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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> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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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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>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
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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 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

[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] 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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[PyMOL] PyMOL + APBS plugin

[Matic Kisovec]

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.


  1.  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?
  2.  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.
  3.  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 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 
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
>
>
> --
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> 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 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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Develop your own process in accordance with the BPMN 2 standard
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<>--
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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

--
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
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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 
To: Thomas Holder  
Cc: "Schubert, Carsten [JRDUS]" ; 
"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 
To: jp d  
Cc: "Schubert, Carsten [JRDUS]" ; 
"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  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]" 
> To: jp d ; "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 
To: jp d  
Cc: "Schubert, Carsten [JRDUS]" ; 
"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  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]" 
> To: jp d ; "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.--
Android apps run on BlackBerry 10
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Now with support for Jelly Bean, Bluetooth, Mapview and more.
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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  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]" 
> To: jp d ; "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.


--
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

[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]" 
To: jp d ; "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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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=124407151&iu=/4140/ostg.clktrk___
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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] 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 wrote:

> 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 :
>
> > 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: (, ImportError('No
> module
> > named pdb2pqr.pdb2pqr',), )
> >  Exception in Tk callback
> >   Function:  at 0x7fd13078e398> (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 
> > 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:
> > : 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.
> >
> >
> >
> --
> > Get 100% visibility into Java/.NET code with AppDynamics Lite
> > It's a free troubleshooting tool designed for production
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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 :
> 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: (, ImportError('No module
> named pdb2pqr.pdb2pqr',), )
>  Exception in Tk callback
>   Function:  at 0x7fd13078e398> (type: )
>   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 
> 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:
> : 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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[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: (, ImportError('No module
named pdb2pqr.pdb2pqr',), )
 Exception in Tk callback
  Function:  at 0x7fd13078e398> (type: )
  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 
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:
: 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 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
wrote:

> 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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-- 
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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 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,

Ricardo.--
WhatsUp Gold - Download Free Network Management Software
The most intuitive, comprehensive, and cost-effective network 
management toolset available today.  Delivers lowest initial 
acquisition cost and overall TCO of any competing solution.
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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

-- 
Justin Lecher
Institute for Neuroscience and Biophysics
ISB 3 - Institute for structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385




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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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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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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 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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-- 
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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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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  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 
> 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.
>>
>>
>> --
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> ___
>> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>
> --
> 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)
>
> --
> Join us December 9, 2009 for the Red Hat Virtual Experience,
> a free event focused on virtualization and cloud computing.
> Attend in-depth sessions from your desk. Your couch. Anywhere.
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> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>

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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 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)
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> National Institutes of Health (NIH)
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> used by anyone who is not the original intended recipient.  If you have
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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


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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

[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

[PyMOL] APBS plugin error

[Ben Eisenbraun]

Hi,

One of our researchers is trying to build an electrostatic map of his model 
using the APBS plugin and is generating the following error.  This is
Pymol 1.0r2 on Linux with APBS 0.5.1.

Any suggestions on how to fix it would be appreciated.

Error: 11
CmdException Exception in Tk callback
  Function:  at 0x41e06e2c> (type: )
  Args: ()
Traceback (innermost last):
  File
"/programs/i386-linux/pymol/1.0r2/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py",
line 1747, in __call__
return apply(self.func, args)
  File
"/programs/i386-linux/pymol/1.0r2/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py",
line 153, in 
command=lambda self=self, name=name: self._doCommand(name))
  File
"/programs/i386-linux/pymol/1.0r2/ext/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwDialog.py",
line 132, in _doCommand
return command(name)
  File "/programs/i386-linux/pymol/1.0r2/modules/pmg_tk/startup/apbs_tools.py",
line 1098, in execute
good = self.generatePqrFile()
  File "/programs/i386-linux/pymol/1.0r2/modules/pmg_tk/startup/apbs_tools.py",
line 1492, in generatePqrFile
assign.missing_c_termini(sel)
  File "/programs/i386-linux/pymol/1.0r2/modules/chempy/champ/assign.py", line
39, in missing_c_termini
while cmd.pop(tmp_sele2,tmp_sele1)>0: # complete the carboxy terminus
  File "/programs/i386-linux/pymol/1.0r2/modules/pymol/selecting.py", line 162,
in pop
if _self._raising(r,_self): raise pymol.CmdException
CmdException: 


Thanks!

-ben

--
Ben Eisenbraun
Structural Biology Grid
http://sbgrid.org/

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

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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[PyMOL] apbs plugin for macpymol

[Andreas Förster]

Hey all,

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


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


Thanks.


Andreas

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

[Gianluigi Caltabiano]

What about the possibility to show the surfaces of just a selection of residues?
Thank You,

Gianluigi Caltabiano, Ph.D.
Lab of Computational Medicine
Autonomic University of Barcelona
Spain

- Messaggio originale -
Da: Michael Lerner 
A: pymol-users@lists.sourceforge.net
Inviato: Giovedì 9 agosto 2007, 23:23:39
Oggetto: [PyMOL] Are there any feature requests for the PyMOL-APBS plugin?

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

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

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[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 plugin in pymol

[Andrea Spitaleri]

Hi,
at this purpose, what kind of range (positive - negative) should be
used in order to visualize correctly the potential surface on a
protein? Normally I used -10 to +10 but I am wondering how you behaves
with this issue too.

Thanks in advance

andrea

2006/11/23, D. Eric Dollins :

Florian,
I had the same problem and I couldnt get everything to work internally
in pymol. I never got pymol to write the *.pqr files. I couldn't
figure it out. However, you can 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 11/22/06, Florian Schmitzberger  wrote:
> Dear All,
>
> I am having a small problem using the apbs plugin in pymol on my pdb (I am
> using fink installed pymol and apbs versions on Mac OSX 10.4.8).
>
> When I try to run apbs I received the following message:
>
> "Unable to assign parameters for 100 atoms in the selection unassigned.
> Please either remove these unassigned atoms and re-start ..."
>
> In principle, I think I understand the problem is that pdb2pqr cannot assign
> charges to certain atoms, in my case posttranslationally modified cysteine
> residues.
>
> My question would be what the best way to fare with those atoms is. Since
> the modification introduces an acidic patch, if possible I would like to
> leave the atoms in (rather than remove them) when calculating surface charge
> representation, as this could be informative.
>
> So perhaps my question boils down to what the optimal way to manually assign
> reasonable charges (in the pqr-file) for this oxidised cysteine (sulfinic
> acid; O-S=O) is.
>
> I also noticed that I get the same error message with residues where
> side-chain atoms have been removed (such as surface lysines), while leaving
> the original residue name. But then I suppose there is no way around this.
>
> Thank you very much in advance for any comments!
>
> Best regards,
>
> Florian
>
> 
> Florian Schmitzberger
> Medical Biochemistry and Biophysics
> Karolinska Institute
> Scheeles vaeg 2
> SE-171 77 Stockholm, Sweden
> Tel: +46-8-524-86875
>
>
>
>
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Duke University Medical Center
Durham, NC 27710
(919)681-1668

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Re: [PyMOL] apbs plugin in pymol

[D. Eric Dollins]

Florian,
I had the same problem and I couldnt get everything to work internally
in pymol. I never got pymol to write the *.pqr files. I couldn't
figure it out. However, you can 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 11/22/06, Florian Schmitzberger  wrote:

Dear All,

I am having a small problem using the apbs plugin in pymol on my pdb (I am
using fink installed pymol and apbs versions on Mac OSX 10.4.8).

When I try to run apbs I received the following message:

"Unable to assign parameters for 100 atoms in the selection unassigned.
Please either remove these unassigned atoms and re-start ..."

In principle, I think I understand the problem is that pdb2pqr cannot assign
charges to certain atoms, in my case posttranslationally modified cysteine
residues.

My question would be what the best way to fare with those atoms is. Since
the modification introduces an acidic patch, if possible I would like to
leave the atoms in (rather than remove them) when calculating surface charge
representation, as this could be informative.

So perhaps my question boils down to what the optimal way to manually assign
reasonable charges (in the pqr-file) for this oxidised cysteine (sulfinic
acid; O-S=O) is.

I also noticed that I get the same error message with residues where
side-chain atoms have been removed (such as surface lysines), while leaving
the original residue name. But then I suppose there is no way around this.

Thank you very much in advance for any comments!

Best regards,

Florian


Florian Schmitzberger
Medical Biochemistry and Biophysics
Karolinska Institute
Scheeles vaeg 2
SE-171 77 Stockholm, Sweden
Tel: +46-8-524-86875




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C266 LSRC, Box 3813
Duke University Medical Center
Durham, NC 27710
(919)681-1668

[PyMOL] apbs plugin in pymol

[Florian Schmitzberger]

Dear All,

I am having a small problem using the apbs plugin in pymol on my pdb  
(I am using fink installed pymol and apbs versions on Mac OSX 10.4.8).


When I try to run apbs I received the following message:

"Unable to assign parameters for 100 atoms in the selection  
unassigned. Please either remove these unassigned atoms and re- 
start ..."


In principle, I think I understand the problem is that pdb2pqr cannot  
assign charges to certain atoms, in my case posttranslationally  
modified cysteine residues.


My question would be what the best way to fare with those atoms is.  
Since the modification introduces an acidic patch, if possible I  
would like to leave the atoms in (rather than remove them) when  
calculating surface charge representation, as this could be informative.


So perhaps my question boils down to what the optimal way to manually  
assign reasonable charges (in the pqr-file) for this oxidised  
cysteine (sulfinic acid; O-S=O) is.


I also noticed that I get the same error message with residues where  
side-chain atoms have been removed (such as surface lysines), while  
leaving the original residue name. But then I suppose there is no way  
around this.


Thank you very much in advance for any comments!

Best regards,

Florian

Florian Schmitzberger
Medical Biochemistry and Biophysics
Karolinska Institute
Scheeles vaeg 2
SE-171 77 Stockholm, Sweden
Tel: +46-8-524-86875

Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[Michael George Lerner]

On Wed, 21 Dec 2005, William Scott wrote:



Dear Michael:

Thanks.

It works great.  Sorry that I stupidly didn't think to check it.


No problem.  I'm glad it works.  Almost everything should be the same. 
APBS has a new required parameter, sdens (Vacc sphere density) that I've 
added to the configuration pane.  As far as I've heard, the default 
setting of 10.0 should be fine for most uses.


If you permit me one whine, I still need to use pdb2pqr (new version of 
that too) in order to do this with nucleic acids.


Allowing the plugin to use pdb2pqr is at the top of my PyMOL-related todo 
list.


-michael

--
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This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|   / \ | mler...@umich




On Tue, 20 Dec 2005, Michael George Lerner wrote:



There's a new version on my website
(http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out
and let me know if it works.  I've tested it on a few systems that I work
with, and it seems fine.  One person has reported some difficulties, but
these may not be related to my plugin.

Thanks,

-michael

--
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it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|   / \ | mler...@umich

On Tue, 20 Dec 2005, William Scott wrote:


I'm not getting very far...

parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
PBEparm_check: SDENS not set!
NOsh:  MG parameters not set correctly!
Error while parsing input file.


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Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[William Scott]

Dear Michael:

Thanks.

It works great.  Sorry that I stupidly didn't think to check it. If you
permit me one whine, I still need to use pdb2pqr (new version of that too)
in order to do this with nucleic acids.

All the best,

Bill



On Tue, 20 Dec 2005, Michael George Lerner wrote:

>
> There's a new version on my website
> (http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out
> and let me know if it works.  I've tested it on a few systems that I work
> with, and it seems fine.  One person has reported some difficulties, but
> these may not be related to my plugin.
>
> Thanks,
>
> -michael
>
> --
> www.umich.edu/~mlerner |_  |Michael Lerner
> This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
> it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
> -Torrence,  Bring It On|   / \ | mler...@umich
>
> On Tue, 20 Dec 2005, William Scott wrote:
>
> > I'm not getting very far...
> >
> > parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> > parsePBE:  Please use "calcforce no" instead.
> > PBEparm_check: SDENS not set!
> > NOsh:  MG parameters not set correctly!
> > Error while parsing input file.
> >
> >
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Re: [PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[Michael George Lerner]

There's a new version on my website 
(http://www.umich.edu/~mlerner/PyMOL/).  Please feel free to try it out 
and let me know if it works.  I've tested it on a few systems that I work 
with, and it seems fine.  One person has reported some difficulties, but 
these may not be related to my plugin.


Thanks,

-michael

--
www.umich.edu/~mlerner |_  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|   / \ | mler...@umich

On Tue, 20 Dec 2005, William Scott wrote:


I'm not getting very far...

parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
PBEparm_check: SDENS not set!
NOsh:  MG parameters not set correctly!
Error while parsing input file.


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[PyMOL] Has anyone got apbs 0.4 to work with the pymol apbs plugin?

[William Scott]

I'm not getting very far...

parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
PBEparm_check: SDENS not set!
NOsh:  MG parameters not set correctly!
Error while parsing input file.
 

[PyMOL] APBS plugin - warnings generating pqr files

[Peter Haebel]

Hi Michael,

i have just updated to the latest version of apbs-0.3.2 and pymol-0.97 under 
debian linux and get the following error messages (see below) + a completely 
positively charged protein surface...

using a pqr-file generated at 'http://nbcr.sdsc.edu/pdb2pqr/index.html' of the 
same protein works, so there seems to be a problem with the build-in 
generation of pqr-files.

i tried 3 different proteins from the PDB with and w/o ligand and water atoms.

any idea what's going wrong? 

cheers,

Peter

--

PDB code 1ini
all waters and ligand atoms removed by hand

...
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated 
Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL generated 
Hydrogens and termini so i am returning pymol-generated.pqr
 WARNING: 5 atoms did not have formal charges assigned
 WARNING: 10 atoms did not have properties assigned
...

This executable compiled on Nov 22 2004 at 15:59:46

Parsing input file pymol-generated.in...
parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
parsePBE:  Please use "bcfl sdh" instead.
NOsh:  Warning -- parsed deprecated statment "chgm 1".
NOsh:  Please use "chgm spl2" instead!
parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
parsePBE:  Please use "srfm smol" instead.
parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
parsePBE:  Please use "calcenergy no" instead.
parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
parsePBE:  Please use "calcforce no" instead.
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from pymol-generated.pqr.
Valist_readPDB:  Unable to parse resSeq token (A) as int!
Valist_readPDB:  Error while parsing residue name!
Valist_readPQR:  Error parsing ATOM field!
Error while reading molecule from pymol-generated.pqr
Error reading molecules!
 ObjectMapLoadDXFile: Loading from 'pymol-generated.dx'.
 DXStrToMap: Dimensions: 129 129 97
 DXStrToMap: Origin   14.554  -48.010   -7.484
 DXStrToMap: Grid0.5790.5230.664
 DXStrToMap: 1614177 data points.
 ObjectMap: Map Read.  Range = 3352.843994 to 12333.959961

 ___

Peter Haebel

Philipps-Universität Marburg
Institut für Pharmazeutische Chemie
Marbacher Weg 6
D-35032 Marburg

phone: +49-6421-28-25072
fax: +49-6421-28-28994

email: peter.hae...@staff.uni-marburg.de
http://www.agklebe.de

NAD3-Workshop 2005 - Divide&Conquer
http://www.agklebe.de/workshop2005

[PyMOL] pymol/apbs plugin rpm

[Cameron Mura]

Hi,
Those of you interested in APBS-based electrostatics in PyMOL via 
Michael Lerner's plugins may be interested in an RPM available at 
"http://mccammon.ucsd.edu/~cmura/PYMOL_examples/pymol-0.96apbs-2rh90.i386.rpm";.  
It is basically a CVS snapshot of a recent version of PyMOL (v0.96beta5; 
05/14/2004) which was compiled with the APBS plugin, and was built on a 
Red Hat 9 Linux system running Python 2.2 (but may work on other distros).

  Cameron


=== Michael George Lerner wrote (on 05/14/2004 02:37 PM): ===


Hi Cameron,

 


hi Michael,

I finally got the APBS plugin to work
(http://mccammon.ucsd.edu/~cmura/PYMOL_examples/apbs_plugin.html).
   



Great! (and nice pictures :))

 


The only catch was that I had to make the following changes near line
500 of your layer4/Cmd.c in order to build the CVS version of PyMOL:
   



Ugh.  This sounds like things changed in CVS between when I put things
online and when you cvs updated.  I'll go ahead and make my changes
relative to version 0.95 and put those up sometime soon.

-michael


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--
Cameron Mura
UCSD