date:20130228

Re: [PyMOL] symmetry operation to generate the whole virus particle

2013-02-28 Thread Sampson, Jared

Hi Yeping -

Try using:

fetch 2buk, type=pdb1, multiplex=1, async=0

This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 
states into separate objects (multiplex=1), and tell PyMOL to wait for all this 
to be completed before moving to the next command in a .pml script (async=0).

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
Old Public Health Building, Room 610
341 East 25th Street
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/




On Feb 28, 2013, at 4:30 AM, yp sun 
mailto:sunyep...@yahoo.com.cn>> wrote:

Dear pymol users:

Usually pymol can show only one chain when you open a pdb file of virus 
particles (such as 2buk,1sva, etc.). I am trying to create the whole virus 
particle and I know it may need applying symmetry operations. And these 
symmetry operation has been given in the pdb files. For example, the follow is 
the symmetry operation of 2buk:

REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350

But I don't understand how to do symmetry operations. Can pymol do these or 
other software is needed? Please help.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

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[PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

2013-02-28 Thread ABEL Stephane 175950

Hi all, 

I am looking for pymol scripts for showing coarse grained representation of 
non-protein molecules. I am currently using the sphere representation for each 
bead, but the bond between two beads are not shown, so it does not nice 
figures.  

Can you help me or give some advices

Thanks you in advance

Stephane
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Re: [PyMOL] symmetry operation to generate the whole virus particle

2013-02-28 Thread Thomas Holder

Hi Yeping and Troels,

symexp is unlikely to give you the REMARK 350 biomolecule, it is for
generating neighboring symmetry mates of the crystallographic packing.

The following scripts from the PyMOLWiki can read REMARK 350 and
generate the biological unit:

http://pymolwiki.org/index.php/Psico -> biomolecule command
http://pymolwiki.org/index.php/BiologicalUnit/Quat
http://pymolwiki.org/index.php/BiologicalUnit

Remember that you can also fetch the biomolecule as type=pdb1 for most
structures. Example:

fetch 2cas, type=pdb1, async=0
as ribbon
set all_states

Hope that helps.

Cheers,
  Thomas

Troels Emtekær Linnet wrote, On 02/28/13 11:38:
> You are probably looking for this:
> 
> http://pymolwiki.org/index.php/Symexp
> 
> Or else you can do it in CCP4.
> Coordinate utilities -> Edit PDB file ->Use pdbset -> generate chains
> via symmetry operations
> 
> Troels Emtekær Linnet
> Ved kløvermarken 9, 1.th 
> 2300 København S
> Mobil: +45 60210234
> 
> 
> 2013/2/28 yp sun mailto:sunyep...@yahoo.com.cn>>
> 
> Dear pymol users:
>  
> Usually pymol can show only one chain when you open a pdb file of
> virus particles (such as 2buk,1sva, etc.). I am trying to create the
> whole virus particle and I know it may need applying symmetry
> operations. And these symmetry operation has been given in the pdb
> files. For example, the follow is the symmetry operation of 2buk:
>  
> REMARK
> 350 
> 
> REMARK 350 GENERATING THE
> BIOMOLECULE  
> REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
> KNOWN  
> REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
> THE   
> REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
> TRANSFORMATIONS 
> REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
> AND 
> REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
> GIVEN.  
> REMARK
> 350 
> 
>  
> But I don't understand how to do symmetry operations. Can pymol do
> these or other software is needed? Please help.
> 
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor

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Re: [PyMOL] symmetry operation to generate the whole virus particle

2013-02-28 Thread Folmer Fredslund

Hi Yeping,

Searching for "pymol biomt" gives this page on the pymol wiki:

http://www.pymolwiki.org/index.php/BiologicalUnit

Should have all the information you need.

Best regards,
Folmer



2013/2/28 yp sun 

> Dear pymol users:
>
> Usually pymol can show only one chain when you open a pdb file of virus
> particles (such as 2buk,1sva, etc.). I am trying to create the whole virus
> particle and I know it may need applying symmetry operations. And these
> symmetry operation has been given in the pdb files. For example, the follow
> is the symmetry operation of 2buk:
>
> REMARK
> 350
> REMARK 350 GENERATING THE
> BIOMOLECULE
> REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE
> KNOWN
> REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF
> THE
> REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT
> TRANSFORMATIONS
> REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC
> AND
> REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE
> GIVEN.
> REMARK
> 350
>
> But I don't understand how to do symmetry operations. Can pymol do these
> or other software is needed? Please help.
>
> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



-- 
Folmer Fredslund
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[PyMOL] symmetry operation to generate the whole virus particle

2013-02-28 Thread yp sun

Dear pymol users:
 
Usually pymol can show only one chain when you open a pdb file of virus 
particles (such as 2buk,1sva, etc.). I am trying to create the whole virus 
particle and I know it may need applying symmetry operations. And these 
symmetry operation has been given in the pdb files. For example, the follow is 
the symmetry operation of 2buk:
 
REMARK 350  
REMARK 350 GENERATING THE BIOMOLECULE   
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN   
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE    
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS  
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND  
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.   
REMARK 350  
 
But I don't understand how to do symmetry operations. Can pymol do these or 
other software is needed? Please help.

Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES 
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] symmetry operation to generate the whole virus particle

[PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

Re: [PyMOL] symmetry operation to generate the whole virus particle

Re: [PyMOL] symmetry operation to generate the whole virus particle

[PyMOL] symmetry operation to generate the whole virus particle

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