Re: [PyMOL] Disulfide Bonds

[Kaushik R. <kx...@ps...>]

Warren,

Thanks for the h-bond tip. A related question, I was wondering if PyMOL 
can protonate  ligands on its own. In other words can it perceive  the 
atom-type. I have been trying to integrate a perception algorithm 
similar to babel with other programs and would like to do it with PyMOL 
as well. However  I could not find  details/examples on the attach 
command in the manual (I did not look through the code yet, I am a new 
user). So can you please give an example of attach command.

Well, the reason I wanted the parser was some programs like  AMBER 
(leap) requires different  names for linked cysteines. It would be 
helpful to get this information from the PDB file since it has it. Also 
there is other information in the PDB file which can be useful if 
displayed somewhere on the viewer like sequence etc. In other words a 
hierarchy window similar to the web-lab viewer. Maybe it does  and just 
have not figured out how to make it work it.

In any case I think this is a terrific program and although I have just 
started using it I am realizing its potential.

Kaushik.

On Friday, September 20, 2002, at 05:24 PM, DeLano, Warren wrote:

> Regarding H-bonds. Funny you should ask -- Hans and I just worked out 
> how to do this here at Sunesis...
>
> There isn't a built-in function yet (it is coming), but you can show 
> H-bonds between two objects using  atom selections so long as hydrogens 
> are present in both molecules.  If you don't have hydrogens, you can 
> use h_add on the proteins or provide ligands with valence information 
> and then use h_add.
>
> Two examples are below.  For clarity, they draw dashes between the 
> heavy atoms and hide the hydrogens.
>
> # EXAMPLE 1: Show hydrogen bonds between protein
> # and docked ligands (which must have hydrogens)
>
> load target.pdb,prot
> load docked_ligs.sdf,lig
>
> # add hydrogens to protein
>
> h_add prot
>
> select don, (elem n,o and (neighbor hydro))
> select acc, (elem o or (elem n and not (neighbor hydro)))
> dist HBA, (lig and acc),(prot and don), 3.2
> dist HBD, (lig and don),(prot and acc), 3.2
> delete don
> delete acc
> hide (hydro)
>
> hide labels,HBA
> hide labels,HBD
>
> # EXAMPLE 2
> # Show hydrogen bonds between two proteins
>
> load prot1.pdb
> load prot2.pdb
>
> h_add prot1
> h_add prot2
>
> select don, (elem n,o and (neighbor hydro))
> select acc, (elem o or (elem n and not (neighbor hydro)))
> dist HBA, (prot1 and acc),(prot2 and don), 3.2
> dist HBD, (prot1 and don),(prot2 and acc), 3.2
> delete don
> delete acc
> hide (hydro)
>
> hide labels,HBA
> hide labels,HBD
>
> # NOTE: that you could also use this approach between two
> # non-overlapping selections within a single object.
>
> As far as SSBOND records go, no PyMOL doesn't currently parse 
> these...does it need to?
>
> Warren
>
> --
> mailto:wa...@su...
> Warren L. DeLano, Ph.D.
>
>> -----Original Message-----
>> From: Kaushik Raha [mailto:kx...@ps...]
>> Sent: Friday, September 20, 2002 1:36 PM
>> To: pym...@li...
>> Subject: Re: [PyMOL] Disulfide Bonds
>>
>>
>> A similar question: Does PyMOL have a PDB file parser that can read
>> disulphide linkages from the file and connect the atoms or one has to
>> explicitly issue bond commands. Also, can PyMOL display
>> hydrogen bonds
>> without the user having to write out a list?
>>
>> thanks,
>>
>> Kaushik Raha.
>> Penn State University.
>>
>> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
>>
>>> Alex,
>>>
>>> 	If the sulfurs are within disulfide bonding distance,
>> PyMOL should
>>> connect them by default.  If this is not happening, please
>> send me the
>>> PDB file so I can take a look-see.
>>>
>>>       Otherwise, you can use the "bond" command to attach them:
>>>
>>> bond 24/sg,26/sg
>>> bond 56/sb,99/sg
>>>
>>> unpick
>>>
>>> (unpick will hide the bond baton which gets displayed)
>>>
>>> Cheers,
>>> Warren
>>>
>>> --
>>> mailto:wa...@su...
>>> Warren L. DeLano, Ph.D.
>>>
>>>> -----Original Message-----
>>>> From: Alex Morla [mailto:al...@ui...]
>>>> Sent: Friday, September 20, 2002 8:48 AM
>>>> To: pym...@li...
>>>> Subject: [PyMOL] Disulfide Bonds
>>>>
>>>>
>>>> Sorry if this is a novice question, but how do I display the
>>>> disulfide bonds
>>>> in my models?
>>>>
>>>> Thanks, and keep up the great work!!
>>>>
>>>> Alex Morla
>>>> Univ. of Illinois, Rockford.
>>>>
>
>
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