pymol-users Mailing List for PyMOL Molecular Graphics System

hi,
do you have any idea of how to represent a dna by its surface?
thanks
Nunzio

Free Api documentation:

#1 is the source code itself (doc strings in modules/pymol/*.py)

#2 are all the commands on pymolwiki.org, which are close to one to  
one with the API

Cheers,
Warren
--
Warren L. DeLano, Ph.D.
wa...@de...

On Feb 27, 2009, at 7:18 AM, "Tsjerk Wassenaar" <ts...@gm...>  
wrote:

> No, but naming is usually fairly intuitive, so you can browse through
> the module properties:
>
> print dir(cmd)
>
> or
>
> /for i in dir(cmd): print i
>
> or even (to get the functions):
>
> /for i in dir(cmd): callable( getattr( cmd, i ) ) and print i
>
> Cheers,
>
> Tsjerk
> On Fri, Feb 27, 2009 at 4:10 PM, Jan Kosinski <ko...@ge...>  
> wrote:
>> Thanks, that works!
>>
>> Is there an API reference to pymol for non-sponsor users?
>>
>>
>> Tsjerk Wassenaar wrote:
>>>
>>> Hi Janek,
>>>
>>> You want:
>>>
>>> cmd.get_object_list()
>>>
>>> For instance, I sometimes want to align a whole lot of things,  
>>> which I do
>>> with:
>>>
>>> /for i in cmd.get_object_list(): cmd.align( i, reference )
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>> On Fri, Feb 27, 2009 at 3:44 PM, Jan Kosinski <ko...@ge...>  
>>> wrote:
>>>
>>>>
>>>> Hi,
>>>>
>>>> I wish to iterate over all objects in my pymol session and for each
>>>> execute some command. Is it possible to do that using pymol  
>>>> commands?
>>>>
>>>> I could do that using python script but: How can I get a list of  
>>>> current
>>>> objects?
>>>>
>>>> Cheers,
>>>> Janek
>>>>
>>>>
>>>> --- 
>>>> --- 
>>>> --- 
>>>> --- 
>>>> ------------------------------------------------------------------
>>>> Open Source Business Conference (OSBC), March 24-25, 2009, San  
>>>> Francisco,
>>>> CA
>>>> -OSBC tackles the biggest issue in open source: Open Sourcing the
>>>> Enterprise
>>>> -Strategies to boost innovation and cut costs with open source
>>>> participation
>>>> -Receive a $600 discount off the registration fee with the source  
>>>> code:
>>>> SFAD
>>>> http://p.sf.net/sfu/XcvMzF8H
>>>> _______________________________________________
>>>> PyMOL-users mailing list
>>>> PyM...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>>
>>>>
>>>
>>>
>>>
>>>
>>
>>
>
>
>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
> --- 
> --- 
> --- 
> ---------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San  
> Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the  
> Enterprise
> -Strategies to boost innovation and cut costs with open source  
> participation
> -Receive a $600 discount off the registration fee with the source  
> code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>

Is it possible to save stick models as .obj files?  I know you can save 
surfaces as .obj, but I'd also like to be able to export the stick 
model.  Thanks,

David Borland

No, but naming is usually fairly intuitive, so you can browse through
the module properties:

print dir(cmd)

or

/for i in dir(cmd): print i

or even (to get the functions):

/for i in dir(cmd): callable( getattr( cmd, i ) ) and print i

Cheers,

Tsjerk
On Fri, Feb 27, 2009 at 4:10 PM, Jan Kosinski <ko...@ge...> wrote:
> Thanks, that works!
>
> Is there an API reference to pymol for non-sponsor users?
>
>
> Tsjerk Wassenaar wrote:
>>
>> Hi Janek,
>>
>> You want:
>>
>> cmd.get_object_list()
>>
>> For instance, I sometimes want to align a whole lot of things, which I do
>> with:
>>
>> /for i in cmd.get_object_list(): cmd.align( i, reference )
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Fri, Feb 27, 2009 at 3:44 PM, Jan Kosinski <ko...@ge...> wrote:
>>
>>>
>>> Hi,
>>>
>>> I wish to iterate over all objects in my pymol session and for each
>>> execute some command. Is it possible to do that using pymol commands?
>>>
>>> I could do that using python script but: How can I get a list of current
>>> objects?
>>>
>>> Cheers,
>>> Janek
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
>>> CA
>>> -OSBC tackles the biggest issue in open source: Open Sourcing the
>>> Enterprise
>>> -Strategies to boost innovation and cut costs with open source
>>> participation
>>> -Receive a $600 discount off the registration fee with the source code:
>>> SFAD
>>> http://p.sf.net/sfu/XcvMzF8H
>>> _______________________________________________
>>> PyMOL-users mailing list
>>> PyM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>
>>>
>>
>>
>>
>>
>
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Thanks, that works!

Is there an API reference to pymol for non-sponsor users?


Tsjerk Wassenaar wrote:
> Hi Janek,
>
> You want:
>
> cmd.get_object_list()
>
> For instance, I sometimes want to align a whole lot of things, which I do with:
>
> /for i in cmd.get_object_list(): cmd.align( i, reference )
>
> Hope it helps,
>
> Tsjerk
>
> On Fri, Feb 27, 2009 at 3:44 PM, Jan Kosinski <ko...@ge...> wrote:
>   
>> Hi,
>>
>> I wish to iterate over all objects in my pymol session and for each
>> execute some command. Is it possible to do that using pymol commands?
>>
>> I could do that using python script but: How can I get a list of current
>> objects?
>>
>> Cheers,
>> Janek
>>
>> ------------------------------------------------------------------------------
>> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
>> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
>> -Strategies to boost innovation and cut costs with open source participation
>> -Receive a $600 discount off the registration fee with the source code: SFAD
>> http://p.sf.net/sfu/XcvMzF8H
>> _______________________________________________
>> PyMOL-users mailing list
>> PyM...@li...
>> https://lists.sourceforge.net/lists/listinfo/pymol-users
>>
>>     
>
>
>
>   

Hi Janek,

You want:

cmd.get_object_list()

For instance, I sometimes want to align a whole lot of things, which I do with:

/for i in cmd.get_object_list(): cmd.align( i, reference )

Hope it helps,

Tsjerk

On Fri, Feb 27, 2009 at 3:44 PM, Jan Kosinski <ko...@ge...> wrote:
> Hi,
>
> I wish to iterate over all objects in my pymol session and for each
> execute some command. Is it possible to do that using pymol commands?
>
> I could do that using python script but: How can I get a list of current
> objects?
>
> Cheers,
> Janek
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

Hi,

I wish to iterate over all objects in my pymol session and for each 
execute some command. Is it possible to do that using pymol commands?

I could do that using python script but: How can I get a list of current 
objects?

Cheers,
Janek

Dan,
 
MacPyMOL is mostly based on PyMOL open-source code, but there are a few Mac-specific proprietary pieces.  
 
So to the extent that your suggestions also apply to the Open-Source version, please consider using the PyMOL Open-Source Trackers linked from the main web site:
 
http://pymol.org
 
Click on "Features" (Tyrosine) and then "Add new" (or Add Artifact in the new version) and complete the form.  Having a SourceForge account will enable you to receive follow up messages, but you can make suggestions anonymously without having an account.
 
For suggestions which pertain to the proprietary aspects of MacPyMOL (e.g. direct QuickTime export, Cocoa-GUI, Mac-only funkyness, etc.), please email those ideas directly to su...@de...
 
Cheers,
Warren

________________________________

From: Dan Kelleher [mailto:Dan...@um...]
Sent: Thu 2/26/2009 11:54 AM
To: pym...@li...
Subject: [PyMOL] Where is the preferred place to E-Mail suggestions to Improve the MacPyMol Software ?



Hello, 
I've Forgotten, 
Where is the preferred place to E-Mail suggestions to Improve the  
MacPyMol Software ? 
-Dan 


------------------------------------------------------------------------------ 
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA 
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise 
-Strategies to boost innovation and cut costs with open source participation 
-Receive a $600 discount off the registration fee with the source code: SFAD 
http://p.sf.net/sfu/XcvMzF8H 
_______________________________________________ 
PyMOL-users mailing list 
PyM...@li... 
https://lists.sourceforge.net/lists/listinfo/pymol-users 

Hello,
I've Forgotten,
Where is the preferred place to E-Mail suggestions to Improve the  
MacPyMol Software ?
-Dan

Bradley,
 
group inner
 
group outer, inner
 
Cheers,
Warren

________________________________

From: Bradley Hintze [mailto:bra...@ag...]
Sent: Tue 2/24/2009 10:46 AM
To: pym...@li...
Subject: [PyMOL] Embedded Groups?


Hi all!

I use the new group objects tool and love it. I was wondering if it is possible to create embedded groups; a group within a group? If not, can that function be added in later releases?

-- 
Bradley J. Hintze
Biochemistry Undergraduate
Utah State University

Hi all!

I use the new group objects tool and love it. I was wondering if it is
possible to create embedded groups; a group within a group? If not, can that
function be added in later releases?

-- 
Bradley J. Hintze
Biochemistry Undergraduate
Utah State University

Anne,
 
In such situations, you probably need to fall back on running APBS manually via the command line (project home: http://apbs.sourceforge.net).  Unfortunately, the PyMOL APBS plugin is only able to handle near-perfect input structures.  However, once you can successfully compute a DX file using APBS, then PyMOL can be of use in visualizing the results.
 
Cheers,
Warren

________________________________

From: LOPES Anne [mailto:ann...@ce...]
Sent: Mon 2/23/2009 9:50 AM
To: pym...@li...
Subject: [PyMOL] error with the APBS plugin




Hello, 

I'm trying to use the APBS plugin to evaluate the electrostatic properties of my protein. 
On the one hand, I've have this error: 
  
 Unable to assign parameters for the 1 atom in selection 'unassigned'. Please either remove 
 thes unassigned atoms and re-start the calculation or fix their parameters in the generated PQR 
 file and run the calculation using the modified PQR file (select 'Use another PQR' in 'Main') 

I tried to remove the selection but it seems that the atom in the selection has not been 
removed and I still obtain the same error message. 

Thus, I tried to edit the PQR file and I removed the atom in the PQR file but in this case I obtain 
a new error message: 

 Reading PQR-format atom data from /home/Models/pymol-generated.pqr. 
 Vio_ctor2: some error occurred. 
 Vio_ctor: Vio_ctor2() failed. 
 Problem opening virtual socket /home/Models/pymol-generated.pqr! 
 Error reading molecules! 
 ObjectMapLoadDXFile-Error: Unable to open file! 

could you explain the problem to me? 
thank you for your help, 

best regards, 

Anne L 



------------------------------------------------------------------------------ 
Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA 
-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise 
-Strategies to boost innovation and cut costs with open source participation 
-Receive a $600 discount off the registration fee with the source code: SFAD 
http://p.sf.net/sfu/XcvMzF8H 
_______________________________________________ 
PyMOL-users mailing list 
PyM...@li... 
https://lists.sourceforge.net/lists/listinfo/pymol-users 

2. When showing a cartoon of DNA the ribose ring in the backbone is 
always there no matter which setting you choose. How can I make the 
phosphates and the ribose rings show as a backbone cartoon "tube" and 
keep just the bases as filled sticks with rinngs? 
 
load nuc_acid.pdb
 
as cartoon
 
set cartoon_ring_mode, 3
 
set cartoon_ring_finder, 2

3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get 
the rings to fill in on selected amino acids (H, W, Y, F) in a protein 
of that same file. Is there a fill amino acid ring setting? 

load $TUT/1hpv.pdb

as cartoon

set cartoon_ring_finger, 4

Cheers,

Warren

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rsa...@an...

 

 

Hello,

I'm trying to use the APBS plugin to evaluate the electrostatic properties of my protein.
On the one hand, I've have this error: 
 
 Unable to assign parameters for the 1 atom in selection 'unassigned'. Please either remove
 thes unassigned atoms and re-start the calculation or fix their parameters in the generated PQR
 file and run the calculation using the modified PQR file (select 'Use another PQR' in 'Main')

I tried to remove the selection but it seems that the atom in the selection has not been
removed and I still obtain the same error message. 

Thus, I tried to edit the PQR file and I removed the atom in the PQR file but in this case I obtain
a new error message:

 Reading PQR-format atom data from /home/Models/pymol-generated.pqr.
 Vio_ctor2: some error occurred.
 Vio_ctor: Vio_ctor2() failed.
 Problem opening virtual socket /home/Models/pymol-generated.pqr!
 Error reading molecules!
 ObjectMapLoadDXFile-Error: Unable to open file!

could you explain the problem to me?
thank you for your help,

best regards,

Anne L

Hello

You can look into 3DNA out of Rutgers
(http://rutchem.rutgers.edu/~xiangjun/3DNA/).  To make the image you
describe you will also need to use Raster3D.  3DNA has some basic
scripts for this but you will need to write your own to get the image
you describe.

Andrew



On Mon, Feb 23, 2009 at 11:29 AM, H. Adam Steinberg <ad...@st...> wrote:
> I have three questions I'm hoping someone can help with.
>
> 1. Does anyone have, or can anyone point me to a program that will
> generate a nice pdb file that contains 50 or so base pairs of random
> sequence B form DNA with hydrogen bonds between the bases or no H bonds?
>
> I need to be able to scultp the DNA and have one strand react to the
> pulling of the other strand. I also want to show the union of the AT and
> GC via H bonds. The H bonds can be regular bonds (and probably will have
> to be if I'm going to be sculpting). I can make the h bonds and make
> them real bonds for the sculpting, I'm just wondering of anyone has
> already done it or has a script around....
>
> 2. When showing a cartoon of DNA the ribose ring in the backbone is
> always there no matter which setting you choose. How can I make the
> phosphates and the ribose rings show as a backbone cartoon "tube" and
> keep just the bases as filled sticks with rinngs?
>
> 3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get
> the rings to fill in on selected amino acids (H, W, Y, F) in a protein
> of that same file. Is there a fill amino acid ring setting?
>
> Thanks in advance for anything you can offer,
>
> Adam
>
> --
> _______________________________________
>
> H. Adam Steinberg
> Artist, Scientist
> <http://adam.steinbergs.us>
>
> Information Technology and Media Center
> Department of Biochemistry
> University of Wisconsin-Madison
> 433 Babcock Drive
> Madison, WI 53706
> 608/265-4982
> _______________________________________
>
>
>
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>

I have three questions I'm hoping someone can help with.

1. Does anyone have, or can anyone point me to a program that will 
generate a nice pdb file that contains 50 or so base pairs of random 
sequence B form DNA with hydrogen bonds between the bases or no H bonds?

I need to be able to scultp the DNA and have one strand react to the 
pulling of the other strand. I also want to show the union of the AT and 
GC via H bonds. The H bonds can be regular bonds (and probably will have 
to be if I'm going to be sculpting). I can make the h bonds and make 
them real bonds for the sculpting, I'm just wondering of anyone has 
already done it or has a script around....

2. When showing a cartoon of DNA the ribose ring in the backbone is 
always there no matter which setting you choose. How can I make the 
phosphates and the ribose rings show as a backbone cartoon "tube" and 
keep just the bases as filled sticks with rinngs?

3. Rings on DNA and RNA can be filled, in cartoon mode. But I can't get 
the rings to fill in on selected amino acids (H, W, Y, F) in a protein 
of that same file. Is there a fill amino acid ring setting?

Thanks in advance for anything you can offer,

Adam

-- 
_______________________________________

H. Adam Steinberg
Artist, Scientist
<http://adam.steinbergs.us>

Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
_______________________________________

Am 20.02.2009 um 17:54 schrieb Pete Meyer:

>> I am trying to fire up a script with pymol -r doit.pml
>
> pymol doit.pml should be sufficient (no need for -r).

Oh ok, without -r it works :-)

Best
	Martin

Martin,

-r is for running Python programs in the __main__ namespace.

For PyMOL command scripts, simply:

pymol doit.pml

Cheers,
Warren


> -----Original Message-----
> From: Martin Höfling [mailto:mar...@gm...]
> Sent: Friday, February 20, 2009 8:50 AM
> To: pym...@li...
> Subject: [PyMOL] running script on startup
> 
> Hey folks,
> 
> I am trying to fire up a script with pymol -r doit.pml
> 
> PyMOL>run doit.pml,main
> Traceback (most recent call last):
>    File "/sw/lib/pymol-py25/modules/pymol/parser.py", line 334, in parse
> 
> parsing
> .run_file(exp_path(layer.args[0]),__main__.__dict__,__main__.__dict__)
>    File "/sw/lib/pymol-py25/modules/pymol/parsing.py", line 455, in
> run_file
>      execfile(file,global_ns,local_ns)
>    File "doit.pml", line 2
>       select resname SOL
>                    ^
>   SyntaxError: invalid syntax
> 
> Can't I use these commands or any ideas what I am doing wrong there? :-)
> 
> Best
> 	Martin
> 
> --------------------------------------------------------------------------
> ----
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
> CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the
> Enterprise
> -Strategies to boost innovation and cut costs with open source
> participation
> -Receive a $600 discount off the registration fee with the source code:
> SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> PyMOL-users mailing list
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> 
> 
> 

> I am trying to fire up a script with pymol -r doit.pml

pymol doit.pml should be sufficient (no need for -r).

>    File "doit.pml", line 2
>       select resname SOL

Unless the syntax has changed, try 'select resname, SOL'.  Does this
script work when run from an already started pymol?

Pete

Hey folks,

I am trying to fire up a script with pymol -r doit.pml

PyMOL>run doit.pml,main
Traceback (most recent call last):
   File "/sw/lib/pymol-py25/modules/pymol/parser.py", line 334, in parse
      
parsing 
.run_file(exp_path(layer.args[0]),__main__.__dict__,__main__.__dict__)
   File "/sw/lib/pymol-py25/modules/pymol/parsing.py", line 455, in  
run_file
     execfile(file,global_ns,local_ns)
   File "doit.pml", line 2
      select resname SOL
                   ^
  SyntaxError: invalid syntax

Can't I use these commands or any ideas what I am doing wrong there? :-)

Best
	Martin

Justin,

Sorry about that...

"svn update" and rebuild.

I believe the warning is gone now.  It should only print if you
specifically request certain stereo modes.

Cheeers,
Warren
 

> -----Original Message-----
> From: Justin Lecher [mailto:j.l...@fz...] 
> Sent: Thursday, February 19, 2009 5:42 AM
> To: pym...@li...
> Subject: [PyMOL] (no subject)
> 
> Hello all especially Warren,
> 
> What does
> 
> "Sorry, time-sequential stereo 3D not available"
> 
> mean. It is printed out when I start pymol. I am using current HEAD.
> 
> Thanks justin
> 
> 
> --
> Justin Lecher
> Institute for  Neuroscience and Biophysics INB 2 - Molecular 
> Biophysics II Research centre Juelich GmbH,
> 52425 Juelich,Germany
> phone: +49 2461 61 5385
> 
> 
> 
> 

Hello all especially Warren,

What does

"Sorry, time-sequential stereo 3D not available"

mean. It is printed out when I start pymol. I am using current HEAD.

Thanks justin


-- 
Justin Lecher
Institute for  Neuroscience and Biophysics
INB 2 - Molecular Biophysics II
Research centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385

Chris,

In answer to your question 1:  Yes, distance with mode=2 runs the polar
contact detection routine between the two selections.

In answer to your question 2, there are two reasons why stick with the
term "polar contacts" instead of "hydrogen bonds":

1) Generally speaking, PyMOL does not have sufficient information to
rigorously determine hydrogen bonds, since typical PDB file are
ambiguous with respect to charge states, bonds, bond valences, and
tautomers.  As it stands, all of those things are guessed heuristically.
Rigorously determining the location of lone pair electrons and proton
coordinates from raw PDB files is a nontrival problem beyond the present
scope of the software (especially when arbitrary small molecule
structures are present).  In addition, PyMOL would also need to consider
the implied coordinate error due to overall structure resolution and
local temperature factors before  rigorously asserting than any specific
hydrogen bond does or does not exist.

2) Furthermore, our hydrogen bond detection machinery was originally
developed for purposes of mimicking Kabsch and Sander's DSSP secondard
structure assignment algorithm (Biopolymers 22, 2577, 1983) which is
based on a rather generous notion of hydrogen bonding (see Kabsch Figure
1). 

Although this approximate capability can be accessed via the distance
command using mode=2, the criteria applied by our implementation may be
based on heavy-atom coordinates (only) and does not necessarily
correspond to anything rigorous or published. 

So the bottom line is that PyMOL merely offers up putative polar
contacts and leaves it to the user to determine whether or not the
interactions present are in fact hydrogen bonds, salt bridges, polar
interactions, or merely artifacts of incorrect assignments (i.e. two
carbonyls hydrogen bonding because they're being treated like
hydroxyls).

With respect to the h_bond_* settings, the angle in question for
h_bond_cutoff_* and h_bond_max_angle is ADH, assuming H exists.  If H
does not exist, then PyMOL will guess a hypothetical coordinate which
may not actually be valid (in plane, etc.).  The other angles you listed
are not directly considered, however, the hydrogen must also lie within
a cone of space with its origin on A (along B->A) and angular width
h_bond_cone.  Since h_bond_cone in 180 by default, the present behavior
is to simply reject any hydrogen bond where the hydrogen would lie
behind the plane defined by the acceptor atom (A) in relation to its
bonded atom(s) B (if any).  In other words, if B is only one atom (e.g.
C=O vs. C-O-C), then by default, HAB cannot be less then 90 degrees.

The two h_bond_power_* settings are merely fitting parameters which
enable PyMOL to reproduce a curve shape reflecting Kabsch Figure 1.  The
endpoints of the effective cutoff curve is a function of the two
h_bond_cutoff_*  setting.

In answer to question 3, with respect to menu actions, the underlying
API call (from modules/pymol/menu.py) is essentially:

cmd.dist(name,selection,selection,quiet=1,mode=2,label=0,reset=1)

Cheers,
Warren

> -----Original Message-----
> From: cmf...@uc... [mailto:cmf...@uc...]
> Sent: Monday, February 16, 2009 11:34 AM
> To: pym...@li...
> Subject: [PyMOL] Hydrogen Bond Parameters
> 
> Hello,
> 
> Any help with the following would be greatly appreciated:
> 
> The online PyMOL documentation
>
(http://delsci.info/dsc/dokuwiki/doku.php?id=setting:h_bond&s=hydrogen%2
0b
> ond)
> 
> describes the h_bond parameters as follows:
> 
> 1. h_bond_cone (float, default: 180.0) is a hydrogen-bond
> geometry parameter.
> 2. h_bond_cutoff_center (float, default: 3.6) is the maximum
> distance for ideal hydrogen bonds.
> 3. h_bond_cutoff_edge (float, default: 3.6) is the maximum
> distance for a marginal hydrogen bond.
> 4. h_bond_exclusion (integer, default: 3) controls suppression
> of hydrogen bonds around adjacent atoms.
> 5. h_bond_max_angle (float, default: 63.0) is the maximum
> angle for a marginal hydrogen bond.
> 6. h_bond_power_a (float, default: 1.6) is a hydrogen-bond
> geometry parameter.
> 7. h_bond_power_b (float, default: 5.0) is a hydrogen-bond
> geometry parameter.
> 
> I was hoping someone (Warren?) might be able to elaborate on
> parameters 1-3 and 5-7 (or alternatively provide a reference
> and/or thread). Specifically, if a hydrogen bond consists of a
> donor (D), hydrogen (H), acceptor (A), and acceptor antecedent
> (B) illustrated as:
> 
> D--H--A--B
> 
> or alternatively:
> 
>   H--A
>  /    \
> D      B
> 
> Then how are parameters 1-3, and 5-7 defined in terms of
> distances (HA, DA) and angles (DHA, DAB, HAB)? I would guess
> that "h_bond_cutoff_center" and "h_bond_cutoff_edge" both
> refer to the donor-acceptor (DA) distance, and I can make
> additional guesses about the other parameters, but I would
> prefer to proceed with a set of exact definitions if possible.
> 
> Three additional questions:
> 
> 1. Once the hydrogen bond parameters have been set, one uses
> the 'dist' command with mode=2 to find all hydrogen bonds,
> correct? For instance, if mc_H is the set generated by the
> command 'select mc_H, name h' and mc_O is the set generated by
> the command 'select mc_O, name o'  then will the following
> command find all main-chain/main-chain hydrogen bonds for a
> given structure (using the previously-defined h_bond
> parameters as selection criteria):
> 
> 	dist mcmc, mc_H, mc_O, mode=2
> ?
> 
> 
> 2. Are hydrogen bonds considered a subset of "polar contacts"
> in PyMOL or are the two sets equivalent ({hydrogen bonds} =
> {polar contacts})?
> 
> 3. At the risk of belaboring the point, what set of commands
> combined with the distance command would yield the same
> results as those generated by following menu selection:
> 
> 	find > polar contacts > within selection
> 
> assuming that the selection under consideration is an entire
> structure?
> 
> Thanks in advance,
> 
> Christopher
> 
>
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> 
> 
> 

Hello,

Any help with the following would be greatly appreciated:

The online PyMOL documentation
(http://delsci.info/dsc/dokuwiki/doku.php?id=setting:h_bond&s=hydrogen%20bond)

describes the h_bond parameters as follows:

1. h_bond_cone (float, default: 180.0) is a hydrogen-bond
geometry parameter.
2. h_bond_cutoff_center (float, default: 3.6) is the maximum
distance for ideal hydrogen bonds.
3. h_bond_cutoff_edge (float, default: 3.6) is the maximum
distance for a marginal hydrogen bond.
4. h_bond_exclusion (integer, default: 3) controls suppression
of hydrogen bonds around adjacent atoms.
5. h_bond_max_angle (float, default: 63.0) is the maximum
angle for a marginal hydrogen bond.
6. h_bond_power_a (float, default: 1.6) is a hydrogen-bond
geometry parameter.
7. h_bond_power_b (float, default: 5.0) is a hydrogen-bond
geometry parameter.

I was hoping someone (Warren?) might be able to elaborate on
parameters 1-3 and 5-7 (or alternatively provide a reference
and/or thread). Specifically, if a hydrogen bond consists of a
donor (D), hydrogen (H), acceptor (A), and acceptor antecedent
(B) illustrated as:

D--H--A--B

or alternatively:
      
  H--A
 /    \
D      B

Then how are parameters 1-3, and 5-7 defined in terms of
distances (HA, DA) and angles (DHA, DAB, HAB)? I would guess
that "h_bond_cutoff_center" and "h_bond_cutoff_edge" both
refer to the donor-acceptor (DA) distance, and I can make
additional guesses about the other parameters, but I would
prefer to proceed with a set of exact definitions if possible.

Three additional questions: 

1. Once the hydrogen bond parameters have been set, one uses
the 'dist' command with mode=2 to find all hydrogen bonds,
correct? For instance, if mc_H is the set generated by the
command 'select mc_H, name h' and mc_O is the set generated by
the command 'select mc_O, name o'  then will the following
command find all main-chain/main-chain hydrogen bonds for a
given structure (using the previously-defined h_bond
parameters as selection criteria):

	dist mcmc, mc_H, mc_O, mode=2
?
	 

2. Are hydrogen bonds considered a subset of "polar contacts"
in PyMOL or are the two sets equivalent ({hydrogen bonds} =
{polar contacts})?

3. At the risk of belaboring the point, what set of commands
combined with the distance command would yield the same
results as those generated by following menu selection:

	find > polar contacts > within selection

assuming that the selection under consideration is an entire
structure?

Thanks in advance,

Christopher