Thread: [PyMOL] please help-how to generate dimer file from monomer file in pymol

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[PyMOL] please help-how to generate dimer file from monomer file in pymol

From: JiangJiang L. <jl...@uw...> - 2010-04-06 04:36:44

  
Hello all,
 
             When I open the  pdb file 1B8E (a homodimer protein) through pymol I can only see a monomer shown in the screen. Now I know the biological dimer is produced through crystallographic symmetry operations in pymol. To generate the dimer, I think I need to convert these remark comands (list below) to be a readable commands by the pymol program. Does anyone know how to do this conversion? Or what's the commands for crystal symmetry operation? 
Thank you very much!
 
Sincerely
Jenna Liu

PS: 
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000       33.43000

Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

From: Jason V. <jas...@sc...> - 2010-04-06 14:47:51

Jenna,

Use PyMOL to download the biological unit:

fetch 1b8e, type=pdb1

split the states out (you'll notice it's a two-state object)

split_states 1b8e

You can also create symmetry expansion via,  A > Generate > Symmetry Mates >
within X A, from your original object.

Cheers,

-- Jason

On Tue, Apr 6, 2010 at 12:36 AM, JiangJiang Liu <jl...@uw...> wrote:

> **
> Hello all,
>
>              When I open the  pdb file 1B8E (a homodimer protein) through
> pymol I can only see a monomer shown in the screen. Now I know the
> biological dimer is produced through crystallographic symmetry operations in
> pymol. To generate the dimer, I think I need to convert these remark comands
> (list below) to be a readable commands by the pymol program. Does anyone
> know how to do this conversion? Or what's the commands for crystal symmetry
> operation?
> Thank you very much!
>
> Sincerely
> Jenna Liu
> PS:
> REMARK 350 BIOMOLECULE:
> 1
> REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT:
> DIMERIC
> REMARK 350 APPLY THE FOLLOWING TO CHAINS:
> A
> REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000
> 0.00000
> REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000
> 0.00000
> REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000
> 0.00000
> REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000
> 0.00000
> REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000
> 0.00000
> REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000
> 33.43000
>
>  <http://www.mail-archive.com/pym...@li.../>
>
> <http://www.mail-archive.com/pym...@li.../>
>
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
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>



-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

From: Robert C. <rob...@qu...> - 2010-04-06 15:09:24

Hello Jenna,

On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu <jl...@uw...> wrote:

>              When I open the  pdb file 1B8E (a homodimer protein) through
> pymol I can only see a monomer shown in the screen. Now I know the
> biological dimer is produced through crystallographic symmetry operations
> in pymol. To generate the dimer, I think I need to convert these remark
> comands (list below) to be a readable commands by the pymol program. Does
> anyone know how to do this conversion? Or what's the commands for crystal
> symmetry operation? Thank you very much! Sincerely Jenna Liu
> 
> PS: 
> REMARK 350 BIOMOLECULE:
> 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT:
> DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS:
> A REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000
> 0.00000 REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000
> 0.00000 REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000
> 0.00000 REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000
> 0.00000 REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000
> 0.00000 REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000
> 33.43000 

Since the file has the crystallographic information in it, you simply have to
tell PyMOL to build the symmetry-related neighbours.  You do this with the
symexp command:

symexp <prefix>, <object>, <selection>, <cutoff>

So if you have an object called 1b8e, you might do:

symexp s_, 1b8e, 1b8e, 3

This will create new objects whose name begins with s_ and is followed by a
label that identifies the symmetry operation.  You can then turn them on and
off until you find the one that is the mate of the original object.  Given
the BIOMT matrix above, this will be the object that is related by a 2-fold
rotation around the crystallographic b-axis (which in this case is parallel
to the Y-axis) followed by a translation of 1/2 of the c-axis.  This is the
object called "s_03-10000" in this case.

Or as Jason has just written, fetch the biological unit directly and then
split out the states.

Cheers,
Rob
-- 
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor 
Botterell Hall Rm 644
Department of Biochemistry, Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821            Fax: 613-533-2497
<rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc

Re: [PyMOL] please help-how to generate dimer file from monomer file in pymol

From: Tsjerk W. <ts...@gm...> - 2010-04-06 19:38:01

Hi Rob, Jenna,

Be aware that the symmetry data (symexp) need not be equal to the
biological unit transformations (remark biomt), even though it will
often match.

And since I'm posting anyway, here's another possibility:

load 1b8e.pdb, A
create B,A
alter_state 1,B,(x,y,z)=(-x,y,33.43-z)

Cheers,

Tsjerk

On Tue, Apr 6, 2010 at 5:09 PM, Robert Campbell
<rob...@qu...> wrote:
> Hello Jenna,
>
> On Tue, 06 Apr 2010 00:36:38 -0400 JiangJiang Liu <jl...@uw...> wrote:
>
>>              When I open the  pdb file 1B8E (a homodimer protein) through
>> pymol I can only see a monomer shown in the screen. Now I know the
>> biological dimer is produced through crystallographic symmetry operations
>> in pymol. To generate the dimer, I think I need to convert these remark
>> comands (list below) to be a readable commands by the pymol program. Does
>> anyone know how to do this conversion? Or what's the commands for crystal
>> symmetry operation? Thank you very much! Sincerely Jenna Liu
>>
>> PS:
>> REMARK 350 BIOMOLECULE:
>> 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT:
>> DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS:
>> A REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000
>> 0.00000 REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000
>> 0.00000 REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000
>> 0.00000 REMARK 350   BIOMT1   2 -1.000000  0.000000  0.000000
>> 0.00000 REMARK 350   BIOMT2   2  0.000000  1.000000  0.000000
>> 0.00000 REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000
>> 33.43000
>
> Since the file has the crystallographic information in it, you simply have to
> tell PyMOL to build the symmetry-related neighbours.  You do this with the
> symexp command:
>
> symexp <prefix>, <object>, <selection>, <cutoff>
>
> So if you have an object called 1b8e, you might do:
>
> symexp s_, 1b8e, 1b8e, 3
>
> This will create new objects whose name begins with s_ and is followed by a
> label that identifies the symmetry operation.  You can then turn them on and
> off until you find the one that is the mate of the original object.  Given
> the BIOMT matrix above, this will be the object that is related by a 2-fold
> rotation around the crystallographic b-axis (which in this case is parallel
> to the Y-axis) followed by a translation of 1/2 of the c-axis.  This is the
> object called "s_03-10000" in this case.
>
> Or as Jason has just written, fetch the biological unit directly and then
> split out the states.
>
> Cheers,
> Rob
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Botterell Hall Rm 644
> Department of Biochemistry, Queen's University,
> Kingston, ON K7L 3N6  Canada
> Tel: 613-533-6821            Fax: 613-533-2497
> <rob...@qu...>    http://pldserver1.biochem.queensu.ca/~rlc
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands