Re: [PyMOL] apbs: program locations

[Matic Kisovec]

Hi Michael,

if you haven't figured it out yet, this thread might help you:
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/EAA6862A-4914-483F-A12F-92B5A1E81233%40schrodinger.com/

It can be done in the configuration file of the plugin.

Best regards!
Matic


On 1. 06. 22 05:26, 
michaelmorgan...@gmail.com wrote:
Dear all,

Can I save the “program locations” information in APBS plugin? Once I exit the 
plugin and open it again, the previous input disappears.
I am using windows version pymol.

Thank you very much.

Michael


[cid:part1.ZgVG4059.i8Jnps8h@ki.si]




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[PyMOL] apbs: program locations

[michaelmorgan937]

Dear all,

 

Can I save the "program locations" information in APBS plugin? Once I exit
the plugin and open it again, the previous input disappears. 

I am using windows version pymol.

 

Thank you very much.

 

Michael

 

 



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Re: [PyMOL] APBS with ions

[Thomas Holder]

Hi Kamil,

The "Selection" field uses "polymer & ..." by default, which excludes
ions. You can use a selection which includes ions instead, for example
"all", "not solvent", or something like "(polymer | name CAL) & ...".

Here an example that works for me:

fetch 1rx1
alter elem Ca, resn="CAL"
alter elem Ca, name="CAL"

In the APBS Electrostatics panel, use "(polymer | name CAL) & 1rx1" as
the selection and "--ff=CHARMM" as pdb2pqr command line option.

Hope that helps.

Cheers,
  Thomas

On Mon, Nov 1, 2021 at 9:21 PM Kamil Steczkiewicz
 wrote:
>
> Hi,
> How to include Ca/Zn ions when using APBS built into Pymol? I'm switching to 
> CHARMM in command line options; CHARMM has CAL and ZN2 atoms already defined 
> in the DAT file. But there's still no difference in electrostatics maps with 
> and without ions in the structure. Also, the default 'prepared01' object 
> lacks the ions.
> Thanks for any clues,
> Kamil
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[PyMOL] APBS with ions

[Kamil Steczkiewicz]

Hi,
How to include Ca/Zn ions when using APBS built into Pymol? I'm switching
to CHARMM in command line options; CHARMM has CAL and ZN2 atoms already
defined in the DAT file. But there's still no difference in electrostatics
maps with and without ions in the structure. Also, the default 'prepared01'
object lacks the ions.
Thanks for any clues,
Kamil
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Re: [PyMOL] APBS plugin for Sugars

[Mario Garcia Urena]

Thank you so much for your quick answer!

Now I can access the file and I was wondering how to get amber data for 
specific molecules. I know that the GLYCAM parameters exist, but as far as I 
understand I can see only bond information. If, for alanine, the amber.dat file 
has the following:

ALA N   -0.415700   1.8240  N
ALA H   0.2719000.6000  H
ALA CA  0.0337001.9080  CT
ALA HA  0.0823001.3870  H1
ALA CB  -0.182500   1.9080  CT
ALA HB1 0.0603001.4870  HC
ALA HB2 0.0603001.4870  HC
ALA HB3 0.0603001.4870  HC
ALA C   0.5973001.9080  C
ALA O   -0.567900   1.6612  O

I was wondering how I could get this info for SIA (Sialic Acid). Is there any 
library where I could get it in this format? Or maybe some tool to get them 
from pdb information (if feasible, I am brainstorming!)

Thanks again for your help and for your help in advance,

Mario

-Original Message-
From: Thomas Holder  
Sent: Monday, June 15, 2020 9:37 AM
To: Mario Garcia Urena 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS plugin for Sugars

Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to 
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, 
the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena  wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For 
> proteins I adapted a code and the dipole moments are correct and work just 
> fine, but for sugars it does not. I am well aware that the problem is that 
> many of the residues are not present in the AMBER force field data (or the 
> force field I want to use.) In APBS it is relatively easy to adapt and 
> introduce the sugars’ information manually, however in the APBS plugin for 
> pymol gets a little bit thorny. I cannot seem to find the files where I 
> should store the sugar information. Has anybody done this before? Any 
> alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
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Re: [PyMOL] APBS plugin for Sugars

[Thomas Holder]

Hi Mario,

Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to 
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux, 
the AMBER force field data files can be found like this:

$ find . -name "AMBER.*"
./lib/python3.7/site-packages/src/dat/AMBER.names
./lib/python3.7/site-packages/src/dat/AMBER.DAT


Hope that helps.

Cheers,
  Thomas


> On Jun 14, 2020, at 6:35 PM, Mario Garcia Urena  wrote:
> 
> Hi all,
>  
> I was trying to generate dipole moments with pymol using the APBS plugin. For 
> proteins I adapted a code and the dipole moments are correct and work just 
> fine, but for sugars it does not. I am well aware that the problem is that 
> many of the residues are not present in the AMBER force field data (or the 
> force field I want to use.) In APBS it is relatively easy to adapt and 
> introduce the sugars’ information manually, however in the APBS plugin for 
> pymol gets a little bit thorny. I cannot seem to find the files where I 
> should store the sugar information. Has anybody done this before? Any 
> alternatives with other programs or approaches are also welcome.
>  
> Thank you in advance,
>  
> Mario
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> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
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PyMOL Principal Developer
Schrödinger, Inc.



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[PyMOL] APBS plugin for Sugars

[Mario Garcia Urena]

Hi all,

I was trying to generate dipole moments with pymol using the APBS plugin. For 
proteins I adapted a code and the dipole moments are correct and work just 
fine, but for sugars it does not. I am well aware that the problem is that many 
of the residues are not present in the AMBER force field data (or the force 
field I want to use.) In APBS it is relatively easy to adapt and introduce the 
sugars' information manually, however in the APBS plugin for pymol gets a 
little bit thorny. I cannot seem to find the files where I should store the 
sugar information. Has anybody done this before? Any alternatives with other 
programs or approaches are also welcome.

Thank you in advance,

Mario
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Re: [PyMOL] Pymol APBS plugin error

[Jack Howarth]

Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to
use an externally generated pqr file. The current mechanism for calling
pdb2pqr from within the APBS Tool results in pdb2pqr running under the same
python as pymol.
Jack

On Mon, Dec 2, 2019 at 5:58 PM Jack Howarth 
wrote:

> You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...
>
>
> https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff
>
> and
>
>
> https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff
>
> applied over Pmw_2_0_0.
> Jack
>
> On Mon, Dec 2, 2019 at 2:43 PM RDirective  wrote:
>
>> Dear all,
>>
>>
>> I get the following errors when trying to launch the APBS plugin from the
>> plugins menu
>>
>>
>> Traceback (most recent call last):
>>
>>   File 
>> "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 
>> 322, in 
>> command = lambda s=self: APBSTools2(s))
>>
>>   File 
>> "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 
>> 617, in __init__
>> self.notebook = Pmw.NoteBook(self.dialog.interior())
>>
>>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py", 
>> line 60, in __init__
>> Pmw.Color.bordercolors(self, self['hull_background'])
>>
>>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py", 
>> line 359, in bordercolors
>> '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
>> TypeError: %x format: an integer is required, not float
>>
>>
>> Pymol source Version 2.4.0a0
>>
>>
>> Best,
>>
>> Quyen
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>
>
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Re: [PyMOL] Pymol APBS plugin error

[Jack Howarth]

You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...

https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff

and

https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff

applied over Pmw_2_0_0.
Jack

On Mon, Dec 2, 2019 at 2:43 PM RDirective  wrote:

> Dear all,
>
>
> I get the following errors when trying to launch the APBS plugin from the
> plugins menu
>
>
> Traceback (most recent call last):
>
>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", 
> line 322, in 
> command = lambda s=self: APBSTools2(s))
>
>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", 
> line 617, in __init__
> self.notebook = Pmw.NoteBook(self.dialog.interior())
>
>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py", 
> line 60, in __init__
> Pmw.Color.bordercolors(self, self['hull_background'])
>
>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py", line 
> 359, in bordercolors
> '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
> TypeError: %x format: an integer is required, not float
>
>
> Pymol source Version 2.4.0a0
>
>
> Best,
>
> Quyen
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[PyMOL] Pymol APBS plugin error

[RDirective]

Dear all,


I get the following errors when trying to launch the APBS plugin from the
plugins menu


Traceback (most recent call last):
  File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 322, in 
command = lambda s=self: APBSTools2(s))
  File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 617, in __init__
self.notebook = Pmw.NoteBook(self.dialog.interior())
  File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py",
line 60, in __init__
Pmw.Color.bordercolors(self, self['hull_background'])
  File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py",
line 359, in bordercolors
'#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
TypeError: %x format: an integer is required, not float


Pymol source Version 2.4.0a0


Best,

Quyen
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[PyMOL] APBS TOOLS 2.1 does not work

[sunyeping via PyMOL-users]

Dear all, 

I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of 
proteins. After I finish "set grid", I press the "set grid" button, I get the 
following error,

(, ImportError('No module named pdb2pqr',), 
)
In show error 2

Could you tell what is the cause of the error and how to fix it?

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[PyMOL] APBS "%x format: an integer is required, not float" error in pymol installed with python 3.7 and "Qt not available, using GLUT/Tk interface" error

[sunyeping via PyMOL-users]

Dear everyone,

I am trying to use the APBS plugin in pymol to calculate protein electrostatic 
potentials. My system is centos 7. The pymol was installed with python 3.7 
(~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1 
from the plugin menu of pymol, a window jumps out which reads: "%x format: an 
integer is required, not float". I've googled it and learned that this error 
may related to python version. So I try to swith to pymol installed with 
python2.7 (/usr/bin/python)
 I install pymol following the guide at 
https://pymolwiki.org/index.php/Linux_Install, with the command:

 /usr/bin/python setup.py  install 
--prefix=~/software/pymol/pymol-python2.7-install

After the installation finished, I tried to lauch pymol, but meet the error:

Qt not available, using GLUT/Tk interface
Traceback (most recent call last):
  File 
"/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py",
 line 65, in 
pymol.launch(args)
  File 
"/home/sunyp/software/pymol/pymol-python2.7-install/lib64/python2.7/site-packages/pymol/__init__.py",
 line 436, in launch
_cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
NotImplementedError: compile with --glut

Acturally the PyQt4 have been install in my system, I don't understand why it 
is not available by pymol. And why pymol installed with python3.7 doesn't have 
such a problem.  Even if I reinstall pymol with --glut option:

 /usr/bin/python setup.py  --glut build install 
--prefix=~/software/pymol/pymol-python2.7-install

the same error still comes out. Could you help me with this problem? Thank you 
in advance.
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[PyMOL] APBS plugin on pymol 1.5 does not work

[Yanni Goudeuk]

Hello

I recently installed PyMOL version 1.5 no my MAC 10.9 using HomeBrew.
There were no problems with the installation at all however the APBS plugin
when loaded it gives me this error:

Error: 4
 Exception in Tk callback
  Function:  at 0x106691758> (type: )
  Args: ()
Traceback (innermost last):
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
line 1753, in __call__
return apply(self.func, args)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
line 265, in 
command = lambda s=self: APBSTools2(s))
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
line 628, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File "", line 1, in pack
None
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-tk/Tkinter.py",
line 1764, in pack_configure
+ self._options(cnf, kw))
: cannot use geometry manager pack inside
.4388449240.4388454480.4388457144.4388479776 which already has slaves
managed by grid

Could someone help me resolve this error please?

Many thanks
goude

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Re: [PyMOL] PyMOL + APBS plugin

[Thomas Holder]

Hi Matic,

1. If you have conflicting (non-unique) file names, you have two options:
  a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
  b) Set the "auto_rename_duplicate_objects" setting

2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days 
ago. If you don't want to recompile, you can also install the updated plugin 
manually from here: http://pymolwiki.org/index.php/Apbsplugin

3. Use the "matrix_copy" command to transfer the transformation matrix from the 
molecular object to the map object after alignment (matrix_copy foo_1, 
foo_1_map)

Hope that helps.

Cheers,
  Thomas 

On 13 Jan 2016, at 13:19, Matic Kisovec  wrote:

> Dear all,
> 
> I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I 
> use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 
> 1.8.0.0.
> 
>   • First I tried to perform a couple of APBS calculations through the 
> APBS plugin window and all went great. Then I did a batch pdb2pqr 
> transformation on my local machine and then a batch apbs calculation also on 
> my local machine. Both directly in terminal (no connection with Pymol). I 
> more or less followed these instructions: http://jamiebaxter.com/blog/?p=890 
> . After the calculations I ended up with all the standard files (.in, .pqr 
> and .dx). The issue was that I was not able to load them in Pymol. After 
> loading .pqr and .dx the tab 'Visualization' in APBS plugin windows kept 
> saying to load a molecule and a map. And after clicking the button 'Update' 
> nothing happened. There was no error reported. First I thought there has to 
> be something wrong with the manual procedure of generating .pqr and .dx 
> files. More or less by accident I figured out the problem is in the names of 
> files. I generated them to be identical and the only difference was the 
> extension (for example foo_1.pqr and foo_1.dx). If I changed one of the names 
> (I just tried .dx for now) and added or deleted a single character everything 
> went smoothly once loaded in Pymol. Is this a problem/bug only in my case 
> since the APBS plugin also creates temporary files with identical names?
>   • Another possible bug is present in the 'Visualization' tab of APBS 
> plugin. If one uses the button 'Update' in the 'Maps and Molecules' field 
> (the one marked in orange in this image: 
> https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses 
> the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and 
> 'Molecular Surface'. They keep on moving downwards until you loose the from 
> the screen (see the image in the previous link to see this). 'Field lines' 
> fields keep appearing after each click on the 'Update' button. Of course one 
> can restrain from using the mentioned 'Update' button since it seems to me 
> that it is not really necessary at all. But still it is a strange behaviour.
>   • This is just a question not an issue really. Is there an easy way to 
> visualise multiple aligned proteins with their electrostatic surfaces 
> simultaneously? I tried 'set grid_mode' and it works but not if I do an 
> alignment after loading the pqr structure and the APBS map. I suppose I 
> could/should align them before doing the calculations but since I didn't it 
> would be great if it is possible to do this during visualization.
> Hopefully somebody can look into this or at least find this through googling 
> and in this way save a couple of minutes or hours.
> All the best,
> Matic Kisovec

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] PyMOL + APBS plugin

[Matic Kisovec]

Dear Thomas,

thank you for these short and perfect answers.

  1.  All fine now.
  2.  Updated the plugin and the GUI bug is gone. One more thing though. 
Whenever I click the button to either set temporary file locations or to set 
program locations in APBS GUI window I immediately get a Segmentation fault 
error (/usr/local/bin/pymol: line 3:  9250 Segmentation fault  (core 
dumped)).
  3.  Also works great.

Thank you again for your quick reply! Your help is invaluable to me (and 
probably to many other users of Pymol).
Keep up the good work!

Kind regards,
Matic


On 13. 01. 2016 20:01, Thomas Holder wrote:

Hi Matic,

1. If you have conflicting (non-unique) file names, you have two options:
  a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
  b) Set the "auto_rename_duplicate_objects" setting

2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days 
ago. If you don't want to recompile, you can also install the updated plugin 
manually from here: http://pymolwiki.org/index.php/Apbsplugin

3. Use the "matrix_copy" command to transfer the transformation matrix from the 
molecular object to the map object after alignment (matrix_copy foo_1, 
foo_1_map)

Hope that helps.

Cheers,
  Thomas

On 13 Jan 2016, at 13:19, Matic Kisovec 
 wrote:



Dear all,

I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I 
use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0.

• First I tried to perform a couple of APBS calculations through the 
APBS plugin window and all went great. Then I did a batch pdb2pqr 
transformation on my local machine and then a batch apbs calculation also on my 
local machine. Both directly in terminal (no connection with Pymol). I more or 
less followed these instructions: http://jamiebaxter.com/blog/?p=890 . After 
the calculations I ended up with all the standard files (.in, .pqr and .dx). 
The issue was that I was not able to load them in Pymol. After loading .pqr and 
.dx the tab 'Visualization' in APBS plugin windows kept saying to load a 
molecule and a map. And after clicking the button 'Update' nothing happened. 
There was no error reported. First I thought there has to be something wrong 
with the manual procedure of generating .pqr and .dx files. More or less by 
accident I figured out the problem is in the names of files. I generated them 
to be iden
tical and the only difference was the extension (for example foo_1.pqr and 
foo_1.dx). If I changed one of the names (I just tried .dx for now) and added 
or deleted a single character everything went smoothly once loaded in Pymol. Is 
this a problem/bug only in my case since the APBS plugin also creates temporary 
files with identical names?
• Another possible bug is present in the 'Visualization' tab of APBS 
plugin. If one uses the button 'Update' in the 'Maps and Molecules' field (the 
one marked in orange in this image: 
https://app.box.com/s/wztcwondd0fiqqczdyekhnd3ltfo0nxa) then one slowly loses 
the option to use the fields 'Positive Isosurface', 'Neg. Isosurface' and 
'Molecular Surface'. They keep on moving downwards until you loose the from the 
screen (see the image in the previous link to see this). 'Field lines' fields 
keep appearing after each click on the 'Update' button. Of course one can 
restrain from using the mentioned 'Update' button since it seems to me that it 
is not really necessary at all. But still it is a strange behaviour.
• This is just a question not an issue really. Is there an easy way to 
visualise multiple aligned proteins with their electrostatic surfaces 
simultaneously? I tried 'set grid_mode' and it works but not if I do an 
alignment after loading the pqr structure and the APBS map. I suppose I 
could/should align them before doing the calculations but since I didn't it 
would be great if it is possible to do this during visualization.
Hopefully somebody can look into this or at least find this through googling 
and in this way save a couple of minutes or hours.
All the best,
Matic Kisovec





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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 plugin not working on both Ubuntu Windows 7

[Brenton Horne]

Hi,

pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or 
1.8 versions; in a previous question I was advised to use the 1.8 
version) and consequently APBS tools doesn't work. I have tried turning 
the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but 
the APBS failed to set up the grid after I did this. Is there any way 
around this?

Thanks for your time,
Brenton

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Re: [PyMOL] APBS plugin not working on both Ubuntu Windows 7

[Matic Kisovec]

Hello Brenton,

I used the pdd2pqr provided by Ubuntu repositories (version 1.8) and installed 
it directly(with Synaptic) from there.
The path on my Xubuntu system is: /usr/share/pdb2pqr/pdb2pqr.py

I also tried setting something up on Windows but gave up eventually.

Good luck and all the best,
Matic


On 14. 04. 2015 08:39, Brenton Horne wrote:

Hi,

pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
1.8 versions; in a previous question I was advised to use the 1.8
version) and consequently APBS tools doesn't work. I have tried turning
the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but
the APBS failed to set up the grid after I did this. Is there any way
around this?

Thanks for your time,
Brenton

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attachment: matic_kisovec.vcf--
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Re: [PyMOL] APBS plugin not working on both Ubuntu Windows 7

[David Hall]

There is an INSTALL file that provides instructions. The first step,
calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in

If you want to manually do it, it just changes the first line in the file
to point to your python installation. But, since there's a whole bunch of
other things ./configure appears to do, I suggest following the steps in
the INSTALL file.

-David


On Tue, Apr 14, 2015 at 2:39 AM, Brenton Horne brentonho...@ymail.com
wrote:

 Hi,

 pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
 1.8 versions; in a previous question I was advised to use the 1.8
 version) and consequently APBS tools doesn't work. I have tried turning
 the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but
 the APBS failed to set up the grid after I did this. Is there any way
 around this?

 Thanks for your time,
 Brenton


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 Develop your own process in accordance with the BPMN 2 standard
 Learn Process modeling best practices with Bonita BPM through live
 exercises
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Re: [PyMOL] apbs error (Error in background function)

[Matic Kisovec]

Dear Thomas,

thank you a lot for your quick reply.
Just to help the users that might find these posts in the future; the path in 
my case was:
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py
and the plugin settings look like this:
...
# Global config variables
#
# To change the default locations, change these to something like
# APBS_BINARY_LOCATION = '/opt/bin/'
#
APBS_BINARY_LOCATION = '/usr/bin/apbs/'
APBS_WEB_LOCATION = None # corresponding environment variable: APBS_WEB_DIR
APBS_PSIZE_LOCATION = '/usr/share/pdb2pqr/src/'
APBS_PDB2PQR_LOCATION = '/usr/share/pdb2pqr/'
TEMPORARY_FILE_DIR = tempfile.gettempdir() # corresponding environment 
variable: TEMP
...

Kind regards,
Matic Kisovec


On 30. 01. 2015 21:21, Thomas Holder wrote:

Dear Matic,

the only option to permanently store those paths is to edit the plugin file. 
Look for apbs_tools.py in the PyMOL installation directory and there for 
Global config variables.

Cheers,
  Thomas

On 30 Jan 2015, at 00:33, Matic Kisovec 
matic.kiso...@ki.simailto:matic.kiso...@ki.si wrote:



Dear Thomas,

thank you for your quick reply.
I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as 
expected.

I do have one more issue. Every time I execute Pymol I get two lines saying:
Could not find default location for file: psize.py
Could not find default location for file: pdb2pqr.py
I manually set up the paths but they get lost when I exit pymol.
Is there a way to permanently store this information?

Kind regards,
Matic

On 28. 01. 2015 16:58, Thomas Holder wrote:


Dear Matic,

this was fixed for 1.7.4:
https://sourceforge.net/p/pymol/code/4099/


Please install the latest version.

Cheers,
  Thomas

On 28 Jan 2015, at 10:04, Matic Kisovec
matic.kiso...@ki.simailto:matic.kiso...@ki.si
 wrote:




Dear Pymol users,

I have recieved the same error as mentioned in the email ate bottom that was 
sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply 
that is a known bug and a link was provided. The bug was filed in March 2013.

The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a 
quick and fresh install inside Virtualbox and after the OS installation 
finished I installed Pymol and its dependencies. Pymol version in Ubuntu 
repositories is 1.7.0. When I select PluginAPBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x7faa60852578 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 
1747, in __call__
return apply(self.func, args)
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /usr/lib/python2.7/lib-tk/Tkinter.py, line 1890, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.140369735891136.140369735892288.140369735980600.140369614990728 which already 
has slaves managed by grid
I am wondering though if this is some problem on my side since it has not been 
mentioned very often online. That is why I tried a fresh installation inside 
Virtualbox and the issue was the same.

Any help would be greatly appreciated.

Kind regards,
Matic



Hello,

 I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package 
manager.  Now, when I initiate the APBS Tools.1 plugin the following error 
occurs:

Error in background function

Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x10cc75230 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
1753, in __call__
return apply(self.func, args)
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
by grid

I brought this to the attention of apbs developers who suggested I post this 
error here as it seems related to PyMol and not apbs.  Not a very savvy user 
here so this may be entirely my fault.

Thank you!





attachment: matic_kisovec.vcf--
Dive 

Re: [PyMOL] apbs error (Error in background function)

[Thomas Holder]

Dear Matic,

the only option to permanently store those paths is to edit the plugin file. 
Look for apbs_tools.py in the PyMOL installation directory and there for 
Global config variables.

Cheers,
  Thomas

On 30 Jan 2015, at 00:33, Matic Kisovec matic.kiso...@ki.si wrote:

 Dear Thomas,
 
 thank you for your quick reply. 
 I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as 
 expected.
 
 I do have one more issue. Every time I execute Pymol I get two lines saying:
 Could not find default location for file: psize.py
 Could not find default location for file: pdb2pqr.py
 I manually set up the paths but they get lost when I exit pymol.
 Is there a way to permanently store this information?
 
 Kind regards,
 Matic
 
 On 28. 01. 2015 16:58, Thomas Holder wrote:
 Dear Matic,
 
 this was fixed for 1.7.4: 
 https://sourceforge.net/p/pymol/code/4099/
 
 
 Please install the latest version.
 
 Cheers,
   Thomas
 
 On 28 Jan 2015, at 10:04, Matic Kisovec 
 matic.kiso...@ki.si
  wrote:
 
 
 Dear Pymol users,
 
 I have recieved the same error as mentioned in the email ate bottom that 
 was sent by DE FALCO JR LOUIS in September 2014 to this list. There was one 
 reply that is a known bug and a link was provided. The bug was filed in 
 March 2013.
 
 The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried 
 a quick and fresh install inside Virtualbox and after the OS installation 
 finished I installed Pymol and its dependencies. Pymol version in Ubuntu 
 repositories is 1.7.0. When I select PluginAPBS Tools2.1 I get a popup 
 with the following error that is almost identical to the one from DE FALCO 
 JR LOUIS:
 Error: 1
 class '_tkinter.TclError' Exception in Tk callback
   Function: function lambda at 0x7faa60852578 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line 314, in lambda
 command = lambda s=self: APBSTools2(s))
   File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line 680, in __init__
 group.pack(fill='both',expand=1, padx=4, pady=5)
   File string, line 1, in pack
 None
   File /usr/lib/python2.7/lib-tk/Tkinter.py, line 1890, in pack_configure
 + self._options(cnf, kw))
 class '_tkinter.TclError': cannot use geometry manager pack inside 
 .140369735891136.140369735892288.140369735980600.140369614990728 which 
 already has slaves managed by grid
 I am wondering though if this is some problem on my side since it has not 
 been mentioned very often online. That is why I tried a fresh installation 
 inside Virtualbox and the issue was the same.
 
 Any help would be greatly appreciated.
 
 Kind regards,
 Matic
 
 
 
 Hello, 
 
  I just updated PyMol Open Source to version 1.7.2.0-2 via the fink 
 package manager.  Now, when I initiate the APBS Tools.1 plugin the 
 following error occurs:
 
 Error in background function
 
 Error: 1
 class '_tkinter.TclError' Exception in Tk callback
   Function: function lambda at 0x10cc75230 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
 1753, in __call__
 return apply(self.func, args)
   File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
 314, in lambda
 command = lambda s=self: APBSTools2(s))
   File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
 680, in __init__
 group.pack(fill='both',expand=1, padx=4, pady=5)
   File string, line 1, in pack
 None
   File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
 + self._options(cnf, kw))
 class '_tkinter.TclError': cannot use geometry manager pack inside 
 .4509565296.4509566808.4509809840.4510083120 which already has slaves 
 managed by grid
 
 I brought this to the attention of apbs developers who suggested I post 
 this error here as it seems related to PyMol and not apbs.  Not a very 
 savvy user here so this may be entirely my fault.
 
 Thank you!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] apbs error (Error in background function)

[Matic Kisovec]

Dear Thomas,

thank you for your quick reply.
I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as 
expected.

I do have one more issue. Every time I execute Pymol I get two lines saying:
Could not find default location for file: psize.py
Could not find default location for file: pdb2pqr.py
I manually set up the paths but they get lost when I exit pymol.
Is there a way to permanently store this information?

Kind regards,
Matic



On 28. 01. 2015 16:58, Thomas Holder wrote:

Dear Matic,

this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/

Please install the latest version.

Cheers,
  Thomas

On 28 Jan 2015, at 10:04, Matic Kisovec 
matic.kiso...@ki.simailto:matic.kiso...@ki.si wrote:



Dear Pymol users,

I have recieved the same error as mentioned in the email ate bottom that was 
sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply 
that is a known bug and a link was provided. The bug was filed in March 2013.

The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a 
quick and fresh install inside Virtualbox and after the OS installation 
finished I installed Pymol and its dependencies. Pymol version in Ubuntu 
repositories is 1.7.0. When I select PluginAPBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x7faa60852578 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 
1747, in __call__
return apply(self.func, args)
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /usr/lib/python2.7/lib-tk/Tkinter.py, line 1890, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.140369735891136.140369735892288.140369735980600.140369614990728 which already 
has slaves managed by grid
I am wondering though if this is some problem on my side since it has not been 
mentioned very often online. That is why I tried a fresh installation inside 
Virtualbox and the issue was the same.

Any help would be greatly appreciated.

Kind regards,
Matic



Hello,

 I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package 
manager.  Now, when I initiate the APBS Tools.1 plugin the following error 
occurs:

Error in background function

Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x10cc75230 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
1753, in __call__
return apply(self.func, args)
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
by grid

I brought this to the attention of apbs developers who suggested I post this 
error here as it seems related to PyMol and not apbs.  Not a very savvy user 
here so this may be entirely my fault.

Thank you!


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Re: [PyMOL] apbs error (Error in background function)

[Matic Kisovec]

Dear Pymol users,

I have recieved the same error as mentioned in the email ate bottom that was 
sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply 
that is a known bug and a link was provided. The bug was filed in March 2013.

The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a 
quick and fresh install inside Virtualbox and after the OS installation 
finished I installed Pymol and its dependencies. Pymol version in Ubuntu 
repositories is 1.7.0. When I select PluginAPBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x7faa60852578 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 
1747, in __call__
return apply(self.func, args)
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /usr/lib/python2.7/lib-tk/Tkinter.py, line 1890, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.140369735891136.140369735892288.140369735980600.140369614990728 which already 
has slaves managed by grid
I am wondering though if this is some problem on my side since it has not been 
mentioned very often online. That is why I tried a fresh installation inside 
Virtualbox and the issue was the same.

Any help would be greatly appreciated.

Kind regards,
Matic




Hello,

 I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package 
manager.  Now, when I initiate the APBS Tools.1 plugin the following error 
occurs:

Error in background function

Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x10cc75230 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
1753, in __call__
return apply(self.func, args)
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
by grid

I brought this to the attention of apbs developers who suggested I post this 
error here as it seems related to PyMol and not apbs.  Not a very savvy user 
here so this may be entirely my fault.

Thank you!

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Re: [PyMOL] apbs error (Error in background function)

[Thomas Holder]

Dear Matic,

this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/

Please install the latest version.

Cheers,
  Thomas

On 28 Jan 2015, at 10:04, Matic Kisovec matic.kiso...@ki.si wrote:

 Dear Pymol users,
 
 I have recieved the same error as mentioned in the email ate bottom that was 
 sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply 
 that is a known bug and a link was provided. The bug was filed in March 2013.
 
 The difference is this time this happened on Ubuntu 14.04.1 OS. So I tried a 
 quick and fresh install inside Virtualbox and after the OS installation 
 finished I installed Pymol and its dependencies. Pymol version in Ubuntu 
 repositories is 1.7.0. When I select PluginAPBS Tools2.1 I get a popup with 
 the following error that is almost identical to the one from DE FALCO JR 
 LOUIS:
 Error: 1
 class '_tkinter.TclError' Exception in Tk callback
   Function: function lambda at 0x7faa60852578 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line 
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
 314, in lambda
 command = lambda s=self: APBSTools2(s))
   File /usr/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line 
 680, in __init__
 group.pack(fill='both',expand=1, padx=4, pady=5)
   File string, line 1, in pack
 None
   File /usr/lib/python2.7/lib-tk/Tkinter.py, line 1890, in pack_configure
 + self._options(cnf, kw))
 class '_tkinter.TclError': cannot use geometry manager pack inside 
 .140369735891136.140369735892288.140369735980600.140369614990728 which 
 already has slaves managed by grid
 I am wondering though if this is some problem on my side since it has not 
 been mentioned very often online. That is why I tried a fresh installation 
 inside Virtualbox and the issue was the same.
 
 Any help would be greatly appreciated.
 
 Kind regards,
 Matic
 
 
 
 Hello, 
 
  I just updated PyMol Open Source to version 1.7.2.0-2 via the fink 
 package manager.  Now, when I initiate the APBS Tools.1 plugin the following 
 error occurs:
 
 Error in background function
 
 Error: 1
 class '_tkinter.TclError' Exception in Tk callback
   Function: function lambda at 0x10cc75230 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
 1753, in __call__
 return apply(self.func, args)
   File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
 314, in lambda
 command = lambda s=self: APBSTools2(s))
   File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
 680, in __init__
 group.pack(fill='both',expand=1, padx=4, pady=5)
   File string, line 1, in pack
 None
   File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
 + self._options(cnf, kw))
 class '_tkinter.TclError': cannot use geometry manager pack inside 
 .4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
 by grid
 
 I brought this to the attention of apbs developers who suggested I post this 
 error here as it seems related to PyMol and not apbs.  Not a very savvy user 
 here so this may be entirely my fault.
 
 Thank you!

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] apbs error (Error in background function)

[Thomas, Jens]

Hi,

I think this is a known bug:

http://sourceforge.net/p/pymolapbsplugin/bugs/1/

There is a fix mentioned but it involves patching the source code for the 
plugin, which worked for me but is somewhat involved. However it might help you 
find a solution or lead someone else to suggest something simpler that might 
work.

Best wishes,

Jens



From: #DE FALCO JR LOUIS# [defa0...@e.ntu.edu.sg]
Sent: 01 September 2014 01:54
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs error (Error in background function)

Hello,

 I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package 
manager.  Now, when I initiate the APBS Tools.1 plugin the following error 
occurs:

Error in background function

Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x10cc75230 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
1753, in __call__
return apply(self.func, args)
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
by grid

I brought this to the attention of apbs developers who suggested I post this 
error here as it seems related to PyMol and not apbs.  Not a very savvy user 
here so this may be entirely my fault.

Thank you!
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[PyMOL] apbs error (Error in background function)

[#DE FALCO JR LOUIS#]

Hello, 

 I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package 
manager.  Now, when I initiate the APBS Tools.1 plugin the following error 
occurs:

Error in background function

Error: 1
class '_tkinter.TclError' Exception in Tk callback
  Function: function lambda at 0x10cc75230 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /sw/lib/python2.7/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py, line 
1753, in __call__
return apply(self.func, args)
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
314, in lambda
command = lambda s=self: APBSTools2(s))
  File /sw/lib/python2.7/site-packages/pmg_tk/startup/apbs_tools.py, line 
680, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File string, line 1, in pack
None
  File /sw/lib/python2.7/lib-tk/Tkinter.py, line 1887, in pack_configure
+ self._options(cnf, kw))
class '_tkinter.TclError': cannot use geometry manager pack inside 
.4509565296.4509566808.4509809840.4510083120 which already has slaves managed 
by grid

I brought this to the attention of apbs developers who suggested I post this 
error here as it seems related to PyMol and not apbs.  Not a very savvy user 
here so this may be entirely my fault.

Thank you!
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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 plugin

[jp d]

hi,
more information:
down in function askfilename
if i change self.activate() to self.show() i can get the file dialogue
to pop up but cant do anything with it.

its also near where tabs and spaces start making for confusing indentation.

that might be the source of the problem.





 From: jp d yo...@yahoo.com
To: Thomas Holder thomas.hol...@schrodinger.com 
Cc: Schubert, Carsten [JRDUS] cschu...@its.jnj.com; 
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net 
Sent: Wednesday, February 12, 2014 11:16 AM
Subject: Re: [PyMOL] apbs plugin
 


hi,
if i enable debugging i get a little more info



get_default_location will search the following :  ['/xtal/programs/pymol/ext', 
'/xtal/programs/pymol/ext/share/pdb2pqr', '/xtal/programs/pymol/ext/bin', 
'/sw/share/pdb2pqr', '/sw/share/apbs/tools/manip', 
'/sw/share/apbs-mpi-openmpi/tools/manip', 
'/sw/share/apbs-mpi-lammpi/tools/manip', '/usr/local/share/tools/manip', 
'/xtal/programs/3dna/x3dna-v2.1/bin', 
'/xtal/programs/xdsme-0.5beta1/bin/noarch', 
'/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/bin', 
'/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/utils', 
'/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/bin', 
'/home/donohue/bin', '/usr/local/sbin', '/usr/local/bin', '/usr/sbin', 
'/usr/bin', '/sbin', '/bin', '/usr/games', '/usr/local/bin', '/opt/local/bin', 
'/sw/bin']
trying /xtal/programs/pymol/ext/pdb2pqr.py
trying /xtal/programs/pymol/ext/pdb2pqr
trying /xtal/programs/pymol/ext/share/pdb2pqr/pdb2pqr.py
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
alloc: invalid block: 0x2c29fb78: 0 0
Abort





 From: Thomas Holder thomas.hol...@schrodinger.com
To: jp d yo...@yahoo.com 
Cc: Schubert, Carsten [JRDUS] cschu...@its.jnj.com; 
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net 
Sent: Wednesday, February 12, 2014 10:35 AM
Subject: Re: [PyMOL] apbs plugin
 

Hi jpd,

I can reproduce this, unfortunately. Thanks for reporting. It's indeed a 
problem with the GUI toolkit and not apbs itself. We are looking into it.

Cheers,
  Thomas


On 11 Feb 2014, at 16:21, jp d yo...@yahoo.com wrote:

 hi,
 good idea, it runs from the command line after adding
 /pymol/ext/lib to my library path
 
 but the plugin still crashes.
 something is odd about my APBS plugin setup.
 if i even just click to change the file locations
 it crashes.
 
 the other plugins seem fine.
 
 thanks
 jpd
 
 From: Schubert, Carsten [JRDUS] cschu...@its.jnj.com
 To: jp d yo...@yahoo.com; pymol-users@lists.sourceforge.net 
 pymol-users@lists.sourceforge.net 
 Sent: Tuesday, February 11, 2014 12:14 PM
 Subject: RE: [PyMOL] apbs plugin
 
 Hi jpd,
  
 try running APBS directly just using the .in file generated from a failed 
 run. That may provide a clue as to where the problem is, i.e. within APBS 
 itself or within the plugin. If it is APBS, which is throwing the error you 
 may
 want to try to grab an updated version or the source code to compile yourself.
  
 HTH
  
 Carsten
  
 From: jp d [mailto:yo...@yahoo.com] 
 Sent: Tuesday, February 11, 2014 2:52 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] apbs plugin
  
 hi,
 anyone else having trouble with the apbs plugin?
 i keep crashing as soon as i try to do anything.
 if i select 'Choose externally generated PQR'
 or 'run APBS' i get this
 In show error 1
 alloc: invalid block: 0x2c29fb78: 0 0
 Abort
  
 this is with pymol 1.7
 ubuntu 12.04
 using 1FAS fetched from the pdb
  
 thanks
 jpd


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.




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Re: [PyMOL] apbs plugin

[Thomas Holder]

Hi jpd,

I can reproduce this, unfortunately. Thanks for reporting. It's indeed a 
problem with the GUI toolkit and not apbs itself. We are looking into it.

Cheers,
  Thomas

On 11 Feb 2014, at 16:21, jp d yo...@yahoo.com wrote:

 hi,
 good idea, it runs from the command line after adding
 /pymol/ext/lib to my library path
 
 but the plugin still crashes.
 something is odd about my APBS plugin setup.
 if i even just click to change the file locations
 it crashes.
 
 the other plugins seem fine.
 
 thanks
 jpd
 
 From: Schubert, Carsten [JRDUS] cschu...@its.jnj.com
 To: jp d yo...@yahoo.com; pymol-users@lists.sourceforge.net 
 pymol-users@lists.sourceforge.net 
 Sent: Tuesday, February 11, 2014 12:14 PM
 Subject: RE: [PyMOL] apbs plugin
 
 Hi jpd,
  
 try running APBS directly just using the .in file generated from a failed 
 run. That may provide a clue as to where the problem is, i.e. within APBS 
 itself or within the plugin. If it is APBS, which is throwing the error you 
 may want to try to grab an updated version or the source code to compile 
 yourself.
  
 HTH
  
 Carsten
  
 From: jp d [mailto:yo...@yahoo.com] 
 Sent: Tuesday, February 11, 2014 2:52 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] apbs plugin
  
 hi,
 anyone else having trouble with the apbs plugin?
 i keep crashing as soon as i try to do anything.
 if i select 'Choose externally generated PQR'
 or 'run APBS' i get this
 In show error 1
 alloc: invalid block: 0x2c29fb78: 0 0
 Abort
  
 this is with pymol 1.7
 ubuntu 12.04
 using 1FAS fetched from the pdb
  
 thanks
 jpd


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
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Re: [PyMOL] apbs plugin

[jp d]

hi,
if i enable debugging i get a little more info



get_default_location will search the following :  ['/xtal/programs/pymol/ext', 
'/xtal/programs/pymol/ext/share/pdb2pqr', '/xtal/programs/pymol/ext/bin', 
'/sw/share/pdb2pqr', '/sw/share/apbs/tools/manip', 
'/sw/share/apbs-mpi-openmpi/tools/manip', 
'/sw/share/apbs-mpi-lammpi/tools/manip', '/usr/local/share/tools/manip', 
'/xtal/programs/3dna/x3dna-v2.1/bin', 
'/xtal/programs/xdsme-0.5beta1/bin/noarch', 
'/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/bin', 
'/xtal/programs/cns_solve_1.21/intel-x86_64bit-linux/utils', 
'/usr/local/phenix-1.8.4-1496/build/intel-linux-2.6-x86_64/bin', 
'/home/donohue/bin', '/usr/local/sbin', '/usr/local/bin', '/usr/sbin', 
'/usr/bin', '/sbin', '/bin', '/usr/games', '/usr/local/bin', '/opt/local/bin', 
'/sw/bin']
trying /xtal/programs/pymol/ext/pdb2pqr.py
trying /xtal/programs/pymol/ext/pdb2pqr
trying /xtal/programs/pymol/ext/share/pdb2pqr/pdb2pqr.py
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
get_default_location will search the following :  ['/tmp', '/tmp', '.']
alloc: invalid block: 0x2c29fb78: 0 0
Abort





 From: Thomas Holder thomas.hol...@schrodinger.com
To: jp d yo...@yahoo.com 
Cc: Schubert, Carsten [JRDUS] cschu...@its.jnj.com; 
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net 
Sent: Wednesday, February 12, 2014 10:35 AM
Subject: Re: [PyMOL] apbs plugin
 

Hi jpd,

I can reproduce this, unfortunately. Thanks for reporting. It's indeed a 
problem with the GUI toolkit and not apbs itself. We are looking into it.

Cheers,
  Thomas


On 11 Feb 2014, at 16:21, jp d yo...@yahoo.com wrote:

 hi,
 good idea, it runs from the command line after adding
 /pymol/ext/lib to my library path
 
 but the plugin still crashes.
 something is odd about my APBS plugin setup.
 if i even just click to change the file locations
 it crashes.
 
 the other plugins seem fine.
 
 thanks
 jpd
 
 From: Schubert, Carsten [JRDUS] cschu...@its.jnj.com
 To: jp d yo...@yahoo.com; pymol-users@lists.sourceforge.net 
 pymol-users@lists.sourceforge.net 
 Sent: Tuesday, February 11, 2014 12:14 PM
 Subject: RE: [PyMOL] apbs plugin
 
 Hi jpd,
  
 try running APBS directly just using the .in file generated from a failed 
 run. That may provide a clue as to where the problem is, i.e. within APBS 
 itself or within the plugin. If it is APBS, which is throwing the error you 
 may want to try to grab an updated version or the source code to compile 
 yourself.
  
 HTH
  
 Carsten
  
 From: jp d [mailto:yo...@yahoo.com] 
 Sent: Tuesday, February 11, 2014 2:52 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] apbs plugin
  
 hi,
 anyone else having trouble with the apbs plugin?
 i keep crashing as soon as i try to do anything.
 if i select 'Choose externally generated PQR'
 or 'run APBS' i get this
 In show error 1
 alloc: invalid block: 0x2c29fb78: 0 0
 Abort
  
 this is with pymol 1.7
 ubuntu 12.04
 using 1FAS fetched from the pdb
  
 thanks
 jpd


-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.--
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[PyMOL] apbs plugin

[jp d]

hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.

if i select 'Choose externally generated PQR'
or 'run APBS' i get this

In show error 1
alloc: invalid block: 0x2c29fb78: 0 0
Abort

this is with pymol 1.7
ubuntu 12.04
using 1FAS fetched from the pdb


thanks
jpd
--
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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Re: [PyMOL] apbs plugin

[Schubert, Carsten [JRDUS]]

Hi jpd,

try running APBS directly just using the .in file generated from a failed run. 
That may provide a clue as to where the problem is, i.e. within APBS itself or 
within the plugin. If it is APBS, which is throwing the error you may want to 
try to grab an updated version or the source code to compile yourself.

HTH

Carsten

From: jp d [mailto:yo...@yahoo.com]
Sent: Tuesday, February 11, 2014 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs plugin

hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.
if i select 'Choose externally generated PQR'
or 'run APBS' i get this
In show error 1
alloc: invalid block: 0x2c29fb78: 0 0
Abort

this is with pymol 1.7
ubuntu 12.04
using 1FAS fetched from the pdb

thanks
jpd
--
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
http://pubads.g.doubleclick.net/gampad/clk?id=124407151iu=/4140/ostg.clktrk___
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Re: [PyMOL] apbs plugin

[jp d]

hi,
good idea, it runs from the command line after adding
/pymol/ext/lib to my library path

but the plugin still crashes.
something is odd about my APBS plugin setup.
if i even just click to change the file locations
it crashes.

the other plugins seem fine.


thanks
jpd




 From: Schubert, Carsten [JRDUS] cschu...@its.jnj.com
To: jp d yo...@yahoo.com; pymol-users@lists.sourceforge.net 
pymol-users@lists.sourceforge.net 
Sent: Tuesday, February 11, 2014 12:14 PM
Subject: RE: [PyMOL] apbs plugin
 


Hi jpd,
 
try running APBS directly just using the .in file generated from a failed run. 
That may provide a clue as to where the problem is, i.e. within APBS itself or 
within the plugin. If it is APBS, which is throwing the error you may want to 
try to grab an updated version or the source code to compile yourself.
 
HTH 
 
Carsten
 
From:jp d [mailto:yo...@yahoo.com] 
Sent: Tuesday, February 11, 2014 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs plugin
 
hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.
if i select 'Choose externally generated PQR'
or 'run APBS' i get this
In show error 1
alloc: invalid block: 0x2c29fb78: 0 0
Abort
 
this is with pymol 1.7
ubuntu 12.04
using 1FAS fetched from the pdb
 
thanks
jpd--
Android apps run on BlackBerry 10
Introducing the new BlackBerry 10.2.1 Runtime for Android apps.
Now with support for Jelly Bean, Bluetooth, Mapview and more.
Get your Android app in front of a whole new audience.  Start now.
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[PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Seth Harris]

Hi all,

I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting
this error with pymol generated files not being found in the tmp directory:

Could not find
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so
searching for
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx'
exist?

It is true that neither of these files exist there, though
pymol-generated.pqr, .in and .pdb are there.

I was attempting this with a PDB file that worked in earlier versions, so I
don't think the problem is with the input. Is it working for others?

Cheers,
Seth


Also, BTW, in the visualization GUI for several versions I've had
misbehaving buttons where some of the update field lines end up actually
controlling the isosurfaces and not doing what they are advertised to do.
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Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Schubert, Carsten [JRDUS]]

Hi Seth,

I had problems with the underlying APBS version (1.4 I believe) under Windows 
in Pymol 1.7. It croaked with an memory allocation error, which I only found 
after I ran the .in file manually in APBS. Try that. You can either install an 
upgraded version of APBS or switch to Pymol 1.8, which has a working APBS 
version.

HTH

Carsten

From: Seth Harris [mailto:set...@gmail.com]
Sent: Wednesday, January 22, 2014 4:16 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi all,

I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting 
this error with pymol generated files not being found in the tmp directory:

Could not find 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so 
searching for 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx' 
exist?
It is true that neither of these files exist there, though pymol-generated.pqr, 
.in and .pdb are there.
I was attempting this with a PDB file that worked in earlier versions, so I 
don't think the problem is with the input. Is it working for others?
Cheers,
Seth

Also, BTW, in the visualization GUI for several versions I've had misbehaving 
buttons where some of the update field lines end up actually controlling the 
isosurfaces and not doing what they are advertised to do.

--
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Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Schubert, Carsten [JRDUS]]

Sorry, I got my versions crossed. I had the same issues with 1.6, it worked 
again with 1.7. Nevertheless I'd try running the .in file separately to debug 
what is going on behind the scenes.

-C.

From: Schubert, Carsten [JRDUS]
Sent: Wednesday, January 22, 2014 4:57 PM
To: Seth Harris; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi Seth,

I had problems with the underlying APBS version (1.4 I believe) under Windows 
in Pymol 1.7. It croaked with an memory allocation error, which I only found 
after I ran the .in file manually in APBS. Try that. You can either install an 
upgraded version of APBS or switch to Pymol 1.8, which has a working APBS 
version.

HTH

Carsten

From: Seth Harris [mailto:set...@gmail.com]
Sent: Wednesday, January 22, 2014 4:16 PM
To: pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

Hi all,

I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting 
this error with pymol generated files not being found in the tmp directory:

Could not find 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so 
searching for 
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx' 
exist?
It is true that neither of these files exist there, though pymol-generated.pqr, 
.in and .pdb are there.
I was attempting this with a PDB file that worked in earlier versions, so I 
don't think the problem is with the input. Is it working for others?
Cheers,
Seth
Also, BTW, in the visualization GUI for several versions I've had misbehaving 
buttons where some of the update field lines end up actually controlling the 
isosurfaces and not doing what they are advertised to do.

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Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7

[Ben Eisenbraun]

Hi Seth,

 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does
 '/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx'
 exist?

 It is true that neither of these files exist there, though
 pymol-generated.pqr, .in and .pdb are there.

You didn't mention what version of OS X you are using, but the apbs
binary included with MacPyMOL doesn't run on versions prior to 10.8.

It's relatively straightforward to compile APBS from source and
replace the binary in the app bundle. It's at pymol/ext/bin/apbs.

-ben

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| SBGrid Consortium  | http://sbgrid.org   |
| Harvard Medical School | http://hms.harvard.edu  |

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[PyMOL] apbs fails in PyMOL 1.6.0 on snow leopard

[Mooers, Blaine H.M. (HSC)]

Dear PyMOLers,

I can set the grid in the apbs_tools gui using the default file locations  
(they are correct; I checked), but I get kernel dump when I try to run apbs.
A gui pops up with the message that MacPyMOL crashed although the PyMOL guis 
are still open and functional. The pop-u gui gives the following error message.

Best regards,

Blaine


Process: MacPyMOL [7673]
Path:/Applications/PyMOLX11Hybrid160.app/Contents/MacOS/MacPyMOL
Identifier:  MacPyMOL
Version: ??? (???)
Code Type:   X86-64 (Native)
Parent Process:  MacPyMOL [7612]

Date/Time:   2013-08-30 09:09:52.027 -0500
OS Version:  Mac OS X 10.6.8 (10K549)
Report Version:  6

Interval Since Last Report:  149553 sec
Crashes Since Last Report:   23
Per-App Crashes Since Last Report:   8
Anonymous UUID:  95441EA8-D0B3-46A9-8BC8-2FD7A7B627D1

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0xfff8
Crashed Thread:  Unknown

Backtrace not available

Unknown thread crashed with X86 Thread State (64-bit):
  rax: 0x0055  rbx: 0x  rcx: 0x  
rdx: 0x
  rdi: 0x  rsi: 0x  rbp: 0x  
rsp: 0x
   r8: 0x   r9: 0x  r10: 0x  
r11: 0x
  r12: 0x  r13: 0x  r14: 0x  
r15: 0x
  rip: 0x7fff5fc01028  rfl: 0x00010203  cr2: 0xfff8

Binary images description not available



Model: MacBookPro6,2, BootROM MBP61.0057.B0C, 2 processors, Intel Core i7, 2.66 
GHz, 8 GB, SMC 1.58f17
Graphics: NVIDIA GeForce GT 330M, NVIDIA GeForce GT 330M, PCIe, 512 MB
Graphics: Intel HD Graphics, Intel HD Graphics, Built-In, 288 MB
Memory Module: global_name
AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x93), Broadcom 
BCM43xx 1.0 (5.10.131.42.4)
Bluetooth: Version 2.4.5f3, 2 service, 12 devices, 1 incoming serial ports
Network Service: Ethernet, Ethernet, en0
Network Service: AirPort, AirPort, en1
Serial ATA Device: ST9500420ASG, 465.76 GB
Serial ATA Device: MATSHITADVD-R   UJ-898
USB Device: Hub, 0x0424  (SMSC), 0x2514, 0xfa10 / 2
USB Device: Apple Internal Keyboard / Trackpad, 0x05ac  (Apple Inc.), 0x0236, 
0xfa12 / 6
USB Device: Hub, 0x05ac  (Apple Inc.), 0x9136, 0xfa14 / 5
USB Device: Ext HDD 1021, 0x1058  (Western Digital Technologies, Inc.), 0x1021, 
0xfa142000 / 14
USB Device: Keyboard Hub, 0x05ac  (Apple Inc.), 0x1006, 0xfa141000 / 8
USB Device: Apple Keyboard, 0x05ac  (Apple Inc.), 0x0220, 0xfa141200 / 13
USB Device: Hub, 0x05ac  (Apple Inc.), 0x9137, 0xfa144000 / 7
USB Device: Apple LED Cinema Display, 0x05ac  (Apple Inc.), 0x9236, 0xfa144300 
/ 12
USB Device: Display Audio, 0x05ac  (Apple Inc.), 0x2912, 0xfa144100 / 11
USB Device: Display iSight, 0x05ac  (Apple Inc.), 0x8508, 0xfa144200 / 10
USB Device: BRCM2070 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0xfa11 / 4
USB Device: Bluetooth USB Host Controller, 0x05ac  (Apple Inc.), 0x8218, 
0xfa113000 / 9
USB Device: Internal Memory Card Reader, 0x05ac  (Apple Inc.), 0x8403, 
0xfa13 / 3
USB Device: Hub, 0x0424  (SMSC), 0x2514, 0xfd10 / 2
USB Device: IR Receiver, 0x05ac  (Apple Inc.), 0x8242, 0xfd12 / 5
USB Device: Built-in iSight, 0x05ac  (Apple Inc.), 0x8507, 0xfd11 / 4
USB Device: Microsoft 3-Button Mouse with IntelliEye(TM), 0x045e  (Microsoft 
Corporation), 0x0040, 0xfd13 / 3



Blaine Mooers
Assistant Professor
Department of Biochemistry and Molecular Biology
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center Rm. 466

Shipping address:
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

Letter address:
P.O. Box 26901, BRC 466
Oklahoma City, OK 73190

office: (405) 271-8300   lab: (405) 271-8313  fax:  (405) 271-3910
e-mail:  blaine-moo...@ouhsc.edumailto:blaine-moo...@ouhsc.edu

Faculty webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/faculty/blaine-mooers-ph-d-

X-ray lab webpage: 
http://www.oumedicine.com/department-of-biochemistry-and-molecular-biology/department-facilities/macromolecular-crystallography-laboratory

Small Angle Scattering webpage: 
http://www.oumedicine.com/docs/default-source/ad-biochemistry-workfiles/small-angle-scattering-links.html?sfvrsn=0

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Re: [PyMOL] APBS error

[Chen Zhao]

Thank you so much Troels,

This solves my problem. But based on this, it seems that APBS In pymol
failed to find PDB2PQR.

Chen


On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet tlin...@gmail.comwrote:

 Have a look on the earlier message on this.

 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
 Wheezy machine. The initialization is successful, but when I hit set
 grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 132, in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval' referenced
 before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
 file, the APBS GUI in pymol is still unable to show the correct path of
 APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] APBS error

[Troels Emtekær Linnet]

Do you have linux or windows?

Do you have PDB2PQR on your system?
http://pymolwiki.org/index.php/Apbsplugin
http://www.poissonboltzmann.org/pdb2pqr


Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Thank you so much Troels,

 This solves my problem. But based on this, it seems that APBS In pymol
 failed to find PDB2PQR.

 Chen


 On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet 
 tlin...@gmail.comwrote:

 Have a look on the earlier message on this.


 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

  Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
 Wheezy machine. The initialization is successful, but when I hit set
 grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 132, in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval'
 referenced before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
 file, the APBS GUI in pymol is still unable to show the correct path of
 APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] APBS error

[Troels Emtekær Linnet]

Hi Chen.

If you are up for it, pdb2pqr exist in the Pymol-script repo.
http://pymolwiki.org/index.php/Git

I have made a automatic compile script.
See here:
http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script

That should fix it for you.
Try to look it through, and just write if you have problems.




Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 I am using Debian linux and I installed PDB2PQR with path specified in
 pymol APBS GUI. However, it seems that there are some problems in python,
 although I don't understand because I am not a programmer. I will try to
 run from command line instead.

 Thank you!

 Chen


 On Tue, Jun 18, 2013 at 11:08 AM, Troels Emtekær Linnet tlin...@gmail.com
  wrote:

 Do you have linux or windows?

 Do you have PDB2PQR on your system?
 http://pymolwiki.org/index.php/Apbsplugin
 http://www.poissonboltzmann.org/pdb2pqr


 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Thank you so much Troels,

 This solves my problem. But based on this, it seems that APBS In pymol
 failed to find PDB2PQR.

 Chen


 On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet 
 tlin...@gmail.com wrote:

 Have a look on the earlier message on this.


 http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



 Troels Emtekær Linnet


 2013/6/18 Chen Zhao chenzhaoh...@gmail.com

  Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a
 Debian Wheezy machine. The initialization is successful, but when I hit
 set grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line 1747, in __call__
 return apply(self.func, args)
   File
 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 153,
 in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File
 /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py, line 132,
 in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, 
 line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval'
 referenced before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in
 apbs_tools.py file, the APBS GUI in pymol is still unable to show the
 correct path of APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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[PyMOL] APBS error

[Chen Zhao]

Dear Pymol Users,

I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
Wheezy machine. The initialization is successful, but when I hit set
grid, I got the error message below:

*error: 1
type 'exceptions.UnboundLocalError' Exception in Tk callback
  Function: function lambda at 0x33a6938 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line 132, in _doCommand
return command(name)
  File
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
1075, in execute
self.runPsize()
  File
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
1096, in runPsize
good = self.generatePqrFile()
  File
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
1007, in generatePqrFile
good = self._generatePdb2pqrPqrFile()
  File
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
1615, in _generatePdb2pqrPqrFile
if retval != 0:
type 'exceptions.UnboundLocalError': local variable 'retval' referenced
before assignment*

Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
file, the APBS GUI in pymol is still unable to show the correct path of
APBS and PDB2PQR.

Thank you so much!

Sincerely,
Chen
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Re: [PyMOL] APBS error

[Troels Emtekær Linnet]

Have a look on the earlier message on this.

http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html



Troels Emtekær Linnet


2013/6/18 Chen Zhao chenzhaoh...@gmail.com

 Dear Pymol Users,

 I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
 Wheezy machine. The initialization is successful, but when I hit set
 grid, I got the error message below:

 *error: 1
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x33a6938 (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line 132, in _doCommand
 return command(name)
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1075, in execute
 self.runPsize()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1096, in runPsize
 good = self.generatePqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1007, in generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File
 /usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py, line
 1615, in _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval' referenced
 before assignment*

 Also, although I specified the PATH of APBS and PDB2PQR in apbs_tools.py
 file, the APBS GUI in pymol is still unable to show the correct path of
 APBS and PDB2PQR.

 Thank you so much!

 Sincerely,
 Chen


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Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

[Troels Emtekær Linnet]

Hej Tobias.

Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)

Orginal version:
http://pymolwiki.org/index.php/APBS

Small modified version:
http://pymolwiki.org/index.php/Apbsplugin

The modified version, is packed into the Pymol-script-repo
http://pymolwiki.org/index.php/Git

I made this installation script some time ago,
http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script

which download the Pymol-script-repo, and sets the path right.

at the moment I can't test it? since:
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly

But maybe you can see from the script, what you have to do.

Best


Troels Emtekær Linnet


2013/5/31 Tobias Beck tobiasb...@gmail.com:
 Dear all,

 I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
 12.10. I have compiled pymol from source
 (http://www.pymolwiki.org/index.php/Linux_Install).

 When running the plugin, I can set the grid, but after clicking on Run
APBS,
 I get the following error:

 Unexpected error: (type 'exceptions.ImportError', ImportError('No module
 named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
 type 'exceptions.UnboundLocalError' Exception in Tk callback
   Function: function lambda at 0x7fd13078e398 (type: type
'function')
   Args: ()
 Traceback (innermost last):
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
 1747, in __call__
 return apply(self.func, args)
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line
 132, in _doCommand
 return command(name)
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1036,
in
 execute
 good = self.generatePqrFile()
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1007,
in
 generatePqrFile
 good = self._generatePdb2pqrPqrFile()
   File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1615,
in
 _generatePdb2pqrPqrFile
 if retval != 0:
 type 'exceptions.UnboundLocalError': local variable 'retval' referenced
 before assignment

 The first line suggests that the pdb2pqr module cannot be loaded. However,
 the grid seems to be set okay. Has anybody encountered this error before
and
 knows how to solve it?

 I have also tried the pymol version that can be installed with apt-get,
but
 same error.

 Thanks for any advice!

 Best wishes, Tobias.



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Re: [PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

[Tobias Beck]

Hi Troels,

Many thanks for your email!

I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?

svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
svn: E210002: Unable to connect to a repository at URL 'svn://
svn.code.sf.net/p/pymol/code/trunk/pymol'
svn: E210002: Network connection closed unexpectedly

Yes, I have also tried to use svn this morning, but got same error.

Thanks again!

Best wishes, Tobias.




On Mon, Jun 3, 2013 at 11:28 AM, Troels Emtekær Linnet tlin...@gmail.comwrote:

 Hej Tobias.

 Some time ago, a year+?, I played around fixing some small things in APBS,
 to make it easier to work. (Most fixing small path things)

 Orginal version:
 http://pymolwiki.org/index.php/APBS

 Small modified version:
 http://pymolwiki.org/index.php/Apbsplugin

 The modified version, is packed into the Pymol-script-repo
 http://pymolwiki.org/index.php/Git

 I made this installation script some time ago,

 http://www.pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script

 which download the Pymol-script-repo, and sets the path right.

 at the moment I can't test it? since:
 svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
 svn: E210002: Unable to connect to a repository at URL 'svn://
 svn.code.sf.net/p/pymol/code/trunk/pymol'
 svn: E210002: Network connection closed unexpectedly

 But maybe you can see from the script, what you have to do.

 Best


 Troels Emtekær Linnet


 2013/5/31 Tobias Beck tobiasb...@gmail.com:

  Dear all,
 
  I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
  12.10. I have compiled pymol from source
  (http://www.pymolwiki.org/index.php/Linux_Install).
 
  When running the plugin, I can set the grid, but after clicking on Run
 APBS,
  I get the following error:
 
  Unexpected error: (type 'exceptions.ImportError', ImportError('No
 module
  named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
  type 'exceptions.UnboundLocalError' Exception in Tk callback
Function: function lambda at 0x7fd13078e398 (type: type
 'function')
Args: ()
  Traceback (innermost last):
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py,
 line
  1747, in __call__
  return apply(self.func, args)
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line
  153, in lambda
  command=lambda self=self, name=name: self._doCommand(name))
File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
 line
  132, in _doCommand
  return command(name)
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
 1036, in
  execute
  good = self.generatePqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
 1007, in
  generatePqrFile
  good = self._generatePdb2pqrPqrFile()
File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line
 1615, in
  _generatePdb2pqrPqrFile
  if retval != 0:
  type 'exceptions.UnboundLocalError': local variable 'retval' referenced
  before assignment
 
  The first line suggests that the pdb2pqr module cannot be loaded.
 However,
  the grid seems to be set okay. Has anybody encountered this error before
 and
  knows how to solve it?
 
  I have also tried the pymol version that can be installed with apt-get,
 but
  same error.
 
  Thanks for any advice!
 
  Best wishes, Tobias.
 
 
 
 --
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  It's a free troubleshooting tool designed for production
  Get down to code-level detail for bottlenecks, with 2% overhead.
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[PyMOL] PyMOL APBS plugin on Ubuntu 12.10 - error after 'run APBS'

[Tobias Beck]

Dear all,

I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source (
http://www.pymolwiki.org/index.php/Linux_Install).

When running the plugin, I can set the grid, but after clicking on Run
APBS, I get the following error:

Unexpected error: (type 'exceptions.ImportError', ImportError('No module
named pdb2pqr.pdb2pqr',), traceback object at 0x7fd130771200)
type 'exceptions.UnboundLocalError' Exception in Tk callback
  Function: function lambda at 0x7fd13078e398 (type: type 'function')
  Args: ()
Traceback (innermost last):
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwBase.py, line
1747, in __call__
return apply(self.func, args)
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
  File /usr/lib/python2.7/dist-packages/Pmw/Pmw_1_3/lib/PmwDialog.py,
line 132, in _doCommand
return command(name)
  File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1036,
in execute
good = self.generatePqrFile()
  File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1007,
in generatePqrFile
good = self._generatePdb2pqrPqrFile()
  File /home/pymol-svn/modules/pmg_tk/startup/apbs_tools.py, line 1615,
in _generatePdb2pqrPqrFile
if retval != 0:
type 'exceptions.UnboundLocalError': local variable 'retval' referenced
before assignment

The first line suggests that the pdb2pqr module cannot be loaded. However,
the grid seems to be set okay. Has anybody encountered this error before
and knows how to solve it?

I have also tried the pymol version that can be installed with apt-get, but
same error.

Thanks for any advice!

Best wishes, Tobias.
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Re: [PyMOL] APBS Tools library error

[Troels Emtekær Linnet]

Hi Christian.

I had a similar problem on my windows machine, but with .
Try to set the temp path.

*reinitialize*
*fetch 4ins, async=0*
*
*
*import os*
*print os.environ['temp']*
*print os.getcwd()*
*os.environ['temp']=os.getcwd()*
and then run the apbs plugin.

My own problem on my windows computer, was that I default had set .py files
to be opened with
notepad++. When I in apbs plugin then executed the Set grid, the pdb2pqr
would be opened in Notepad++
instead of executing the script.
I had to default opening of .py files to python before it worked.

I dont know if these problems would be meaning full on CentOS ?

Please report how it goes :-)

Best
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2012/9/27 Christian Roth christian.r...@bbz.uni-leipzig.de

 Dear all,

 we have with our system Ubuntu a problem with APBS in the new pymol 1.5.
 We use exactyl this version:
 This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
  The following error occurs:
 PDB2PQR - a Python-based structural conversion utility
 --
 Please cite your use of PDB2PQR as:
   Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
   PDB2PQR: an automated pipeline for the setup, execution,
   and analysis of Poisson-Boltzmann electrostatics calculations.
   Nucleic Acids Research 32 W665-W667 (2004).

 ran main.mainCommand
 Erasing contents of pymol-generated.pqr in order to clean it up
 I WILL RETURN TRUE from pdb2pqr
 GENERATED
 Running:
 prog=/software/linuxsoft/pymol/freemol/bin/apbs.exe
 args=('/software/linuxsoft/pymol/freemol/bin/apbs.exe', '
 pymol-generated.in')
 Results were:
 Return value: 127
 Output:
 /software/linuxsoft/pymol/freemol/bin/apbs.exe: symbol lookup error:
 /software/linuxsoft/ifc/compiler60/ia32/lib/libimf.so: undefined symbol:
 __aullshr

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

 It seems to be a very strange error within the intelfortan compiler
 library.
 However we cannot find so far  solution.
 So far we did not find a usable new library version to overcome the
 problem.
 Interestingly the APBS version within pymol build 1.2r3pre using APBS
 It works. This was a centos45 version of pymol.

 Does anyone has encountered a similar error and found a more elegant
 solution
 than just using an old pymol for such calculations?

 Thank you very much in advance for your help an suggestions.

 Best Regards

 Christian
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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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[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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[PyMOL] APBS Plugin: protein out of grid

[Ricardo O. S. Soares]

Dear users,

there's a particular case where I'm using the APBS plugin and the resultant 
grid 
leaves a portion of the protein out of it. This portion is show in full white 
because no potential is calculated there.
Why isnt the grid centered as usual? Changing the values by hand and them 
recaulculating does not seem to change the grid at all.

Thanks,

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Re: [PyMOL] APBS Plugin: protein out of grid

[Michael Lerner]

Can you send me the files (off list) so that I can take a look?

Thanks,

-Michael

On Thu, May 5, 2011 at 5:11 PM, Ricardo O. S. Soares
ross_...@yahoo.com.brwrote:

 Dear users,

 there's a particular case where I'm using the APBS plugin and the resultant
 grid leaves a portion of the protein out of it. This portion is show in full
 white because no potential is calculated there.
 Why isnt the grid centered as usual? Changing the values by hand and them
 recaulculating does not seem to change the grid at all.

 Thanks,

 Ricardo.



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Re: [PyMOL] APBS values

[Michael Zimmermann]

I am replying since your question did not get addressed in the past, but
know that I am not intimately familiar with PyMOL code or python.  I do have
a thought, though, if using a grid approximation would work.  I have done
some work with using MRC density map format in pymol, partly in anticipation
of the v1.4 improvements that will come (I wanted to link to them, but can't
find it...).  There is a 3D grid described by these files, usually encoding
density information.  I have edited (or created) these maps to encode other
types of data.  You could use them to record the potential value at each
point in the grid.  Then the comparison of your two (or more) equal volume
structures is just comparing grid points with the same [x,y,z] triple.

On Tue, Mar 15, 2011 at 3:39 PM, Matteo Pendleton znfin...@gmail.comwrote:

 I posed this question some while back and thought I'd submit it again as my
 question wasn't answered completely.

 Is it possible to have APBS spit out a list of values for points on the
 surface? I'd like to be able to quantitatively compare surface
 electrostatics of volumetrically identical proteins. I've been able to
 export a mesh of points on the solvent accessible surface but would also
 like to have electrostatic potential values at those points.

 Thanks!

 Matt Pendleton


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[PyMOL] APBS values

[Matteo Pendleton]

I posed this question some while back and thought I'd submit it again as my
question wasn't answered completely.

Is it possible to have APBS spit out a list of values for points on the
surface? I'd like to be able to quantitatively compare surface
electrostatics of volumetrically identical proteins. I've been able to
export a mesh of points on the solvent accessible surface but would also
like to have electrostatic potential values at those points.

Thanks!

Matt Pendleton
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Re: [PyMOL] APBS surface data export

[Michael Lerner]

Hi Matt,

PyMOL does not currently allow you to export the data mapped to the surface.
However, the dx format is very straightforward. It follows a subset of the
OpenDX standard, as described on the APBS site (
http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
).

I don't know much about surface file formats, but the PyMOL wiki mentions (
http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File)
that you can save surface coordinates to a file. It might be possible for a
developer (you?) to convince PyMOL to write out the electrostatic potential
along with whatever else it's writing to the .wrl file.

Hope that helps,

-Michael

On Mon, Jan 31, 2011 at 7:03 PM, Matteo Pendleton znfin...@gmail.comwrote:

 Greetings,

 I'm looking to use an electrostatic surface map for downstream calculations
 and was wondering whether it's currently possible (after using APBSv2 to
 calculate a surface potential map) to export a mesh of data points in a list
 format with each data point's associated potential? If not, does anyone have
 an outline of the file layout for the pymol-generated.dx file so I could
 write my own script to do it?

 Thank you kindly,

 Matt Pendleton

 Independent Researcher
 New York, NY


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[PyMOL] APBS surface data export

[Matteo Pendleton]

Greetings,

I'm looking to use an electrostatic surface map for downstream calculations
and was wondering whether it's currently possible (after using APBSv2 to
calculate a surface potential map) to export a mesh of data points in a list
format with each data point's associated potential? If not, does anyone have
an outline of the file layout for the pymol-generated.dx file so I could
write my own script to do it?

Thank you kindly,

Matt Pendleton

Independent Researcher
New York, NY
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[PyMOL] APBS in PyMOL

[耿存亮]

Dear PyMOL users,
I want to compute electrostatic with APBS plugin, and I create PQR file in 
http://pdb2pqr-1.wustl.edu/pdb2pqr/ .
When I run APBS in PyMOL, it displays the errors as followed:

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

Does anyone  know how to solve this problem?

Thanks,
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[PyMOL] APBS Tools2 (v1.3) vs APBS Tools (v1.2r3) issue

[Noinaj, Nicholas (NIH/NIDDK) [F]]

Hi,

I have noticed an 'odd' behavior when calculating electrostatic surface 
potential representations between the APBS Tools (v1.2r3) and APBS Tools2 
(v1.3) where the results are significantly different depending on which version 
of Pymol I use (recently upgraded to 1.3 and noticed this when re-making a 
figure that was originally made using 1.2r3)!

I am just wondering, has anyone else observed similar behavior?  The results 
from v1.3 look more accurate, which worries me somewhat about the figures I 
have previously made using the v1.2r3 APBS plugin!  While i am happy using v1.3 
(which agrees reasonably well with other programs), people currently using 
v1.2r3 or the like might want to investigate further by comparing their results 
to v1.3.

Thanks in advance for any feedback!





Cheers,
Nick










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noin...@niddk.nih.govmailto:noin...@niddk.nih.gov

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[PyMOL] Pre-release version of the PyMOL-APBS plugin

[Michael Lerner]

Hi all,

I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release. There are three big advantages of
the new version:

* It's been tested modern OS X, Windows and Linux systems and fixes several
long-standing bugs.
* It allows you to call through to PDB2PQR directly.
* It has two visualization panels to aid in showing multiple potential
surfaces at once.

I've also upped the default maximum allowed memory since typical users have
bigger and faster computers these days.

The main reason that I'm sending this out now is to get bug reports. I think
it runs everywhere, but *please* let me know if you have problems with it.
Once it's shown to be stable, it'll be included in the next PyMOL release.

A slightly longer list of changes is included below.

== How to get it ==

There are two ways to get the new plugin

* If you have subversion installed, you can always get the latest version
via

svn co
https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/pymolapbsplugin

* You can download the it from
http://pymolapbsplugin.svn.sourceforge.net/viewvc/pymolapbsplugin/trunk/src/apbsplugin.py

That should give you a file called apbsplugin.py

Once you have the plugin, you can install it via PyMOL's plugin installer:
Plugin -- Manage Plugins -- Install

Note that the plugin will be installed as APBS Tools2 so that you can
continue to use your old version.

== Longer feature list ==

* The ability to call through directly to PDB2PQR
* More modern apbs input files
* Two visualization panels. It's often quite useful to look at two different
electrostatic potentials at once. It's also quite useful to look at
electrostatic potentials mapped onto two different surfaces at once.
Multiple visualization panels makes this a snap: just set up one surface on
panel 1 and another surface on panel 2.
* Fixes several bugs that caused crashes on both OS X and Linux systems
* Increased maximum allowed memory
* Switch from os.system to subprocess for running external programs
* Deals with paths on Windows properly
* Gives better diagnostic information so that PyMOL/APBS developers can find
bugs more easily
* Lots of internal code cleanup

You can find this same information on the PyMOL wiki:
http://pymolwiki.org/index.php/User:Mglerner

Thanks,

-Michael

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Re: [PyMOL] Pre-release version of the PyMOL-APBS plugin

[Justin Lecher]

On 28/01/10 21:31, Michael Lerner wrote:
 Hi all,
 
 I've been working with Jason Vertrees on a new version of the PyMOL-APBS
 plugin and it's now ready for pre-release.

Hi,

that's really good news, that you are going to develop the plugin in a
more public accessible manner!

For all gentoo user, you can find the plugin in the sci overlay as

sci-chemistry/pymol-apbs-plugin.

There is a version for revision 11 as well as a live ebuild available.

Thanks justin

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Re: [PyMOL] APBS plugin woes

[Michael Lerner]

We solved the problem this afternoon. The version of APBS that comes with
PyMOL does not work on Tiger (10.4). Neither does the universal binary of
apbs-1.2.1b available on sourceforge.

An older version of apbs (0.5) worked. We are in the middle of installing
APBS via MacPorts, as it seems like that should work too.

I've added some troubleshooting instructions to both

http://pymolwiki.org/index.php/APBS
and
http://pymolwiki.org/index.php/User:Mglerner

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote:

 I download and install macpymol-1_2r2.tgz.

 I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
 up.

 Load a pdb file after removing HETATM lines.

 Open APBS Tools and set grid:
 Log:
 Maximum number of grid points exceeded.  Old grid dimensions were
 [129, 97, 129]
 Fine grid points rounded down from [117, 87, 117]
 New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

 Click Run APBS, see hydrogens appear, see residues being selected
 and unselected, then the display says:

 Log:
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


 Help?
 PowerBook, PPC, 10.4.11

 Dave


 --
 David N. Garboczi, PhD
 Phone: 301-496-4773
 Head, Structural Biology Section (SBS)
 Research Technologies Branch (RTB)
 National Institute of Allergy and Infectious Diseases (NIAID)
 National Institutes of Health (NIH)
 Twinbrook 2/Room 110
 12441 Parklawn Drive
 Rockville, Maryland 20852-1742
 Fax:301-402-0284
 Email: dgarbo...@niaid.nih.gov


 The information in this e-mail and any of its attachments is
 confidential and may contain sensitive information. It should not be
 used by anyone who is not the original intended recipient.  If you have
 received this e-mail in error please inform the sender and delete it
 from your mailbox or any other storage devices.  The National Institute
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[PyMOL] APBS plugin woes

[David Garboczi]

I download and install macpymol-1_2r2.tgz.

I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up.

Load a pdb file after removing HETATM lines.

Open APBS Tools and set grid:
Log:
Maximum number of grid points exceeded.  Old grid dimensions were 
[129, 97, 129]
Fine grid points rounded down from [117, 87, 117]
New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

Click Run APBS, see hydrogens appear, see residues being selected 
and unselected, then the display says:

Log:
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


Help?
PowerBook, PPC, 10.4.11

Dave


-- 
David N. Garboczi, PhD
Phone: 301-496-4773
Head, Structural Biology Section (SBS)
Research Technologies Branch (RTB)
National Institute of Allergy and Infectious Diseases (NIAID)
National Institutes of Health (NIH)
Twinbrook 2/Room 110
12441 Parklawn Drive
Rockville, Maryland 20852-1742
Fax:301-402-0284
Email: dgarbo...@niaid.nih.gov


The information in this e-mail and any of its attachments is
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used by anyone who is not the original intended recipient.  If you have
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Re: [PyMOL] APBS plugin woes

[Michael Lerner]

Can you go to the Program Locations tab and find out which version of APBS
you're using? There's a problem with the one in
/Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

I've added instructions for fixing this problem to
http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
top of the page, under APBS Plugin FAQ. Could you try them out and see if
they work for you?

Thanks,

-Michael

On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.govwrote:

 I download and install macpymol-1_2r2.tgz.

 I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
 up.

 Load a pdb file after removing HETATM lines.

 Open APBS Tools and set grid:
 Log:
 Maximum number of grid points exceeded.  Old grid dimensions were
 [129, 97, 129]
 Fine grid points rounded down from [117, 87, 117]
 New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

 Click Run APBS, see hydrogens appear, see residues being selected
 and unselected, then the display says:

 Log:
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


 Help?
 PowerBook, PPC, 10.4.11

 Dave


 --
 David N. Garboczi, PhD
 Phone: 301-496-4773
 Head, Structural Biology Section (SBS)
 Research Technologies Branch (RTB)
 National Institute of Allergy and Infectious Diseases (NIAID)
 National Institutes of Health (NIH)
 Twinbrook 2/Room 110
 12441 Parklawn Drive
 Rockville, Maryland 20852-1742
 Fax:301-402-0284
 Email: dgarbo...@niaid.nih.gov


 The information in this e-mail and any of its attachments is
 confidential and may contain sensitive information. It should not be
 used by anyone who is not the original intended recipient.  If you have
 received this e-mail in error please inform the sender and delete it
 from your mailbox or any other storage devices.  The National Institute
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 on behalf of the NIAID by one of its representatives.


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5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)
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Re: [PyMOL] APBS plugin woes

[Jason Vertrees]

FYI, that worked for me.  I just copied the binary to /usr/local/lib.

-- Jason

--
Jason Vertrees, PhD

PyMOLWiki -- http://www.pymolwiki.org



On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner mgler...@gmail.com wrote:
 Can you go to the Program Locations tab and find out which version of APBS
 you're using? There's a problem with the one in
 /Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.

 I've added instructions for fixing this problem to
 http://pymolwiki.org/index.php/User:Mglerner . The instructions are near the
 top of the page, under APBS Plugin FAQ. Could you try them out and see if
 they work for you?

 Thanks,

 -Michael

 On Mon, Nov 30, 2009 at 2:21 PM, David Garboczi dgarbo...@niaid.nih.gov
 wrote:

 I download and install macpymol-1_2r2.tgz.

 I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it
 up.

 Load a pdb file after removing HETATM lines.

 Open APBS Tools and set grid:
 Log:
 Maximum number of grid points exceeded.  Old grid dimensions were
 [129, 97, 129]
 Fine grid points rounded down from [117, 87, 117]
 New grid dimensions are [97, 65, 97]
  APBS Tools: coarse grid: (76.908,61.259,77.489)
  APBS Tools: fine grid: (65.240,56.035,65.582)
  APBS Tools: center: (-22.620,-1.106,-3.967)
  APBS Tools: fine grid points (97,65,97)

 Click Run APBS, see hydrogens appear, see residues being selected
 and unselected, then the display says:

 Log:
 ObjectMapLoadDXFile-Error: Unable to open file!
 ObjectMapLoadDXFile: Does 'pymol-generated.dx' exist?


 Help?
 PowerBook, PPC, 10.4.11

 Dave


 --
 David N. Garboczi, PhD
 Phone: 301-496-4773
 Head, Structural Biology Section (SBS)
 Research Technologies Branch (RTB)
 National Institute of Allergy and Infectious Diseases (NIAID)
 National Institutes of Health (NIH)
 Twinbrook 2/Room 110
 12441 Parklawn Drive
 Rockville, Maryland 20852-1742
 Fax:    301-402-0284
 Email: dgarbo...@niaid.nih.gov


 The information in this e-mail and any of its attachments is
 confidential and may contain sensitive information. It should not be
 used by anyone who is not the original intended recipient.  If you have
 received this e-mail in error please inform the sender and delete it
 from your mailbox or any other storage devices.  The National Institute
 of Allergy and Infectious Diseases (NIAID) shall not accept liability
 for any statement made that are the sender's own and not expressly made
 on behalf of the NIAID by one of its representatives.


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 --
 Michael Lerner, Ph.D.
 IRTA Postdoctoral Fellow
 Laboratory of Computational Biology NIH/NHLBI
 5635 Fishers Lane, Room T909, MSC 9314
 Rockville, MD 20852 (UPS/FedEx/Reality)
 Bethesda MD 20892-9314 (USPS)

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[PyMOL] APBS in pymol1.2

[Hugo G. de Teran]

Hi,

I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
compiled with no problem APBS, but when I try to start a calculation I
get the following error:
  File
/usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py,
line 998, in __init__
from freemol import apbs
ImportError: No module named freemol
/usr/local/bin/pymol: line 2:   798 Segmentation fault 
/usr/bin/python
/usr/local/lib64/python2.6/site-packages/pymol/__init__.py $@

I have read previous posts about freemol, but I do not want to mess up with
beta-versions so I only would like to make APBS work with pymol.

Thanks for help,

Hugo


-- 
Hugo G. de Teran, PhD.
Parga Pondal Research fellow
Fundación Pública Galega de Medicina Xenómica - SERGAS
Santiago de Compostela (SPAIN) 

Phone +34 981563100 ext 13873
e-mail:hugo.te...@usc.es   http://web.usc.es/~hugogdt   



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Re: [PyMOL] APBS in pymol1.2

[Warren DeLano]

Hugo,

If building PyMOL from source, then please get APBS in source or binary form 
from the APBS sourceforge project:  http://apbs.sourceforge.net  

Cheers,
Warren

 -Original Message-
 From: Hugo G. de Teran [mailto:hugo.te...@usc.es]
 Sent: Thursday, August 27, 2009 10:06 AM
 Cc: apbs-us...@lists.sourceforge.net; pymol-users@lists.sourceforge.net
 Subject: [PyMOL] APBS in pymol1.2
 
 Hi,
 
 I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
 compiled with no problem APBS, but when I try to start a calculation I
 get the following error:
   File
 /usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py,
 line 998, in __init__
 from freemol import apbs
 ImportError: No module named freemol
 /usr/local/bin/pymol: line 2:   798 Segmentation fault
 /usr/bin/python
 /usr/local/lib64/python2.6/site-packages/pymol/__init__.py $@
 
 I have read previous posts about freemol, but I do not want to mess up
 with
 beta-versions so I only would like to make APBS work with pymol.
 
 Thanks for help,
 
 Hugo
 
 
 --
 Hugo G. de Teran, PhD.
 Parga Pondal Research fellow
 Fundación Pública Galega de Medicina Xenómica - SERGAS
 Santiago de Compostela (SPAIN)
 
 Phone +34 981563100 ext 13873
 e-mail:hugo.te...@usc.es   http://web.usc.es/~hugogdt
 
 
 
 --
 
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[PyMOL] APBS hangs upon exit

[Kelly-Anne Twist]

Hi,

I just installed pymol-py25 and APBS via fink.
I can use APBS to generate some beautiful electrostatic potential maps but
when I exit APBS the pymol command line is frozen. I can move molecules
around in the Pymol viewer but I cannot save the images or files.

Can anyone suggest a fix for this?
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[PyMOL] apbs plugin for MacPyMOL?

[Paul Shannon]

I've installed apbs and used it from the command line.  Now I'd like  
to run it (more conveniently)

as a MacPyMOL plugin.

Anybody know how I can set this up?

Thanks!

 - Paul

Re: [PyMOL] apbs plugin for MacPyMOL?

[Justin]

Paul Shannon schrieb:
I've installed apbs and used it from the command line.  Now I'd like  
to run it (more conveniently)

as a MacPyMOL plugin.

Anybody know how I can set this up?

Thanks!

  - Paul

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Here is all you need to know:

http://pymolwiki.org/index.php/APBS



signature.asc
Description: OpenPGP digital signature

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Gilles Truan]

Thank you Tom!
Well, I can change my APBS script to remove all alternate conformations 
from b to d or e!!!

Thank you again for pulling out the information.
Gilles

Thomas Stout a écrit :

To follow up on one of Gilles least important questions: I was convinced that the PDB 
must contain structures for which there are more than two alternate conformations.  I 
downloaded all structures with resolutions between 0.5 and 1.0A and with a bit of regexp 
grepping, quickly found the following set of examples with at least three alternate 
conformers (I didn't find any with more than four, and the few that had four looked 
suspicious):

1BXO, 1BYI, 1CBN, 1CEX, 1DY5,
1EB6, 1EJG, 1EM0, 1EN8, 1EN9,
1ENE, 1ENN, 1ET1, 1EXR, 1F9Y,
1FN8, 1FY4, 1FY5, 1GCI, 1GDN,
1GWE, 1IX9, 1IXB, 1JFB, 1JXT,
1JXU, 1JXW, 1JXX, 1JXY, 1KTH,
1M40, 1MSO, 1MUW, 1MWQ, 1MXT,
1N1P, 1N4U, 1N4V, 1N4W, 1N55,
1N9B, 1OD3, 1PJX, 1PQ5, 1PQ8,
1R6J, 1S5M, 1S5N, 1SSX, 1TG0,
1US0, 1UZV, 1V0L, 1V6P, 1VB0,
1W0N, 1X6X, 1X6Z, 1XG0, 1XVO,
1YK4, 2AT0, 2BV4, 2BW4, 2CNQ,
2CWS, 2DDX, 2E4T, 2FWH, 2GEW,
2GG2, 2H5C, 2H5D, 2I16, 2I17,
2IXT, 2IZQ, 2NLS, 2NMZ, 2NRL,
2O7A, 2P74, 2PEV, 2PF8, 2PFH,
2PPP, 2PWA, 2PYA, 2QCP, 2QXW,
2RH2, 2V8B, 2VB1, 2Z6W, 3AL1,
3B3R, 3C78, 3CNJ, 3D1P, 8A3H

Cheers!
-Tom


-Original Message-
From: Gilles Truan [mailto:gilles.tr...@cgm.cnrs-gif.fr]
Sent: Mon 9/22/2008 6:14 AM
To: Nathan Baker
Cc: David Gohara; apbs-us...@lists.sourceforge.net list; 
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users]  Strange behaviour with APBS
 
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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Gilles Truan]

I think I found the problem with reading externally generated pqr files...

When pymol generates by itself the pqr file, it puts it in the working 
directory, hence the pymol-generated.in used for apbs and the pqr file 
are in the same directory. In the pymol-generated.in the file name of 
the pqr is given directly without any path given. On the contrary, when 
an externally generated pqr file is given in apbs plugin, the 
pymol-generated.in puts the entire path of the file, and in my case the 
path has spaces in its directory name...

The APBS manual is quite clear about that:

/|path|/

   The location of the molecular data file. This pathname should not
   include spaces.

And therefore APBS cannot read the pqr file!

Well, I think it really does not matter for now, as the different 
methods to work with the APBS plugin should work readilt. If for any 
reason some atoms are not assigned charges with pymo, I can still 
generated the pqr file, the apbs ini file and calculate the potential 
with apbs and read it with pymol


Gilles


Gilles Truan a écrit :

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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Gilles Truan]

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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Yong Huang]

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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Thomas Stout]

To follow up on one of Gilles least important questions: I was convinced that 
the PDB must contain structures for which there are more than two alternate 
conformations.  I downloaded all structures with resolutions between 0.5 and 
1.0A and with a bit of regexp grepping, quickly found the following set of 
examples with at least three alternate conformers (I didn't find any with more 
than four, and the few that had four looked suspicious):

1BXO, 1BYI, 1CBN, 1CEX, 1DY5,
1EB6, 1EJG, 1EM0, 1EN8, 1EN9,
1ENE, 1ENN, 1ET1, 1EXR, 1F9Y,
1FN8, 1FY4, 1FY5, 1GCI, 1GDN,
1GWE, 1IX9, 1IXB, 1JFB, 1JXT,
1JXU, 1JXW, 1JXX, 1JXY, 1KTH,
1M40, 1MSO, 1MUW, 1MWQ, 1MXT,
1N1P, 1N4U, 1N4V, 1N4W, 1N55,
1N9B, 1OD3, 1PJX, 1PQ5, 1PQ8,
1R6J, 1S5M, 1S5N, 1SSX, 1TG0,
1US0, 1UZV, 1V0L, 1V6P, 1VB0,
1W0N, 1X6X, 1X6Z, 1XG0, 1XVO,
1YK4, 2AT0, 2BV4, 2BW4, 2CNQ,
2CWS, 2DDX, 2E4T, 2FWH, 2GEW,
2GG2, 2H5C, 2H5D, 2I16, 2I17,
2IXT, 2IZQ, 2NLS, 2NMZ, 2NRL,
2O7A, 2P74, 2PEV, 2PF8, 2PFH,
2PPP, 2PWA, 2PYA, 2QCP, 2QXW,
2RH2, 2V8B, 2VB1, 2Z6W, 3AL1,
3B3R, 3C78, 3CNJ, 3D1P, 8A3H

Cheers!
-Tom


-Original Message-
From: Gilles Truan [mailto:gilles.tr...@cgm.cnrs-gif.fr]
Sent: Mon 9/22/2008 6:14 AM
To: Nathan Baker
Cc: David Gohara; apbs-us...@lists.sourceforge.net list; 
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users]  Strange behaviour with APBS
 
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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Gilles Truan]

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...


PyMOLfetch 1ehb
PyMOLremove 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: Grid0.5830.5360.591
DXStrToMap: 912673 data points.
PyMOLdelete all
PyMOLfetch 1cjc
PyMOLremove 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?
PyMOLdelete all
PyMOLfetch 1ehb
PyMOLremove 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: Grid0.5830.5360.591
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

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Nathan Baker]

Hi Warren --


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.


This might be a good reason to start moving towards distribution of  
APBS and PDB2PQR with PyMOL! :)


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.


I agree completely.  However, I think we can remain flexible with the  
PQR format while still allowing this.



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.


OK.

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.


This seems like a reasonable guess but I can't think of a component of  
PDB2PQR that is sensitive to this.  Gilles, can you confirm that you  
used PDB2PQR to generate the PQR file for your calculation?


Thanks,

Nathan


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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Re: [PyMOL] [Apbs-users] Plan for FreeMOL: APBS/PQR2PDB + MENGINE + MPEG movie creation

[Nathan Baker]

Hi Warren --

That's fantastic news!  It sounds like a great plan; please let me  
know if we can do anything to help out, particularly with the  
interface, annoying ObjectMapLoadDXFile-Error messages and related  
verbosity, etc.


Thanks!

-- Nathan

On Sep 18, 2008, at 2:32 PM, DeLano Scientific wrote:




This might be a good reason to start moving towards distribution of
APBS and PDB2PQR with PyMOL! :)


Indeed, along those lines, here is the plan:

Starting with PyMOL 1.2, we will start distributing an accompanying
open-source compilation named FreeMOL, which includes several  
packages many

users would like to be able to call upon when using PyMOL.  They are:

(a) an electrostatics package (APBS / PDB2PQR of course).

(b) an MMFF forcefield  minimizer (mengine) for small molecule  
building and

peptide modeling.

(C) an MPEG movie generator (mpeg_encode, most likely).

In each case, we are doing the upfront compilation, integration, and  
testing

to ensure that what ships actually interoperates reliably, on Mac, on
Windows, and on Linux.  With this effort, I am determined that we  
will get
to a point where all this stuff just works together without major  
issues.


Well.  That is the plan at least.  Nothing in software can ever be  
taken for
granted until it has shipped.  At present, we about two thirds of  
the way
there, so hopefully the rest will have come together before the end  
of the

year.  Betas will be out much sooner of course...

By the way, just to be absolutely crystal clear:  FreeMOL is and  
will remain
a 100% free-software  open-source project, distributed under full  
compliance
with each component's own open-source licensing terms.  As such,  
FreeMOL is
and must be kept well-separated from our closed-source PyMOL  
derivatives.


Cheers,
Warren

PS. I suspect I am not the only one looking forward to the day when  
we stop
seeing all those repeated ObjectMapLoadDXFile-Errors clogging up  
the APBS

 PyMOL mailing lists...


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-
boun...@lists.sourceforge.net] On Behalf Of Nathan Baker
Sent: Thursday, September 18, 2008 11:54 AM
To: DeLano Scientific
Cc: apbs-us...@lists.sourceforge.net; gilles.tr...@cgm.cnrs-gif.fr;  
pymol-

us...@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

Hi Warren --


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.


This might be a good reason to start moving towards distribution of
APBS and PDB2PQR with PyMOL! :)


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.


I agree completely.  However, I think we can remain flexible with the
PQR format while still allowing this.

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.


OK.


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.


This seems like a reasonable guess but I can't think of a component  
of

PDB2PQR that is sensitive to this.  Gilles, can you confirm that you
used PDB2PQR to generate the PQR file for your calculation?

Thanks,

Nathan





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Web: http://cholla.wustl.edu/

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Chris Swain]

Hi,

I noticed the latest version of the PDB file format description was  
posted today.


http://www.wwpdb.org/docs.html

Chris


On 17 Sep 2008, at 20:21, DeLano Scientific wrote:



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.

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[Nathan Baker]

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!!!


-
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
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Web: http://cholla.wustl.edu/

Re: [PyMOL] [Apbs-users] Strange behaviour with APBS

[DeLano Scientific]

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!!!


 --
 --- 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=100url=/
 ___
 apbs-users mailing list
 apbs-us...@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/apbs-users

--
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for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/

[PyMOL] distorted electrostatic surface color with PyMOL/APBS

[Douglas Kojetin]

Hi All,

I am having some problems with surface display of the output from the  
APBS plugin distributed with PyMOL (version 1.1r0) using the color by  
potential on sol. acc. surf. option.  Steps to reproduce the problem:


1. Load in a structure.

2. Perform the APBS calculation (execute Set grid and Run APBS  
functions/buttons).


3. Show the electrostatics on the molecular surface under the  
Visualization tab.  I used the following options


Low = -5
High = 5
solvent accessible surface = selected
color by potential on sol. acc. surf. = selected

The initial surface displayed looks OK, and there are no problems if I  
rotate the molecule using the mouse.  However, if I attempt to rotate  
the molecule using a command such as rotate y, 180,, the surface  
coloring is distorted.  If I execute rotate y, 180 again, then  
rotate by hand, the distortion on the problematic surface-side  
disappears.  However, if I execute rotate y, 180 once, or some  
iteration != 360, then rotate the molecule using the mouse, the color  
distortion is present and will not disappear with subsequent rotate  
commands.


Thanks in advance for help,

Doug

Re: [PyMOL] distorted electrostatic surface color with PyMOL/APBS

[DeLano Scientific]

Doug,

Rotate transforms atomic coordinates (relative to the precomputed field).
Try using turn to move the camera instead.

turn y,180

etc.

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Douglas
Kojetin
Sent: Tuesday, July 22, 2008 9:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] distorted electrostatic surface color with PyMOL/APBS

Hi All,

I am having some problems with surface display of the output from the APBS
plugin distributed with PyMOL (version 1.1r0) using the color by potential
on sol. acc. surf. option.  Steps to reproduce the problem:

1. Load in a structure.

2. Perform the APBS calculation (execute Set grid and Run APBS  
functions/buttons).

3. Show the electrostatics on the molecular surface under the Visualization
tab.  I used the following options

Low = -5
High = 5
solvent accessible surface = selected
color by potential on sol. acc. surf. = selected

The initial surface displayed looks OK, and there are no problems if I
rotate the molecule using the mouse.  However, if I attempt to rotate the
molecule using a command such as rotate y, 180,, the surface coloring is
distorted.  If I execute rotate y, 180 again, then rotate by hand, the
distortion on the problematic surface-side disappears.  However, if I
execute rotate y, 180 once, or some iteration != 360, then rotate the
molecule using the mouse, the color distortion is present and will not
disappear with subsequent rotate commands.

Thanks in advance for help,

Doug

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[PyMOL] APBS error

[Thomas Juettemann]

Dear all,

when trying to use the APBS plugin I experience the following problem


The first time I tried to run it it the error message was simply
ObjectMapLoadDXFile-Error:  Unable to open file!
Now the second time it pops up an error log:

Error: 1
WindowsError Exception in Tk callback
 Function: bound method PmwFileDialog.okbutton of
pmg_tk.startup.apbs_tools.PmwFileDialog instance at 0x05961A30
(type: type 'instancemethod')
 Args: ()
Traceback (innermost last):
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 1747, in
__call__
   return apply(self.func, args)
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1711, in
okbutton
   self.setfilename(fn)
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1745, in
setfilename
   self.configure(directory=dir,filename=value)
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py, line 729, in
configureapbs.exe
   func()
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1769, in
newdir
   self.fillit()
 File d:\Program Files\DeLano
Scientific\PyMOL/modules\pmg_tk\startup\apbs_tools.py, line 1836, in
fillit
   fl=os.listdir(dir)
WindowsError: [Errno 123] The filename, directory name, or volume
label syntax is incorrect: 'd:APBS-0.5.1\\bin\\d:APBS-0.5.1\\bin/*.*'

Both pymol (1.0edu1) and apbs (0.5.1)are fresh and clean installations.
APBS is installed in D:\APBS-0.5.1

I experienced similiar problems on another Windows machine and a Mac,
but both without the error log above.

I was realizing that when choosing the location of APBS binary pymol
writes: d:APBS-0.5.1 where it should be d:\APBS-0.5.1
I tried to put the correct path manually d:\APBS-0.5.1\bin\apbs.exe,
but did not help.


Any suggestions?


Many thanks,
Thomas

Re: [PyMOL] apbs plugin for macpymol

[Michael Lerner]

 I would like to use apbs from within PyMOL.  I have downloaded and
 installed the latest version of apbs, and apbs_tools.py exists in
 $PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no plugins entry
 in any of the PyMOL menus.

I think that you need to rename the application bundle to
PyMOLX11Hybrid in order to use plugins.

 Am I blind or daft?  But the question I'd
 really like to have answered is how do I get abps to work.

I would suggest

1) register APBS here http://agave.wustl.edu/apbs/download/
2) Install fink ( http://finkproject.org/ ) and then use it to install
apbs (e.g. by typing fink install apbs on the command line).

hope that helps,

-michael


 I'm using educational MacPyMOL, which integrates and extends
 Open-Source PyMOL 1.0r1.

 Thanks.


 Andreas

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http://www.umich.edu/~mlerner

Re: [PyMOL] apbs plugin for macpymol

[Andreas Förster]

Thanks to Michael and Warren for a quick and correct but somewhat 
baffling solution.  In OSX, one renames an application and it starts up 
looking quite dissimilar from before.  I'm still new to the Gospel 
according to Steve, and I wouldn't mind enlightenment.


In any case, using MacPyMOL as PyMOLHybrid also solves the problem of 
physically separating the viewer from the external gui, without which 
one couldn't fully harness the power of multiple screens.


A side note regarding Michael's instructions:  APBS doesn't require 
fink.  (I haven't even figured out what fink is yet.  Some sort of yum 
for OSX?)  One can just download the Mac OSX binary from WUSTL and 
install it as per default.  Works like a charm, as does APBS itself. 
Much better than on my Fedora 7 system, I'm embarrassed to admit ;-)



Andreas


Michael Lerner wrote:

I would like to use apbs from within PyMOL.  I have downloaded and
installed the latest version of apbs, and apbs_tools.py exists in
$PYMOL_PATH/modules/pmg_tk/startup/.  However, I find no plugins entry
in any of the PyMOL menus.


I think that you need to rename the application bundle to
PyMOLX11Hybrid in order to use plugins.


Am I blind or daft?  But the question I'd
really like to have answered is how do I get abps to work.


I would suggest

1) register APBS here http://agave.wustl.edu/apbs/download/
2) Install fink ( http://finkproject.org/ ) and then use it to install
apbs (e.g. by typing fink install apbs on the command line).

hope that helps,

-michael


I'm using educational MacPyMOL, which integrates and extends
Open-Source PyMOL 1.0r1.

Thanks.


Andreas

[PyMOL] APBS - Net charge and contour level

[Janet Deane]

Dear all,

I have posted this message also to the APBS list but have not yet had
a response so if anyone here can help I'd be most grateful.

We are using APBS tools in Pymol to compare the electrostatic surfaces
of two related proteins. We are concerned about the correct way to
display these so that the comparison is meaningful. Our question
relates to the effect of the overall charge of the protein and the
contours at which the electrostatic potential is displayed.
Specifically, the calculated net charge of one of the proteins is -18
and the other is -11 and if both are contoured between 4 and -4 one
surface looks as though the charge density is exaggerated, i.e. there
are very few patches without strong positive or negative charge.
Should the net charge be considered when choosing how to contour the
electrostatic surface?

Cheers,
Janet


-- 
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Postdoctoral Researcher
Sir William Dunn School of Pathology
South Parks Rd
University of Oxford OX1 3RE
United Kingdom
Phone: +44 1865 275385
Email: janet.de...@path.ox.ac.uk

Re: [PyMOL] APBS - Net charge and contour level

[DeLano Scientific]

Janet,

This is really a question for the electrostatics experts, but it sounds
reasonable to expect that a protein with a larger net charge would have more
regions showing a strong negative potential.  Given the large difference in
net charge, a simple visual juxtaposition of potentials may not be all that
informative.  

Cheers,
Warren

--
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Subscriber Support Services
mailto:del...@delsci.info
 
Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@delsci.com to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor! -WLD
 

 -Original Message-
 From: pymol-users-boun...@lists.sourceforge.net 
 [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf 
 Of Janet Deane
 Sent: Friday, October 19, 2007 2:59 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] APBS - Net charge and contour level
 
 Dear all,
 
 I have posted this message also to the APBS list but have not 
 yet had a response so if anyone here can help I'd be most grateful.
 
 We are using APBS tools in Pymol to compare the electrostatic 
 surfaces of two related proteins. We are concerned about the 
 correct way to display these so that the comparison is 
 meaningful. Our question relates to the effect of the overall 
 charge of the protein and the contours at which the 
 electrostatic potential is displayed.
 Specifically, the calculated net charge of one of the 
 proteins is -18 and the other is -11 and if both are 
 contoured between 4 and -4 one surface looks as though the 
 charge density is exaggerated, i.e. there are very few 
 patches without strong positive or negative charge.
 Should the net charge be considered when choosing how to 
 contour the electrostatic surface?
 
 Cheers,
 Janet
 
 
 --
 Dr Janet Deane
 Postdoctoral Researcher
 Sir William Dunn School of Pathology
 South Parks Rd
 University of Oxford OX1 3RE
 United Kingdom
 Phone: +44 1865 275385
 Email: janet.de...@path.ox.ac.uk
 
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Re: [PyMOL] APBS-electrostatics

[Michael Lerner]

It looks like quite a few people are actually still using the
electrostatics wizard, so I updated the code on my website
(http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use
the visualization pane of the APBS plugin these days, but I understand
if the wizard is a little cleaner for some purposes.

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner


On 10/4/07, DeLano Scientific del...@delsci.info wrote:


 Gianluigi,

 The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances
 in a single Python interpreter -- your wizard needs to be updated so that
 the init method takes a _self keyword argument:

 def __init__(, _self=cmd):
...


 --
 DeLano Scientific LLC
 Subscriber Support Services
 mailto:del...@delsci.info

 Not yet a PyMOL Subscriber, but want to support the project?  Email
 sa...@delsci.com to quote your lab, school, or employer.  Thank you for
 sponsoring this open-source endeavor! -WLD



  
  From: pymol-users-boun...@lists.sourceforge.net
 [mailto:pymol-users-boun...@lists.sourceforge.net] On
 Behalf Of Gianluigi Caltabiano
 Sent: Thursday, October 04, 2007 7:55 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] APBS-electrostatics



 Hi everybody,
 I am trying to use the electrostatic wizard to read some .dx file I made.
 It always worked..since I up-graded to pymol 1.0.
 Now it doesn't work ( I have already checked the modification in
 __init__.py file, it's fine).
 The message it give to me is:

 Traceback (most recent call last):
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\parser.py, line 251, in
 parse
 self.result=apply(layer.kw[0],layer.args,layer.kw_args)
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in
 wizard
 r = _wizard(name,arg,kwd,0)
   File C:\Archivos de programa\DeLano
 Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in
 _wizard
 wiz = apply(getattr(mod_obj,oname),arg,kwd)
 TypeError: __init__() got an unexpected keyword argument '_self'

 Thank you for your help

 Gianluigi Caltabiano


  
  
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[PyMOL] APBS-electrostatics

[Gianluigi Caltabiano]

Hi everybody,
  I am trying to use the electrostatic wizard to read some .dx file I made.
  It always worked..since I up-graded to pymol 1.0.
  Now it doesn't work ( I have already checked the modification in 
__init__.py file, it's fine).
  The message it give to me is:
   
  Traceback (most recent call last):
  File C:\Archivos de programa\DeLano 
Scientific\PyMOL/modules\pymol\parser.py, line 251, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File C:\Archivos de programa\DeLano 
Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in wizard
r = _wizard(name,arg,kwd,0)
  File C:\Archivos de programa\DeLano 
Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in _wizard
wiz = apply(getattr(mod_obj,oname),arg,kwd)
TypeError: __init__() got an unexpected keyword argument '_self'
   
  Thank you for your help
   
  Gianluigi Caltabiano
   

   
-

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Re: [PyMOL] APBS-electrostatics

[DeLano Scientific]

Gianluigi,
 
The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances
in a single Python interpreter -- your wizard needs to be updated so that
the init method takes a _self keyword argument:
 
def __init__(, _self=cmd):
   ...
 
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
 
Not yet a PyMOL Subscriber, but want to support the project?  Email
sa...@delsci.com to quote your lab, school, or employer.  Thank you for
sponsoring this open-source endeavor! -WLD
 


  _  

From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Gianluigi
Caltabiano
Sent: Thursday, October 04, 2007 7:55 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS-electrostatics


Hi everybody,
I am trying to use the electrostatic wizard to read some .dx file I made.
It always worked..since I up-graded to pymol 1.0.
Now it doesn't work ( I have already checked the modification in
__init__.py file, it's fine).
The message it give to me is:
 
Traceback (most recent call last):
  File C:\Archivos de programa\DeLano
Scientific\PyMOL/modules\pymol\parser.py, line 251, in parse
self.result=apply(layer.kw[0],layer.args,layer.kw_args)
  File C:\Archivos de programa\DeLano
Scientific\PyMOL/modules\pymol\wizarding.py, line 86, in wizard
r = _wizard(name,arg,kwd,0)
  File C:\Archivos de programa\DeLano
Scientific\PyMOL/modules\pymol\wizarding.py, line 45, in _wizard
wiz = apply(getattr(mod_obj,oname),arg,kwd)
TypeError: __init__() got an unexpected keyword argument '_self'
 
Thank you for your help
 
Gianluigi Caltabiano
 



  _  


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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] Are there any feature requests for the PyMOL-APBS plugin?

[Michael Lerner]

Hi,

I'm working on an update to the PyMOL-APBS plugin. Are there any
features that you would like to see included? As an example, I'm
including the ability to use PDB2PQR to generate PQR files in the next
version. Please request anything you'd like, no matter how
trivial/difficult you think it might be to implement (that's not a
promise that I'll implement it .. just that I'll consider it :) ).

Thanks,

-Michael Lerner

-- 
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner

Re: [PyMOL] APBS

[Oganesyan, Vaheh]

Dear Robert,

Thank you for your note. You were right. I downloaded i386 for my Linux
computer and it runs. The funny part is that my computer has 64 bit
Xeon processor.
Go figure ...

Vaheh Oganesyan

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of Robert
Campbell
Sent: Wednesday, May 30, 2007 11:06 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS

Hi Vaheh,

* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
 I did not get much luck with those recommendations either. I was doing
exactly the same. Something is phishy with my pymol and/or APBS
installation. I did check for different pdb files, so it is not pdb
related. The roor message is below:


==
 Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs',
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
 OSError Exception in Tk callback
   Function: function lambda at 0xf608448c (type: type
'function')
   Args: ()
 Traceback (innermost last):
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.
py, line 1747, in __call__
 return apply(self.func, args)
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py, line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialo
g.py, line 132, in _doCommand
 return command(name)
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line
1101, in execute
 (retval,progout) =
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),
))
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line
317, in run
 retcode =
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOU
T)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in
call
 return Popen(*args, **kwargs).wait()
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in
__init__
 errread, errwrite)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in
_execute_child
 raise child_exception
 OSError: [Errno 8] Exec format error

 ^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.ca
http://pldserver1.biochem.queensu.ca/~rlc


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Re: [PyMOL] APBS

[Oganesyan, Vaheh]

I did not get much luck with those recommendations either. I was doing exactly 
the same. Something is phishy with my pymol and/or APBS installation. I did 
check for different pdb files, so it is not pdb related. The roor message is 
below:
==
Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', 
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
OSError Exception in Tk callback
  Function: function lambda at 0xf608448c (type: type 'function')
  Args: ()
Traceback (innermost last):
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, 
line 1747, in __call__
return apply(self.func, args)
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 132, in _doCommand
return command(name)
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 1101, in 
execute
(retval,progout) = 
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 317, in run
retcode = 
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in call
return Popen(*args, **kwargs).wait()
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in __init__
errread, errwrite)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in 
_execute_child
raise child_exception
OSError: [Errno 8] Exec format error
==
Comments and solutions are appreciated.

VO

-Original Message-
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
 
I also continually had this problem unless I got pqr coordinates  
(with hydrogens)

below is the instructions I wrote for myself and group so that I  
would be able to do it again next time (getting old and the memory  
isn't what it used to be)

pqr corrdinates - Can do it on the web at

http://pdb2pqr.sourceforge.net/

http://agave.wustl.edu/pdb2pqr/server.html

I just used the defaults


Under plugins go to APBS tools

Choose use another PQR.  (maybe if you select Use PDB2PQR it might do  
this automatically without first going on line to do it?)


default configuration



Each time I've always had to set the APBS binary location.  The other  
sections leave blank



default Temporary File Locations



To start APBS 1st select Set Grid, then do Run APBS - I don't know  
why the buttons are placed in that order.  Also, it seems you must  
click on Run APBS twice before it launches.  Run Top in unix window  
to make sure it runs

For Hfq, ~400 residues, APBS took about a minute.

Go to Visualization and click on Update



For most reasonable looking Molecular Surfaces I turn off Solvent  
Accessible Surface and turn on Color by potential on sol. acc. surf.   
Select Show.  If you change the range you must also click on Update


When I tried to do this with another loaded structure, it actually  
looked like it mapped the first EPS onto the surface of the second  
structure.


Make sure to remove waters (and probably everyother non-protein  
residue).  EP on the left was done with waters in structure.  Notice  
red surface where ever water molecules appeare


non-linear Bolzman

Linear Bolzman

On May 24, 2007, at 1:16 PM, Michael Lerner wrote:

 Hi,

 Can you try installing the most recent version of my plugin from
 http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
 the normal Install Plugin menu option .. there's no need to do things
 by hand anymore)?  It fixes some problems and gives better error
 messages on others.

 Thanks,

 -Michael

 -- 
 Biophysics Graduate Student
 Carlson Lab, University of Michigan
 http://www.umich.edu/~mlerner


 On 5/24/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote:




 I'll appreciate some help with APBS plugin.



 In both Win or Lin the same error appears:



 ObjectMapLoadDXFile-Error: Unable to open file!



 After googling with this error message I've checked all of the
 possibilities:

 Map file is loaded OK, folders with apbs.exe and psize.py files do  
 not
 contain blanks,

 the *.pqr file is created using pdb2pqr server with and without chain
 identifier.



 At this point I do not know what else to try. Before (about 1 year  
 ago) I've
 used it with no problems.

 Could someone point me to the problem?

 Windows version is 0_99rc6 installed using binaries.

 Thanks in advance.



 Vaheh Oganesyan


 - 
 
 This SF.net

Re: [PyMOL] APBS

[D. Eric Dollins]

You can try this:
Give your pdb to the PDB2PQR server:
http://agave.wustl.edu/pdb2pqr/server.html
Strip the waters/ligands and load in your pdb. Choose that you want to
create an APBS input file. You get 2 files: *.pqr and *.in.  Rename
without .txt extension (if the output has them. My mac put them on).
You can load input pdb (the one with waters/ligands stripped).  Change
the temp file locations (temp.pqr, *.pdb, and APBS input file). Don't
change the pymol generated dx.  Under main, choose use another
pqr.  Choose externally generated pqr and browse for your x.pqr.
Click set grid. Click run APBS.  That will spit out a
pymol-generated.dx. In pymol type load_dx [file].dx. In APBS window,
go to the visualization tab and choose show mol. surface.  Change
levels and update.
Perhaps not the best way to get this to work, but it will give you a
surface to look at. Good luck,
Eric

On 5/30/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote:

I did not get much luck with those recommendations either. I was doing exactly 
the same. Something is phishy with my pymol and/or APBS installation. I did 
check for different pdb files, so it is not pdb related. The roor message is 
below:
==
Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', 
'/home/Vaheh/Work/Fc3M/pymol-generated.in')
OSError Exception in Tk callback
  Function: function lambda at 0xf608448c (type: type 'function')
  Args: ()
Traceback (innermost last):
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, 
line 1747, in __call__
return apply(self.func, args)
  File /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 153, in lambda
command=lambda self=self, name=name: self._doCommand(name))
  File 
/usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py, 
line 132, in _doCommand
return command(name)
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 1101, in 
execute
(retval,progout) = 
run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
  File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 317, in run
retcode = 
subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in call
return Popen(*args, **kwargs).wait()
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in __init__
errread, errwrite)
  File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in 
_execute_child
raise child_exception
OSError: [Errno 8] Exec format error
==
Comments and solutions are appreciated.

VO

-Original Message-
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS

I also continually had this problem unless I got pqr coordinates
(with hydrogens)

below is the instructions I wrote for myself and group so that I
would be able to do it again next time (getting old and the memory
isn't what it used to be)

pqr corrdinates - Can do it on the web at

http://pdb2pqr.sourceforge.net/

http://agave.wustl.edu/pdb2pqr/server.html

I just used the defaults


Under plugins go to APBS tools

Choose use another PQR.  (maybe if you select Use PDB2PQR it might do
this automatically without first going on line to do it?)


default configuration



Each time I've always had to set the APBS binary location.  The other
sections leave blank



default Temporary File Locations



To start APBS 1st select Set Grid, then do Run APBS - I don't know
why the buttons are placed in that order.  Also, it seems you must
click on Run APBS twice before it launches.  Run Top in unix window
to make sure it runs

For Hfq, ~400 residues, APBS took about a minute.

Go to Visualization and click on Update



For most reasonable looking Molecular Surfaces I turn off Solvent
Accessible Surface and turn on Color by potential on sol. acc. surf.
Select Show.  If you change the range you must also click on Update


When I tried to do this with another loaded structure, it actually
looked like it mapped the first EPS onto the surface of the second
structure.


Make sure to remove waters (and probably everyother non-protein
residue).  EP on the left was done with waters in structure.  Notice
red surface where ever water molecules appeare


non-linear Bolzman

Linear Bolzman

On May 24, 2007, at 1:16 PM, Michael Lerner wrote:

 Hi,

 Can you try installing the most recent version of my plugin from
 http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
 the normal Install Plugin menu option .. there's no need to do things
 by hand anymore)?  It fixes some problems and gives better error
 messages on others.

 Thanks

Re: [PyMOL] APBS

[Robert Campbell]

Hi Vaheh,

* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
 I did not get much luck with those recommendations either. I was doing 
 exactly the same. Something is phishy with my pymol and/or APBS installation. 
 I did check for different pdb files, so it is not pdb related. The roor 
 message is below:
 ==
 Running ('/usr/bin/APBS/apbs-0.5.0/bin/apbs', 
 '/home/Vaheh/Work/Fc3M/pymol-generated.in')
 OSError Exception in Tk callback
   Function: function lambda at 0xf608448c (type: type 'function')
   Args: ()
 Traceback (innermost last):
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py, 
 line 1747, in __call__
 return apply(self.func, args)
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py,
  line 153, in lambda
 command=lambda self=self, name=name: self._doCommand(name))
   File 
 /usr/bin/pymol/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py,
  line 132, in _doCommand
 return command(name)
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 1101, in 
 execute
 (retval,progout) = 
 run(self.binary.getvalue(),(self.pymol_generated_in_filename.getvalue(),))
   File /usr/bin/pymol/modules/pmg_tk/startup/apbs_tools.py, line 317, in run
 retcode = 
 subprocess.call(args,stdout=output_file.fileno(),stderr=subprocess.STDOUT)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 412, in call
 return Popen(*args, **kwargs).wait()
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 542, in __init__
 errread, errwrite)
   File /usr/bin/pymol/ext/lib/python2.4/subprocess.py, line 975, in 
 _execute_child
 raise child_exception
 OSError: [Errno 8] Exec format error

 ^^

This error would seem to indicate that you are running PyMOL on one kind
of computer but the apbs executable was compiled for a different one.
Are you perhaps mixing i686 and x86_64 Linuxes, for example?

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821Fax: 613-533-2497
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] APBS

[Todd M. Link]

I also continually had this problem unless I got pqr coordinates  
(with hydrogens)


below is the instructions I wrote for myself and group so that I  
would be able to do it again next time (getting old and the memory  
isn't what it used to be)


pqr corrdinates - Can do it on the web at

http://pdb2pqr.sourceforge.net/

http://agave.wustl.edu/pdb2pqr/server.html

I just used the defaults


Under plugins go to APBS tools

Choose use another PQR.  (maybe if you select Use PDB2PQR it might do  
this automatically without first going on line to do it?)



default configuration



Each time I’ve always had to set the APBS binary location.  The other  
sections leave blank




default Temporary File Locations



To start APBS 1st select Set Grid, then do Run APBS – I don’t know  
why the buttons are placed in that order.  Also, it seems you must  
click on Run APBS twice before it launches.  Run Top in unix window  
to make sure it runs


For Hfq, ~400 residues, APBS took about a minute.

Go to Visualization and click on Update



For most reasonable looking Molecular Surfaces I turn off Solvent  
Accessible Surface and turn on Color by potential on sol. acc. surf.   
Select Show.  If you change the range you must also click on Update



When I tried to do this with another loaded structure, it actually  
looked like it mapped the first EPS onto the surface of the second  
structure.



Make sure to remove waters (and probably everyother non-protein  
residue).  EP on the left was done with waters in structure.  Notice  
red surface where ever water molecules appeare



non-linear Bolzman

Linear Bolzman

On May 24, 2007, at 1:16 PM, Michael Lerner wrote:


Hi,

Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)?  It fixes some problems and gives better error
messages on others.

Thanks,

-Michael

--
Biophysics Graduate Student
Carlson Lab, University of Michigan
http://www.umich.edu/~mlerner


On 5/24/07, Oganesyan, Vaheh oganesy...@medimmune.com wrote:





I'll appreciate some help with APBS plugin.



In both Win or Lin the same error appears:



ObjectMapLoadDXFile-Error: Unable to open file!



After googling with this error message I've checked all of the
possibilities:

Map file is loaded OK, folders with apbs.exe and psize.py files do  
not

contain blanks,

the *.pqr file is created using pdb2pqr server with and without chain
identifier.



At this point I do not know what else to try. Before (about 1 year  
ago) I've

used it with no problems.

Could someone point me to the problem?

Windows version is 0_99rc6 installed using binaries.

Thanks in advance.



Vaheh Oganesyan


- 


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