Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of Molprobity in PyMol???

2014-10-22 Thread Schubert, Carsten [JRDUS] 
Tim: Good suggestion, I would second this effort. Thanks for raising the issue

Cheers,

Carsten

From: Tim Schulte [mailto:tim.schu...@ki.se]
Sent: Wednesday, October 22, 2014 2:11 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of 
Molprobity in PyMol???

Hej everybody,
my question is related to this post.
I am just analyzing a structure and really like the way Molprobity puts out 
information about hydrogen bonds and vdW contacts and so on.

It is also possible to take advantage of this analysis in phenix during/after 
refinement, because Coot provides a graphical interface for visualization of 
the Molprobity output - however, Coot is not my favorite program for making 
nice figures.

So I just wonder whether it might be of general interest to the pymol community 
if someone would write a plug-in to integrate the Molprobity output in PyMol?

I can definitely not do it, but maybe this could be an interesting feature 
request to the PyMol developers?

All the best,
Tim



Am 30/08/14 01:53, schrieb Robert Immormino:
Hi Bondurant,

I really like the merging of the graphic beauty of pymol with the detailed 
depictions of reduce and probe.  I have a method that is a bit clunky for doing 
what you ask, but I don't know if it ever made it to the mainstream in 
MolProbity.  The caveat of wanting to work with a ligand makes it a bit harder 
to explain so my apologies in advance if things aren't 100% clear but here 
goes

1. Make sure you have a reduce definition file for your ligand.  If the ligand 
had been deposited in the PDB before ~2012 then the reduce_wwPDB_het_dict file 
found (http://kinemage.biochem.duke.edu/software/reduce.php)  should have it, 
otherwise here's an example:

RESIDUE   ACP  11
CONECT  P  4 O1   O2   O3   O4
CONECT  O1 1 P
CONECT  O2 1 P
CONECT  O3 1 P
CONECT  O4 2 PC1
CONECT  C1 3 O4   O5   C2
CONECT  O5 1 C1
CONECT  C2 4 C1  HC1  HC2  HC3
CONECT HCH11 C2
CONECT HCH21 C2
CONECT HCH31 C2
END
HETACP  8
HETNAM ACP ACETYL PHOSPHATE
FORMUL  ACPC2 H3 O5 P1 2-

2. download the reduce and probe executables also from 
http://kinemage.biochem.duke.edu/

3.  run reduce make sure to use the -DB flag to input your ligand dictionary

4. run probe with a command something like:
probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" CheY_A88T_AcP_H.pdb
Where chain A in this case is the protein and the hydroxyl of Thr 88 is the 
only relevant interacting group with chain X the ligand.

5. convert the probe output to a python script to render the cgo objects in 
pymol using the attached perl script.  ./probe_to_cgo [input probe dots] 
[output pymol cgo]

6. use the run command in pymol to execute the python script and draw the cgo 
output.

If this all works the first go then amazing!  If not I can try to help get 
things working, but it's been a few years since I last used these tools.

Best of Luck!
-bob


On Fri, Aug 29, 2014 at 10:30 AM, Bondurant 
mailto:bondurant...@gmail.com>> wrote:
Hello community,
I would like to draw a figure similar to this one
http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
showing the clashes between a potential ligand and the protein. The only way i 
know how to do this in pymol is using the show_bumps plugin, but i don't really 
like the "red disks" format.
Could anyone tell me how i could easily draw something similar to those red 
spikes from the example to represent the clashes in pymol or any other program? 
I'm able to do it using molprobity and kinemage, but there's no much 
possibilities for editing and to get it in printing quality.
Thanks

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Re: [PyMOL] How to draw clashes in pymol -> integration/plug-in of Molprobity in PyMol???

2014-10-22 Thread Tim Schulte 

Hej everybody,
my question is related to this post.
I am just analyzing a structure and really like the way Molprobity puts 
out information about hydrogen bonds and vdW contacts and so on.


It is also possible to take advantage of this analysis in phenix 
during/after refinement, because Coot provides a graphical interface for 
visualization of the Molprobity output - however, Coot is not my 
favorite program for making nice figures.


So I just wonder whether it might be of general interest to the pymol 
community if someone would write a plug-in to integrate the Molprobity 
output in PyMol?


I can definitely not do it, but maybe this could be an interesting 
feature request to the PyMol developers?


All the best,
Tim



Am 30/08/14 01:53, schrieb Robert Immormino:

Hi Bondurant,

I really like the merging of the graphic beauty of pymol with the 
detailed depictions of reduce and probe.  I have a method that is a 
bit clunky for doing what you ask, but I don't know if it ever made it 
to the mainstream in MolProbity.  The caveat of wanting to work with a 
ligand makes it a bit harder to explain so my apologies in advance if 
things aren't 100% clear but here goes


1. Make sure you have a reduce definition file for your ligand.  If 
the ligand had been deposited in the PDB before ~2012 then the 
reduce_wwPDB_het_dict file found 
(http://kinemage.biochem.duke.edu/software/reduce.php)  should have 
it, otherwise here's an example:


RESIDUE   ACP  11
CONECT  P  4 O1   O2   O3   O4
CONECT  O1 1 P
CONECT  O2 1 P
CONECT  O3 1 P
CONECT  O4 2 PC1
CONECT  C1 3 O4   O5   C2
CONECT  O5 1 C1
CONECT  C2 4 C1  HC1  HC2  HC3
CONECT HCH11 C2
CONECT HCH21 C2
CONECT HCH31 C2
END
HETACP  8
HETNAM ACP ACETYL PHOSPHATE
FORMUL  ACPC2 H3 O5 P1 2-

2. download the reduce and probe executables also from 
http://kinemage.biochem.duke.edu/


3.  run reduce make sure to use the -DB flag to input your ligand 
dictionary


4. run probe with a command something like:
probe -both "chaina 88 (ATOM_OG1 | ATOM_HG1)" "chainx 1" 
CheY_A88T_AcP_H.pdb
Where chain A in this case is the protein and the hydroxyl of Thr 88 
is the only relevant interacting group with chain X the ligand.


5. convert the probe output to a python script to render the cgo 
objects in pymol using the attached perl script.  ./probe_to_cgo 
[input probe dots] [output pymol cgo]


6. use the run command in pymol to execute the python script and draw 
the cgo output.


If this all works the first go then amazing!  If not I can try to help 
get things working, but it's been a few years since I last used these 
tools.


Best of Luck!
-bob



On Fri, Aug 29, 2014 at 10:30 AM, Bondurant > wrote:


Hello community,
I would like to draw a figure similar to this one
http://www.cell.com/cms/attachment/615980/4968633/gr1.jpg
showing the clashes between a potential ligand and the protein.
The only way i know how to do this in pymol is using the
show_bumps plugin, but i don't really like the "red disks" format.
Could anyone tell me how i could easily draw something similar to
those red spikes from the example to represent the clashes in
pymol or any other program? I'm able to do it using molprobity and
kinemage, but there's no much possibilities for editing and to get
it in printing quality.
Thanks


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Re: [PyMOL] Can not open APBS plugin in PyMol 1.7.2.0 (Open Source, Fink, OS X 10.10)

2014-10-22 Thread Xiaoguang Xue 
This is the system info

Also include the following system information:

Package manager version: 0.38.1

Distribution version: selfupdate-rsync Sun Oct 22 10:00:35 2014, 10.10,
x86_64

Trees: local/main stable/main stable/crypto

Xcode.app: 6.1.0

Xcode command-line tools: 6.1.0.0.1.1413057044

Max. Fink build jobs:  4

On Wed, Oct 22, 2014 at 10:06 AM, Xiaoguang Xue  wrote:

> Hi, All
>
> I can't open apbs plugin in pymol 1.7.2.0 (installed by Fink on OS X
> 10.10). I got the following error.
>
> Error: 2
>  Exception in Tk callback
>   Function:  at 0x110cde320> (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
> .4584592016.4584592880.4584616592.4584671568 which already has slaves
> managed by grid
>
>
>
>
> --
> Xiaoguang Xue, PhD student
> Utrecht University
> Crystal & Structural Chemistry
> Padualaan 8. Room N807
> 3584 CH Utrecht
> The Netherlands
> Tel. +31-30-253-2383
>



-- 
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Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383
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[PyMOL] Can not open APBS plugin in PyMol 1.7.2.0 (Open Source, Fink, OS X 10.10)

2014-10-22 Thread Xiaoguang Xue 
Hi, All

I can't open apbs plugin in pymol 1.7.2.0 (installed by Fink on OS X
10.10). I got the following error.

Error: 2
 Exception in Tk callback
  Function:  at 0x110cde320> (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
.4584592016.4584592880.4584616592.4584671568 which already has slaves
managed by grid




-- 
Xiaoguang Xue, PhD student
Utrecht University
Crystal & Structural Chemistry
Padualaan 8. Room N807
3584 CH Utrecht
The Netherlands
Tel. +31-30-253-2383
--
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho___
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