Re: [PyMOL] Editing of the pdb structure

[Jason V. <jas...@sc...>]

James,

I can't think of a clever way at the moment, so here's a simple
solution. Just create a temporary copy of the ligand from state 2 into
state 1. Then, create the new object from the protein and new_ligand:

# create a new one-state ligand from state 2 of the original

create new_ligand, old_ligand, 1, 2

# create the new_obj from

create new_obj, (new_ligand or protein), 1, 1

The object, new_obj, will have the ligand and protein both, now, in state 1.

Alternatively, you load the multi-state structure using the multiplex
flag and use create on the new objects:

load some_file.pdb, multiplex=1

create new_obj, (some_file1 or some_file2)

Cheers,

-- Jason


On Wed, Jul 18, 2012 at 12:57 PM, James Starlight
<jms...@gm...> wrote:
> Dear all!
>
>
> I have input multi state structure consisted of protein in one state
> and ligand in the second state generated by Chimera. I want to merge
> both of that objects in one common object. How I could do it?
>
>
> James
>
> 2012/7/18 James Starlight <jms...@gm...>:
>> Dear all!
>>
>>
>> I have input multi state structure consisted of protein in one state
>> and ligand in the second state generated by Chimera. I want to merge
>> both of that objects in one common object. How I could do it?
>>
>>
>> James
>>
>> 2012/4/30 Thomas Holder <sp...@us...>:
>>> Hi James and Joel,
>>>
>>> I would use a homology modeling tool to add missing atoms (basically rebuild
>>> the structure, given the incomplete structure as template).
>>>
>>> Examples for web servers:
>>>  * http://toolkit.tuebingen.mpg.de/modeller
>>>  * http://swissmodel.expasy.org/
>>>
>>> pdb2pqr can also add a limited number of missing atoms, see
>>> http://www.poissonboltzmann.org/pdb2pqr/d/web-servers
>>>
>>>
>>> Hope that helps.
>>>
>>> Cheers,
>>>   Thomas
>>>
>>> Joel Tyndall wrote, On 04/30/12 00:07:
>>>
>>>> Surely you could use pymol mutagenesis wizard to do tis.
>>>>
>>>> Also James, It is a good practice to  start a new thread (new email with
>>>> new subject for each set of questions you have
>>>>
>>>> Regards
>>>>
>>>> Joel
>>>>
>>>> From: James Starlight [mailto:jms...@gm...]
>>>> Sent: Friday, 27 April 2012 8:25 p.m.
>>>> To: pymol-users
>>>> Subject: Re: [PyMOL] Editing of the pdb structure
>>>>
>>>> Dear all!
>>>>
>>>> I want to prepare my pdb structure for MD simulation. I've done all
>>>> required things but my protein consist of some missing heavy atoms the list
>>>> of which I've obtained from my pdb hedader
>>>>
>>>> REMARK 470   M RES CSSEQI  ATOMS
>>>> REMARK 470     ARG A 220    CG   CD   NE   CZ   NH1  NH2
>>>> REMARK 470     ARG A 222    CG   CD   NE   CZ   NH1  NH2
>>>> REMARK 470     ASN B 212    O    CG   OD1  ND2
>>>> REMARK 470     LYS C  43    CG   CD   CE   NZ
>>>> REMARK 470     GLY C 225    O
>>>> I've heard that there are some web servers wich could be usefull to build
>>>> such missing atoms.
>>>> In particular in my structure there are lack not only side chain atoms but
>>>> also two backbone Oxygens in the Gly and Asn wich could be the main problem
>>>> of such task.
>>>>
>>>> In any case I'll be very thankfull if you provide me with such server
>>>> James
>>>
>>>
>>> --
>>> Thomas Holder
>>> MPI for Developmental Biology
>>> Spemannstr. 35
>>> D-72076 Tübingen
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, LLC

(e) Jas...@sc...
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