
REMARK   5  7255 C5 in CTP 902
REMARK   5  7256 C6 in CTP 902
REMARK   5  7257 O2 in CTP 902
REMARK   5  7258 N4 in CTP 902
REMARK   5  7259 C1' in CTP 902
REMARK   5  7260 C2' in CTP 902
REMARK   5  7261 O2' in CTP 902
REMARK   5  7262 C3' in CTP 902
REMARK   5  7263 C4' in CTP 902
REMARK   5  7264 O4' in CTP 902
REMARK   5  7265 O3' in CTP 902
REMARK   5  7266 C5' in CTP 902
REMARK   5  7267 O5' in CTP 902
REMARK   5  7268 PA in CTP 902
REMARK   5  7269 O1A in CTP 902
REMARK   5  7270 O2A in CTP 902
REMARK   5  7271 O3A in CTP 902
REMARK   5  7272 PB in CTP 902
REMARK   5  7273 O1B in CTP 902
REMARK   5  7274 O2B in CTP 902
REMARK   5  7275 O3B in CTP 902
REMARK   5  7276 PG in CTP 902
REMARK   5  7277 O1G in CTP 902
REMARK   5  7278 O2G in CTP 902
REMARK   5  7279 O3G in CTP 902
REMARK   5
REMARK   6 Total charge on this protein: -10. e
REMARK   6

Bill

On Fri, 21 Sep 2007 08:46:43 -0700
DeLano Scientific del...@delsci.info wrote:

  Evan,
  
 This appears to be a problem with file format incompatibility between PyMOL
 and the psize.py script.  I suspect that rounding off the atom coordinates
 will eliminate it:
  
 alter_state 1, all, (x,y,z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
 int(z*1000)/1000.0)
  
 Cheers,
 Warren
   _  
 
 From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
 Kantrowitz
 Sent: Friday, September 21, 2007 7:28 AM
 To: PyMOL-users@lists.sourceforge.net
 Subject: [PyMOL] Pymol apbs problem
 
 
 
 With a certain file 1za1 from pdb when I try to run apbs I get the errors
 below. Other files are OK. Any suggestions? 
 
 error: 1
 ValueError Exception in Tk callback
 Function: function lambda at 0x182892b0 (type: type 'function')
 Args: ()
 Traceback (innermost last):
 File
 
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
 Base.py, line 1747, in __call__
 return apply(self.func, args)
 File
 
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
 Dialog.py, line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
 File
 
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/Pmw/Pmw_1_2/lib/Pmw
 Dialog.py, line 132, in _doCommand
 return command(name)
 File
 
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
 _tools.py, line , in execute
 self.runPsize()
 File
 
/Applications/MacPyMol/PyMOLX11Hybrid.app/pymol/modules/pmg_tk/startup/apbs
 _tools.py, line 1155, in runPsize
 size.runPsize(pdb_filename)
 File /sw/share/xtal/bin/psize.py, line 267, in runPsize
 self.parseInput(filename)
 File /sw/share/xtal/bin/psize.py, line 102, in parseInput
 self.parseLines(file.readlines())
 File /sw/share/xtal/bin/psize.py, line

[PyMOL] apbs problem

[Ashwini Mishra]

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 input from PDB  
file. Same problem. Any suggestion would be appreciated.

Thanks
Ashwini

Re: [PyMOL] apbs problem

[J. Evan Sadler]

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 processor apbs 3.2 but an older version of the mac/x11 hybrid pymol,
using the same pdb files.


Evan Sadler

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Washington University
660 S. Euclid Ave., Box 8022
St. Louis, MO   63110
Tel: 314-362-9067
FAX: 314-454-3012
email: esad...@im.wustl.edu




On 11/21/05 10:36 AM, Ashwini Mishra ashwini.mis...@umassmed.edu wrote:

 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 input from PDB
 file. Same problem. Any suggestion would be appreciated.
 Thanks
 Ashwini
 
 
 
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