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 
 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

 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 Plugin>APBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
 Exception in Tk callback
  Function:  at 0x7faa60852578> (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/pmg_tk/startup/apbs_tools.py", line 
314, in 
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 "", line 1, in pack
None
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
+ self._options(cnf, kw))
: 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
 Exception in Tk callback
  Function:  at 0x10cc75230> (type: )
  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 
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 "", line 1, in pack
None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
+ self._options(cnf, kw))
: 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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things parallel software development, from weekly thought leaders

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  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 
>> 
>>  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 Plugin>APBS Tools2.1 I get a popup 
>>> with the following error that is almost identical to the one from DE FALCO 
>>> JR LOUIS:
>>> Error: 1
>>>  Exception in Tk callback
>>>   Function:  at 0x7faa60852578> (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/pmg_tk/startup/apbs_tools.py", 
>>> line 314, in 
>>> 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 "", line 1, in pack
>>> None
>>>   File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
>>> + self._options(cnf, kw))
>>> : 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
>>>  Exception in Tk callback
>>>   Function:  at 0x10cc75230> (type: )
>>>   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 
>>> 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 "", line 1, in pack
>>> None
>>>   File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
>>> + self._options(cnf, kw))
>>> : 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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hub for all things parallel software development, from weekly thought
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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 
 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 Plugin>APBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
 Exception in Tk callback
  Function:  at 0x7faa60852578> (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/pmg_tk/startup/apbs_tools.py", line 
314, in 
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 "", line 1, in pack
None
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
+ self._options(cnf, kw))
: 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
 Exception in Tk callback
  Function:  at 0x10cc75230> (type: )
  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 
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 "", line 1, in pack
None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
+ self._options(cnf, kw))
: 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!


<>--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/___
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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  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 Plugin>APBS Tools2.1 I get a popup with 
> the following error that is almost identical to the one from DE FALCO JR 
> LOUIS:
> Error: 1
>  Exception in Tk callback
>   Function:  at 0x7faa60852578> (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/pmg_tk/startup/apbs_tools.py", line 
> 314, in 
> 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 "", line 1, in pack
> None
>   File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
> + self._options(cnf, kw))
> : 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
>  Exception in Tk callback
>   Function:  at 0x10cc75230> (type: )
>   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 
> 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 "", line 1, in pack
> None
>   File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
> + self._options(cnf, kw))
> : 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.


--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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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 Plugin>APBS Tools2.1 I get a popup with 
the following error that is almost identical to the one from DE FALCO JR LOUIS:
Error: 1
 Exception in Tk callback
  Function:  at 0x7faa60852578> (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/pmg_tk/startup/apbs_tools.py", line 
314, in 
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 "", line 1, in pack
None
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1890, in pack_configure
+ self._options(cnf, kw))
: 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
 Exception in Tk callback
  Function:  at 0x10cc75230> (type: )
  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 
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 "", line 1, in pack
None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
+ self._options(cnf, kw))
: 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!

<>--
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/___
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Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

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
 Exception in Tk callback
  Function:  at 0x10cc75230> (type: )
  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 
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 "", line 1, in pack
None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
+ self._options(cnf, kw))
: 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
 Exception in Tk callback
  Function:  at 0x10cc75230> (type: )
  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 
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 "", line 1, in pack
None
  File "/sw/lib/python2.7/lib-tk/Tkinter.py", line 1887, in pack_configure
+ self._options(cnf, kw))
: 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

[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 

> 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  > 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 
>>
>>> 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 

>  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
>  Exception in Tk callback
>   Function:  at 0x33a6938> (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
> "/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:
> : 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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>


>>>
>>
>
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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 

> 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 
> 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 
>>
>>>  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
>>>  Exception in Tk callback
>>>   Function:  at 0x33a6938> (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
>>> "/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:
>>> : 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
>>>
>>>
>>> --
>>> This SF.net email is sponsored by Windows:
>>>
>>> Build for Windows Store.
>>>
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>>>
>>
>>
>
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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 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 
>
>> 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
>>  Exception in Tk callback
>>   Function:  at 0x33a6938> (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
>> "/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:
>> : 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
>>
>>
>> --
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
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>>
>
>
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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 

> 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
>  Exception in Tk callback
>   Function:  at 0x33a6938> (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
> "/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:
> : 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
>
>
> --
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
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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
 Exception in Tk callback
  Function:  at 0x33a6938> (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
"/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:
: 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

[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: >
(type: )
 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 error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

[Sabuj Pattanayek]

Yeah that's perfect. Just what I was looking for!

One other thing, anyone know how to turn the stereo visual off 
completely so that pymol doesn't load into an opengl stereo visual even 
if pymol detects that you have stereo capable hardware? Even when stereo 
is turned off the screen flickers like its in stereo mode. Is there some 
kind of pymol startup switch or environment variable to disable loading 
into a stereo window?



Michael George Lerner wrote:


Hi,

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Mr. Lerner,

Thanks for letting me know about the PDB2PQR server. I was able to 
generate a pqr from the NBCR website that then works with APBS to 
generate the dx map.


I'm not sure how to get the same electrostatic gradient effect on the 
molecule surface generated using APBS tools using the isosurface 
command. I really like the potential mapping to molecular surface 
visual and it would be nice if it could be done with more than one 
molecule (from separate pdb files). I guess I can just render one 
molecule at a time and then crop multiple images into a single 
document so it looks like one system.



Oops .. my fault.  I was reading quickly, and I thought you wanted 
different isosurfaces for each molecule, not different molecular 
surfaces. The APBS plugin can't handle what you want, but you can do 
it.  You need to load a map and a molecule, create a ramp that controls 
the coloring and attach that ramp to the molecule's surface.  Here's an 
example (assuming you have pdb files firstmol.pdb and secondmol.pdb and 
dx maps firstmap.dx and secondmap.dx):


-- begin --

# load the molecules and maps
load firstmol.pdb
load firstmap.dx
load secondmol.pdb
load secondmap.dx

# create the ramps and show the surfaces
ramp_new firstramp, firstmap, [-10,0,10]
set surface_color, firstramp, firstmol
show surface, firstmol

ramp_new secondramp, secondmap, [-10,0,10]
set surface_color, secondramp, secondmol
show surface, secondmol

--- end ---

This is kind of ugly, though: it creates both of the ramps in the same 
place, and i don't know how to move them.  So, if you want to change the 
scales, you probably need to delete the ramp and give a new set of 
ramp_new, set and show commands.


Does that help?

Question: do people want the APBS plugin to support multiple molecules?  
I can probably put something in, but it would take a bit of work (and 
I'll have to think about how to keep the interface small enough for 
"normal" screen sizes).


-michael



Thank you very much,
Sabuj Pattanayek

Michael George Lerner wrote:



Hi,

I've been meaning to update APBS tools so that some of the warnings 
are larger and better explained.



WARNING: 53 atoms did not have properties assigned




means that PyMOL couldn't automatically assign properties for 53 
atoms in yoru molecule.  This is usually because you have 
non-standard protein residues (or because you're not using a protein 
at all).  In this case, you'll need to teach PyMOL about your 
molecule (via chempy .. it's a little involved.  I think Warren 
posted something about it recently) or use another program to 
generate the PQR file.


If you can get a good PQR file from another source (e.g. there's an 
APBS web portal at https://gridport.npaci.edu/apbs/ that probably 
understands more molecules than PyMOL), then you can use APBS tools 
directly with that PQR file.


For your second question, you'll have to have to make the surfaces 
yourself, as the APBS Plugin only supports one molecule/map at a time 
right now.  Have you looked at the help information for isosurface?  
You may also have to create two different dx maps and load them in by 
hand so that they have different names.  You can use the 
'Configuration' pane of the APBS plugin to make sure that they get 
reasonable names when you create them (then you just use PyMOL's load 
command to load them).


Is that enough to get you started?

-michael

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

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Pymol users,

I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first 
clicking the Set grid button, then clicking run APBS, but I get the 
error message shown below.


coarsedim is [119.03399429321288, 109.91349792480469, 
143.63640098571776]

finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.454237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties as

Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

[Michael George Lerner]

Hi,

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Mr. Lerner,

Thanks for letting me know about the PDB2PQR server. I was able to generate a 
pqr from the NBCR website that then works with APBS to generate the dx map.


I'm not sure how to get the same electrostatic gradient effect on the 
molecule surface generated using APBS tools using the isosurface command. I 
really like the potential mapping to molecular surface visual and it would be 
nice if it could be done with more than one molecule (from separate pdb 
files). I guess I can just render one molecule at a time and then crop 
multiple images into a single document so it looks like one system.


Oops .. my fault.  I was reading quickly, and I thought you wanted 
different isosurfaces for each molecule, not different molecular surfaces. 
The APBS plugin can't handle what you want, but you can do it.  You need 
to load a map and a molecule, create a ramp that controls the coloring and 
attach that ramp to the molecule's surface.  Here's an example (assuming 
you have pdb files firstmol.pdb and secondmol.pdb and dx maps firstmap.dx 
and secondmap.dx):


-- begin --

# load the molecules and maps
load firstmol.pdb
load firstmap.dx
load secondmol.pdb
load secondmap.dx

# create the ramps and show the surfaces
ramp_new firstramp, firstmap, [-10,0,10]
set surface_color, firstramp, firstmol
show surface, firstmol

ramp_new secondramp, secondmap, [-10,0,10]
set surface_color, secondramp, secondmol
show surface, secondmol

--- end ---

This is kind of ugly, though: it creates both of the ramps in the same 
place, and i don't know how to move them.  So, if you want to change the 
scales, you probably need to delete the ramp and give a new set of 
ramp_new, set and show commands.


Does that help?

Question: do people want the APBS plugin to support multiple molecules?  I 
can probably put something in, but it would take a bit of work (and I'll 
have to think about how to keep the interface small enough for "normal" 
screen sizes).


-michael



Thank you very much,
Sabuj Pattanayek

Michael George Lerner wrote:


Hi,

I've been meaning to update APBS tools so that some of the warnings are 
larger and better explained.



WARNING: 53 atoms did not have properties assigned



means that PyMOL couldn't automatically assign properties for 53 atoms in 
yoru molecule.  This is usually because you have non-standard protein 
residues (or because you're not using a protein at all).  In this case, 
you'll need to teach PyMOL about your molecule (via chempy .. it's a little 
involved.  I think Warren posted something about it recently) or use 
another program to generate the PQR file.


If you can get a good PQR file from another source (e.g. there's an APBS 
web portal at https://gridport.npaci.edu/apbs/ that probably understands 
more molecules than PyMOL), then you can use APBS tools directly with that 
PQR file.


For your second question, you'll have to have to make the surfaces 
yourself, as the APBS Plugin only supports one molecule/map at a time right 
now.  Have you looked at the help information for isosurface?  You may also 
have to create two different dx maps and load them in by hand so that they 
have different names.  You can use the 'Configuration' pane of the APBS 
plugin to make sure that they get reasonable names when you create them 
(then you just use PyMOL's load command to load them).


Is that enough to get you started?

-michael

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

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Pymol users,

I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking the 
Set grid button, then clicking run APBS, but I get the error message shown 
below.


coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.454237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!

Another problem I've come across when trying to load phi maps exported 
from Grasp is described below:


1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with molecule x, 
set values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks 
as it should.

4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize

Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

[Sabuj Pattanayek]

Dear Mr. Lerner,

Thanks for letting me know about the PDB2PQR server. I was able to 
generate a pqr from the NBCR website that then works with APBS to 
generate the dx map.


I'm not sure how to get the same electrostatic gradient effect on the 
molecule surface generated using APBS tools using the isosurface 
command. I really like the potential mapping to molecular surface visual 
and it would be nice if it could be done with more than one molecule 
(from separate pdb files). I guess I can just render one molecule at a 
time and then crop multiple images into a single document so it looks 
like one system.


Thank you very much,
Sabuj Pattanayek

Michael George Lerner wrote:


Hi,

I've been meaning to update APBS tools so that some of the warnings are 
larger and better explained.



WARNING: 53 atoms did not have properties assigned



means that PyMOL couldn't automatically assign properties for 53 atoms 
in yoru molecule.  This is usually because you have non-standard protein 
residues (or because you're not using a protein at all).  In this case, 
you'll need to teach PyMOL about your molecule (via chempy .. it's a 
little involved.  I think Warren posted something about it recently) or 
use another program to generate the PQR file.


If you can get a good PQR file from another source (e.g. there's an APBS 
web portal at https://gridport.npaci.edu/apbs/ that probably understands 
more molecules than PyMOL), then you can use APBS tools directly with 
that PQR file.


For your second question, you'll have to have to make the surfaces 
yourself, as the APBS Plugin only supports one molecule/map at a time 
right now.  Have you looked at the help information for isosurface?  You 
may also have to create two different dx maps and load them in by hand 
so that they have different names.  You can use the 'Configuration' pane 
of the APBS plugin to make sure that they get reasonable names when you 
create them (then you just use PyMOL's load command to load them).


Is that enough to get you started?

-michael

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

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Pymol users,

I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking 
the Set grid button, then clicking run APBS, but I get the error 
message shown below.


coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.454237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!

Another problem I've come across when trying to load phi maps exported 
from Grasp is described below:


1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with molecule 
x, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this 
looks as it should.

4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize, set phi map y to correlate with molecule 
y, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this 
looks as it should for pdb y but the remaining isosurface from phi map 
y gets mapped onto pdb x and the x surface no longer looks like it 
should.


..so is there anyway to load two phi maps and map them to the surfaces 
of their correlating molecules without exceeeding their respective 
surface boundaries?


Thanks,
Sabuj Pattanayek



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Re: [PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

[Michael George Lerner]

Hi,

I've been meaning to update APBS tools so that some of the warnings are 
larger and better explained.



WARNING: 53 atoms did not have properties assigned


means that PyMOL couldn't automatically assign properties for 53 atoms in 
yoru molecule.  This is usually because you have non-standard protein 
residues (or because you're not using a protein at all).  In this case, 
you'll need to teach PyMOL about your molecule (via chempy .. it's a 
little involved.  I think Warren posted something about it recently) or 
use another program to generate the PQR file.


If you can get a good PQR file from another source (e.g. there's an APBS 
web portal at https://gridport.npaci.edu/apbs/ that probably understands 
more molecules than PyMOL), then you can use APBS tools directly with that 
PQR file.


For your second question, you'll have to have to make the surfaces 
yourself, as the APBS Plugin only supports one molecule/map at a time 
right now.  Have you looked at the help information for isosurface?  You 
may also have to create two different dx maps and load them in by hand so 
that they have different names.  You can use the 'Configuration' pane of 
the APBS plugin to make sure that they get reasonable names when you 
create them (then you just use PyMOL's load command to load them).


Is that enough to get you started?

-michael

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

On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:


Dear Pymol users,

I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking the 
Set grid button, then clicking run APBS, but I get the error message shown 
below.


coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.454237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!

Another problem I've come across when trying to load phi maps exported from 
Grasp is described below:


1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with molecule x, set 
values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks as it 
should.

4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize, set phi map y to correlate with molecule y, set 
values for say -16kt/e, 0, 16 kt/e, and show the surface, this looks as it 
should for pdb y but the remaining isosurface from phi map y gets mapped onto 
pdb x and the x surface no longer looks like it should.


..so is there anyway to load two phi maps and map them to the surfaces of 
their correlating molecules without exceeeding their respective surface 
boundaries?


Thanks,
Sabuj Pattanayek



---
This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
Tool for open source databases. Create drag-&-drop reports. Save time
by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
Download a FREE copy at http://www.intelliview.com/go/osdn_nl
___
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PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users

[PyMOL] apbs error ObjectMapLoadDXFile-Error: Unable to open file! / multiple electrostatics maps overlapping

[Sabuj Pattanayek]

Dear Pymol users,

I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking 
the Set grid button, then clicking run APBS, but I get the error message 
shown below.


coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.454237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!

Another problem I've come across when trying to load phi maps exported 
from Grasp is described below:


1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with molecule 
x, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this 
looks as it should.

4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize, set phi map y to correlate with molecule 
y, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this 
looks as it should for pdb y but the remaining isosurface from phi map y 
gets mapped onto pdb x and the x surface no longer looks like it should.


..so is there anyway to load two phi maps and map them to the surfaces 
of their correlating molecules without exceeeding their respective 
surface boundaries?


Thanks,
Sabuj Pattanayek