pymol-users Mailing List for PyMOL Molecular Graphics System

Hi Chad, Kanika,
Symexp is for generating symmetry mates, not for (re)constructing
biological assemblies.
If the BIOMT record gives an identity matrix, it means that there is
no further information for building a biological unit. The biological
unit is most likely contained in the PDB file. Note that it may be
part of the structure in the PDB file, as those may contain an
asymmetric crystallographic unit.
Kanika,
You come up with a different protein every time, which makes it a bit
confusing for us, but probably also for yourself. Maybe it's good to
first get to understand the basics, the file formats, biological
units, pymol, etc. Otherwise, provide a more full account of what
you're trying to do, what you've tried to do yourself getting there
and where you got stuck.
Cheers,
Tsjerk
On Mon, Feb 28, 2011 at 1:06 PM, Chad Davis <cha...@gm...> wrote:
> I thought symexp() would accomplish this, no?
> From:
> http://pymol.sourceforge.net/newman/user/S0400xtal.html
>
> Something like:
>
> fetch 3hhz
> symexp mysymm, 3hhz, (3hhz), 2.75
>
> (I came up with 2.75 by trail-and-error as 2.5 generates no symmetry
> mates and 3.0 generated too many)
>
> In the case of 3m2m, the header you pasted shows there are 12
> potential biological assemblies, 1 through 8 are all monomeric,
> however. 9 through 12 are the dimeric assemblies. If you need a dimer,
> you need to download any one of 9 through 12, which are probably all
> equivalent to one another. Note that PISA seems to believe that this
> is a monomer. I would be sure that you have other evidence that this
> is a dimer, as there are other crystal contacts in the deposited 3m2m.
>
> These might also help
> http://www.pymolwiki.org/index.php/Symexp
> http://www.pymolwiki.org/index.php/BiologicalUnit
>
> -Chad
>
>
> On Mon, Feb 28, 2011 at 12:20, kanika sharma <ksh...@gm...> wrote:
>> I have a dimeric protein 3HHZ.....to generate the dimer foll transformations
>> have to be made....the problem is that this is an identity matrix,so will
>> not change anything...can anyone help with this??
>> how can i get the asymmetric unit to generate dimer??
>>
>> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>>
>> 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
>> On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu
>> <hon...@bi...> wrote:
>>>
>>> Hi, Kanika,
>>>
>>> are you looking for biological units of proteins when you say stable
>>> dimer? If this is the case, I recommend the page:
>>>
>>> http://pdbwiki.org/index.php/Biological_unit
>>> at the bottom of the page you can find four very useful servers for the
>>> determination of biological units of proteins (PQS is not updated anymore):
>>>  The Protein Quaternary Structure Server (PQS) [2] or [3]
>>>  The Macro-Molecular Structure Database (MSD) [4] or [5]
>>>  The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
>>>  Protein quaternary structure investigation (PiQSi) [7]
>>>
>>> As a matter of fact, the PDB also provides the biological assembly of each
>>> PDB entry for download. More information can be found at:
>>>
>>> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
>>>
>>> If your protein is not from the PDB, you can still try pisa (
>>> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein
>>> coordinate files uploaded by the users and determines the "stable dimer" or
>>> else-mer of your protein.
>>>
>>> hope these help!
>>> hongbo
>>>
>>> On 02/25/2011 01:46 PM, kanika sharma wrote:
>>>>
>>>> Hi,
>>>> i am working to generate a dimer of my protein..I have made a duplicate
>>>> of my protein....Can any one tell me how to rotate my molecule to get
>>>> maximum stability..???
>>>>
>>>>
>>>> Regards..
>>>> Kanika
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Free Software Download: Index, Search& Analyze Logs and other IT data in
>>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>>>> data
>>>> generated by your applications, servers and devices whether physical,
>>>> virtual
>>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> PyMOL-users mailing list (PyM...@li...)
>>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>>> Archives: http://www.mail-archive.com/pym...@li...
>>>
>>> --
>>> Hongbo ZHU
>>> Postdoctoral Researcher
>>> Structural Bioinformatics
>>>
>>> Technische Universität Dresden
>>> Biotechnology Center
>>> Tatzberg 47/49
>>> 01307 Dresden, Germany
>>>
>>> Tel.: +49 (0) 351 463-40083
>>> Fax: +49 (0) 351 463-40087
>>> E-Mail: hon...@bi...-dresden
>>> Webpage: www.biotec.tu-dresden.de
>>
>>
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
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> 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
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

the symexp data may not always be consistent with the biomt
transformations..although they turn out to be..
considering the case of 3hh7...the biological unit and asymm unit are
same...to form a dimer of this protein...i cannot find a clue by biomt data
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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

I thought symexp() would accomplish this, no?
From:
http://pymol.sourceforge.net/newman/user/S0400xtal.html
Something like:
fetch 3hhz
symexp mysymm, 3hhz, (3hhz), 2.75
(I came up with 2.75 by trail-and-error as 2.5 generates no symmetry
mates and 3.0 generated too many)
In the case of 3m2m, the header you pasted shows there are 12
potential biological assemblies, 1 through 8 are all monomeric,
however. 9 through 12 are the dimeric assemblies. If you need a dimer,
you need to download any one of 9 through 12, which are probably all
equivalent to one another. Note that PISA seems to believe that this
is a monomer. I would be sure that you have other evidence that this
is a dimer, as there are other crystal contacts in the deposited 3m2m.
These might also help
http://www.pymolwiki.org/index.php/Symexp
http://www.pymolwiki.org/index.php/BiologicalUnit
-Chad
On Mon, Feb 28, 2011 at 12:20, kanika sharma <ksh...@gm...> wrote:
> I have a dimeric protein 3HHZ.....to generate the dimer foll transformations
> have to be made....the problem is that this is an identity matrix,so will
> not change anything...can anyone help with this??
> how can i get the asymmetric unit to generate dimer??
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>
> 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
> On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu
> <hon...@bi...> wrote:
>>
>> Hi, Kanika,
>>
>> are you looking for biological units of proteins when you say stable
>> dimer? If this is the case, I recommend the page:
>>
>> http://pdbwiki.org/index.php/Biological_unit
>> at the bottom of the page you can find four very useful servers for the
>> determination of biological units of proteins (PQS is not updated anymore):
>>  The Protein Quaternary Structure Server (PQS) [2] or [3]
>>  The Macro-Molecular Structure Database (MSD) [4] or [5]
>>  The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
>>  Protein quaternary structure investigation (PiQSi) [7]
>>
>> As a matter of fact, the PDB also provides the biological assembly of each
>> PDB entry for download. More information can be found at:
>>
>> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
>>
>> If your protein is not from the PDB, you can still try pisa (
>> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein
>> coordinate files uploaded by the users and determines the "stable dimer" or
>> else-mer of your protein.
>>
>> hope these help!
>> hongbo
>>
>> On 02/25/2011 01:46 PM, kanika sharma wrote:
>>>
>>> Hi,
>>> i am working to generate a dimer of my protein..I have made a duplicate
>>> of my protein....Can any one tell me how to rotate my molecule to get
>>> maximum stability..???
>>>
>>>
>>> Regards..
>>> Kanika
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Free Software Download: Index, Search& Analyze Logs and other IT data in
>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>>> data
>>> generated by your applications, servers and devices whether physical,
>>> virtual
>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>>
>>>
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>> --
>> Hongbo ZHU
>> Postdoctoral Researcher
>> Structural Bioinformatics
>>
>> Technische Universität Dresden
>> Biotechnology Center
>> Tatzberg 47/49
>> 01307 Dresden, Germany
>>
>> Tel.: +49 (0) 351 463-40083
>> Fax: +49 (0) 351 463-40087
>> E-Mail: hon...@bi...-dresden
>> Webpage: www.biotec.tu-dresden.de
>
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT
> data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>

my protein is 3m2m..iv downloaded the biological assembly 1 for this..
http://www.rcsb.org/pdb/explore/explore.do?structureId=3M2M
to generate dimer for this the BIOMT data is like this from the pdb
file....i dont know how will this work if its an identity matrix..
REMARK 350 BIOMOLECULE: 1
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
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
REMARK 350 BIOMOLECULE: 3
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C
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
REMARK 350 BIOMOLECULE: 4
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: D
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
REMARK 350 BIOMOLECULE: 5
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: E
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
REMARK 350 BIOMOLECULE: 6
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: F
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
REMARK 350 BIOMOLECULE: 7
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: G
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
REMARK 350 BIOMOLECULE: 8
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: H
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
REMARK 350 BIOMOLECULE: 9
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
REMARK 350 BIOMOLECULE: 10
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
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
REMARK 350 BIOMOLECULE: 11
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F
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
REMARK 350 BIOMOLECULE: 12
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H
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

Hi Kanika,
In 3HHZ.pdb, I find:
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N,
REMARK 350 AND CHAINS: O, R
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 0.00000
So there are two BIOMT records. One identity, indicating that the
coordinates as the are are also part of the biological assembly, and
one giving the transformation to be applied to a copy. From the
previous posts, you should already know how to do that...
Cheers,
Tsjerk
On Mon, Feb 28, 2011 at 12:20 PM, kanika sharma <ksh...@gm...> wrote:
> I have a dimeric protein 3HHZ.....to generate the dimer foll transformations
> have to be made....the problem is that this is an identity matrix,so will
> not change anything...can anyone help with this??
> how can i get the asymmetric unit to generate dimer??
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>
> 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
> On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu
> <hon...@bi...> wrote:
>>
>> Hi, Kanika,
>>
>> are you looking for biological units of proteins when you say stable
>> dimer? If this is the case, I recommend the page:
>>
>> http://pdbwiki.org/index.php/Biological_unit
>> at the bottom of the page you can find four very useful servers for the
>> determination of biological units of proteins (PQS is not updated anymore):
>>  The Protein Quaternary Structure Server (PQS) [2] or [3]
>>  The Macro-Molecular Structure Database (MSD) [4] or [5]
>>  The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
>>  Protein quaternary structure investigation (PiQSi) [7]
>>
>> As a matter of fact, the PDB also provides the biological assembly of each
>> PDB entry for download. More information can be found at:
>>
>> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
>>
>> If your protein is not from the PDB, you can still try pisa (
>> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts protein
>> coordinate files uploaded by the users and determines the "stable dimer" or
>> else-mer of your protein.
>>
>> hope these help!
>> hongbo
>>
>> On 02/25/2011 01:46 PM, kanika sharma wrote:
>>>
>>> Hi,
>>> i am working to generate a dimer of my protein..I have made a duplicate
>>> of my protein....Can any one tell me how to rotate my molecule to get
>>> maximum stability..???
>>>
>>>
>>> Regards..
>>> Kanika
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Free Software Download: Index, Search& Analyze Logs and other IT data in
>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>>> data
>>> generated by your applications, servers and devices whether physical,
>>> virtual
>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>>
>>>
>>>
>>> _______________________________________________
>>> PyMOL-users mailing list (PyM...@li...)
>>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>>> Archives: http://www.mail-archive.com/pym...@li...
>>
>> --
>> Hongbo ZHU
>> Postdoctoral Researcher
>> Structural Bioinformatics
>>
>> Technische Universität Dresden
>> Biotechnology Center
>> Tatzberg 47/49
>> 01307 Dresden, Germany
>>
>> Tel.: +49 (0) 351 463-40083
>> Fax: +49 (0) 351 463-40087
>> E-Mail: hon...@bi...-dresden
>> Webpage: www.biotec.tu-dresden.de
>
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT
> data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> 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
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

I have a dimeric protein 3HHZ.....to generate the dimer foll transformations
have to be made....the problem is that this is an identity matrix,so will
not change anything...can anyone help with this??
how can i get the asymmetric unit to generate dimer??
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
On Fri, Feb 25, 2011 at 6:40 PM, Hongbo Zhu <hon...@bi...
> wrote:
> Hi, Kanika,
>
> are you looking for biological units of proteins when you say stable dimer?
> If this is the case, I recommend the page:
>
> http://pdbwiki.org/index.php/Biological_unit
> at the bottom of the page you can find four very useful servers for the
> determination of biological units of proteins (PQS is not updated anymore):
> The Protein Quaternary Structure Server (PQS) [2] or [3]
> The Macro-Molecular Structure Database (MSD) [4] or [5]
> The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
> Protein quaternary structure investigation (PiQSi) [7]
>
> As a matter of fact, the PDB also provides the biological assembly of each
> PDB entry for download. More information can be found at:
>
> http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
>
> If your protein is not from the PDB, you can still try pisa (
> http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts
> protein coordinate files uploaded by the users and determines the "stable
> dimer" or else-mer of your protein.
>
> hope these help!
> hongbo
>
>
> On 02/25/2011 01:46 PM, kanika sharma wrote:
>
>> Hi,
>> i am working to generate a dimer of my protein..I have made a duplicate
>> of my protein....Can any one tell me how to rotate my molecule to get
>> maximum stability..???
>>
>>
>> Regards..
>> Kanika
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search& Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT
>> data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
> --
> Hongbo ZHU
> Postdoctoral Researcher
> Structural Bioinformatics
>
> Technische Universität Dresden
> Biotechnology Center
> Tatzberg 47/49
> 01307 Dresden, Germany
>
> Tel.: +49 (0) 351 463-40083
> Fax: +49 (0) 351 463-40087
> E-Mail: hon...@bi...-dresden
> Webpage: www.biotec.tu-dresden.de
>

this is an identity matrix so will not make any change,i think....but the
file says so...
can any one help me...!!
Regards,
Kanika
On Mon, Feb 28, 2011 at 1:26 PM, kanika sharma <ksh...@gm...> wrote:
> M really sorry for the wrong information guys...script helped a lot..
>
> If my protein is a dimer...Chain A,B....How can i apply the script
> here?....i dun know for 2 chains....
>
> Thank you..in advance....apologies for previous mistake...
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
>
> 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
> Thank you...
>
>
>
> On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar <ts...@gm...>wrote:
>
>> Hi Kanika,
>>
>> 'b' is a selection keyword. For that reason it doesn't make a good
>> object identifier. Try
>>
>> load 1b8e.pdb, 1b8e_A
>> create 1b8e_B,1b8e_A
>> alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z)
>>
>> Not that the numbers are different. In 1b8e.pdb I find:
>>
>> 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
>>
>> That's quite different from the record you gave previously. If you
>> want to have good help, especially when it's urgent to you, better do
>> your best in providing correct information and thinking along.
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>> On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma <ksh...@gm...>
>> wrote:
>> > Iv applied the foll eq:
>> >
>> > load 1b8e.pdb, A
>> > create B,A
>> > alter_state 1,B,(x,y,z)=(x,-y,40.60-z)
>> >
>> > it should form a dimer of my protein but the object "B" is same as my
>> > monomer with no change... i am unable to find the error..
>> >
>> > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar <ts...@gm...>
>> > wrote:
>> >>
>> >> Hi Kanika,
>> >>
>> >> Let's say your protein is called 'protein'. Then you can obtain the
>> other
>> >> unit corresponding to your second biomt operation as:
>> >>
>> >> create unit2, protein
>> >> alter_state 1,unit2,(y,z)=(-y,40.6-z)
>> >>
>> >> Note this is a shorthand specific to your case. For a full biomt record
>> (R
>> >> t), with R being the rotation matrix (first three columns) and t the
>> >> translation vector (last column), you would have to make the equation
>> >> reflect the matrix operation Rp+t.
>> >>
>> >> Hope it helps,
>> >>
>> >> Tsjerk
>> >>
>> >> On Feb 28, 2011 6:46 AM, "kanika sharma" <ksh...@gm...> wrote:
>> >>
>> >>> ok, I know that a dimer can be generated from the BIOMT operationon
>> >>> monomeric unit of protein.
>> >>
>> >> I have this protein....but its unclear to me how to apply these
>> >> transformations and what do they represent....
>> >> If somebody knows then please let me know...Its really urgent...
>> >>
>> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
>> >>
>> >>
>> >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
>> >> REMARK 350 BIOMT...
>> >>
>> >> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000
>> >>
>> >>
>> >> Best Regards,
>> >> Kanika
>> >
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>
>

M really sorry for the wrong information guys...script helped a lot..
If my protein is a dimer...Chain A,B....How can i apply the script
here?....i dun know for 2 chains....
Thank you..in advance....apologies for previous mistake...
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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
Thank you...
On Mon, Feb 28, 2011 at 1:00 PM, Tsjerk Wassenaar <ts...@gm...> wrote:
> Hi Kanika,
>
> 'b' is a selection keyword. For that reason it doesn't make a good
> object identifier. Try
>
> load 1b8e.pdb, 1b8e_A
> create 1b8e_B,1b8e_A
> alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z)
>
> Not that the numbers are different. In 1b8e.pdb I find:
>
> 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
>
> That's quite different from the record you gave previously. If you
> want to have good help, especially when it's urgent to you, better do
> your best in providing correct information and thinking along.
>
> Cheers,
>
> Tsjerk
>
>
> On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma <ksh...@gm...>
> wrote:
> > Iv applied the foll eq:
> >
> > load 1b8e.pdb, A
> > create B,A
> > alter_state 1,B,(x,y,z)=(x,-y,40.60-z)
> >
> > it should form a dimer of my protein but the object "B" is same as my
> > monomer with no change... i am unable to find the error..
> >
> > On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar <ts...@gm...>
> > wrote:
> >>
> >> Hi Kanika,
> >>
> >> Let's say your protein is called 'protein'. Then you can obtain the
> other
> >> unit corresponding to your second biomt operation as:
> >>
> >> create unit2, protein
> >> alter_state 1,unit2,(y,z)=(-y,40.6-z)
> >>
> >> Note this is a shorthand specific to your case. For a full biomt record
> (R
> >> t), with R being the rotation matrix (first three columns) and t the
> >> translation vector (last column), you would have to make the equation
> >> reflect the matrix operation Rp+t.
> >>
> >> Hope it helps,
> >>
> >> Tsjerk
> >>
> >> On Feb 28, 2011 6:46 AM, "kanika sharma" <ksh...@gm...> wrote:
> >>
> >>> ok, I know that a dimer can be generated from the BIOMT operationon
> >>> monomeric unit of protein.
> >>
> >> I have this protein....but its unclear to me how to apply these
> >> transformations and what do they represent....
> >> If somebody knows then please let me know...Its really urgent...
> >>
> >> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
> >>
> >>
> >> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
> >> REMARK 350 BIOMT...
> >>
> >> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000
> >>
> >>
> >> Best Regards,
> >> Kanika
> >
> >
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>

Hi Kanika,
'b' is a selection keyword. For that reason it doesn't make a good
object identifier. Try
load 1b8e.pdb, 1b8e_A
create 1b8e_B,1b8e_A
alter_state 1,1b8e_B,(x,y,z)=(-x,y,33.43-/z)
Not that the numbers are different. In 1b8e.pdb I find:
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
That's quite different from the record you gave previously. If you
want to have good help, especially when it's urgent to you, better do
your best in providing correct information and thinking along.
Cheers,
Tsjerk
On Mon, Feb 28, 2011 at 8:16 AM, kanika sharma <ksh...@gm...> wrote:
> Iv applied the foll eq:
>
> load 1b8e.pdb, A
> create B,A
> alter_state 1,B,(x,y,z)=(x,-y,40.60-z)
>
> it should form a dimer of my protein but the object "B" is same as my
> monomer with no change... i am unable to find the error..
>
> On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
>>
>> Hi Kanika,
>>
>> Let's say your protein is called 'protein'. Then you can obtain the other
>> unit corresponding to your second biomt operation as:
>>
>> create unit2, protein
>> alter_state 1,unit2,(y,z)=(-y,40.6-z)
>>
>> Note this is a shorthand specific to your case. For a full biomt record (R
>> t), with R being the rotation matrix (first three columns) and t the
>> translation vector (last column), you would have to make the equation
>> reflect the matrix operation Rp+t.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Feb 28, 2011 6:46 AM, "kanika sharma" <ksh...@gm...> wrote:
>>
>>> ok, I know that a dimer can be generated from the BIOMT operationon
>>> monomeric unit of protein.
>>
>> I have this protein....but its unclear to me how to apply these
>> transformations and what do they represent....
>> If somebody knows then please let me know...Its really urgent...
>>
>> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
>>
>>
>> REMARK 350  BIOMT1  1 1.000000 0.000000 0.000000    0.00000
>>    REMARK 350  BIOMT...
>>
>> REMARK 350  BIOMT3  2 0.000000 0.000000 -1.000000    40.60000
>>
>>
>> Best Regards,
>> Kanika
>
>
-- 
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

Iv applied the foll eq:
load 1b8e.pdb, A
create B,A
alter_state 1,B,(x,y,z)=(x,-y,40.60-z)
it should form a dimer of my protein but the object "B" is same as my
monomer with no change... i am unable to find the error..
On Mon, Feb 28, 2011 at 12:39 PM, Tsjerk Wassenaar <ts...@gm...>wrote:
> Hi Kanika,
>
> Let's say your protein is called 'protein'. Then you can obtain the other
> unit corresponding to your second biomt operation as:
>
> create unit2, protein
> alter_state 1,unit2,(y,z)=(-y,40.6-z)
>
> Note this is a shorthand specific to your case. For a full biomt record (R
> t), with R being the rotation matrix (first three columns) and t the
> translation vector (last column), you would have to make the equation
> reflect the matrix operation Rp+t.
>
>
> Hope it helps,
>
>
> Tsjerk
>
>
> On Feb 28, 2011 6:46 AM, "kanika sharma" <ksh...@gm...> wrote:
>
> ok, I know that a dimer can be generated from the BIOMT operationon
>> monomeric unit of protein.
>>
>> I have this protein....but its unclear to me how to apply these
> transformations and what do they represent....
>
> If somebody knows then please let me know...Its really urgent...
>
> REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
>
>
> REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
> REMARK 350 BIOMT...
> REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000
>
>
>
> Best Regards,
> Kanika
>
>

Hi Kanika,
Let's say your protein is called 'protein'. Then you can obtain the other
unit corresponding to your second biomt operation as:
create unit2, protein
alter_state 1,unit2,(y,z)=(-y,40.6-z)
Note this is a shorthand specific to your case. For a full biomt record (R
t), with R being the rotation matrix (first three columns) and t the
translation vector (last column), you would have to make the equation
reflect the matrix operation Rp+t.
Hope it helps,
Tsjerk
On Feb 28, 2011 6:46 AM, "kanika sharma" <ksh...@gm...> wrote:
ok, I know that a dimer can be generated from the BIOMT operationon
> monomeric unit of protein.
>
> I have this protein....but its unclear to me how to apply these
transformations and what do they represent....
If somebody knows then please let me know...Its really urgent...
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
 REMARK 350 BIOMT...
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.60000
Best Regards,
Kanika

Jason Vertrees wrote:
> Hi Francios,
> 
> Someone recently asked about this and the answer was that this should
> be a setting, but isn't currently available. If I have time, I'll try
> to sneak this in the upcoming PyMOL v1.4 release.
Please, send me an e-mail if it is done some day.
Other software, like Jmol, don't suffer from such bug so this is just
preventing people from using Pymol on some applications.
As the surface is computed for a PDB that was read in,
I don't see why it is exported after undergoing some rotation
and a translation that has nothing to do with the input PDB.
Regards,
F.
> Cheers,
> 
> -- Jason
> 
> On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger <ber...@ri...> wrote:
>> Hello,
>>
>> Is it possible to save the Connolly surface
>> computed by Pymol without any rotation and translation
>> added compared to the PDB from which the atom coordinates were read?
>>
>> I looked at the .obj file output and find there was some centering
>> done and also some rotation added.
>>
>> Thanks a lot,
>> F.
>>
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>> generated by your applications, servers and devices whether physical, virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives: http://www.mail-archive.com/pym...@li...
>>
> 
> 
> 

Hi Roberto,
It's nice to see people learning how to script and putting PyMOL
through its paces.
> trying to use a pseudoatom as label I met several problems:
>
> 1) How to move the label (pseudoatom) to a target residue?
>    Is there a simple command to do?
The easiest way would be to get the coordinates of the target residue,
I'd choose the alpha carbon (replace "X" with your residue number):
# query residue X's alpha carbon, store the position in targetResPosition
targetResPosition = cmd.get_atom_coords("resi X and n. CA")
# next, just assign that position to the pseudoatom:
cmd.alter_state(1, "myPseudoAtom", "(x,y,z) = targetResPosition")
> 2) How to change the label without messaging the user?
>    The 'label' command appears not have a 'quiet' option.
This is interesting, and not what I'd expect from PyMOL, however it works:
# make a new text label as a Python string
newLabel = "New Pseudoatom label"
# assign that label
cmd.label("myPseudoAtom", "newLabel")
Interestingly, PyMOL picks up the 2nd parameter as a variable name.
Also, label does have a quiet option:
# assign that label, quietly
cmd.label("myPseudoAtom", "newLabel", quiet=1)
> 3) (less important) How to hide the pseudoatom?
>    I wish not have the pseudoatom listed among models in the GUI panel.
To hide a pseudoatom (just the + symbol):
hide nonbonded, myPseudoAtom
# or, just hide the labels
hide labels, myPseudoAtom
# or, hide all
hide everything, myPseudoAtom
> 4) (less important) I need to execute all these operations by script (mdo
> commands during a movie)
>    To simplify the movie I wish use only one mdo command
>
> def doAll()
>  .. all my script here ..
>
>    extending the cmd just before the movie start
>
> cmd.extend('doAll', doAll)
>
>    and clearing the cmd just at the end of the movie but I don't know
> how.
>    Is there a way to clear a command?
The mdo command takes a frame number and a string. For that frame it
stores the string, and then applies it prior to setting the scene.
PyMOL overwrites the string each time, so you need to cache all your
commands for one frame and use the mdo command once per fram. Create
a small class that stores all the mdo commands as one string. Then,
when you want those command executed ask the class to call mdo on the
given frame, using that long string. That might look something like:
mcache 50, "show sticks"
mcache 50, "as spheres, het"
mcache 50, "show surface, poly within 10 or org"
...
store scenes, plan movie, etc.
...
mCacheApply 50
I made something similar for making movie fades, just cache the string
an apply it when necessary.
Cheers,
-- Jason
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Francios,
Someone recently asked about this and the answer was that this should
be a setting, but isn't currently available. If I have time, I'll try
to sneak this in the upcoming PyMOL v1.4 release.
Cheers,
-- Jason
On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger <ber...@ri...> wrote:
> Hello,
>
> Is it possible to save the Connolly surface
> computed by Pymol without any rotation and translation
> added compared to the PDB from which the atom coordinates were read?
>
> I looked at the .obj file output and find there was some centering
> done and also some rotation added.
>
> Thanks a lot,
> F.
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pym...@li...
>
-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jas...@sc...
(o) +1 (603) 374-7120

Hi Carsten,
thanks for the answer. 
Yes is for scripted mode. 
I searched pyMOLWiki for a simple command to move the label to the target 
(something like 'super', 'fit' ) but I didn't find.
So I searched for 'get' to have the coordinates of the target atom and for 
'alter' to change the coordinates of the label but I was quite confused: I 
didn't find names like x, y, z in the name space of both 'get' and 'alter' 
commands. So I am still searching .. 
Could you please tell me how to get and set x, y, z coordinates?
About the 'label' command: is there a way to not message the user? I didn't 
find a 'quiet' option for this command. Is there another way?
Thanks for your hint about '_' prefix to hide an object.
roberto
>----Messaggio originale----
>Da: CSC...@it...
>Data: 27/02/2011 17.44
>A: <rv...@li...>, <pym...@li...>
>Ogg: RE: [PyMOL] labeling by a pseudoatom
>
>Roberto, 
>
>partial answer to point 3. Adding a "_" before an object name hides it
>from the panel.
>
>For points 1 or 2. Could you please expand on your question? Is this for
>interactive
>or scripted mode? 
>For scripted mode you could modify the coordinates of the pseudoatom to
>be closer to the target atom or not? Otherwise look up the commands in
>"Edit" mode. BTW in Edit mode you can actually mode regular labels with
>the mouse as well (Edit Mode: CTRL Middle click)
>
>Hope it helps somewhat
>
>Carsten
>
>> -----Original Message-----
>> From: rv...@li... [mailto:rv...@li...]
>> Sent: Friday, February 25, 2011 5:00 PM
>> To: pym...@li...
>> Subject: [PyMOL] labeling by a pseudoatom
>> 
>> Hello everyone,
>> 
>> trying to use a pseudoatom as label I met several problems:
>> 
>> 1) How to move the label (pseudoatom) to a target residue?
>> Is there a simple command to do?
>> 
>> 2) How to change the label without messaging the user?
>> The 'label' command appears not have a 'quiet' option.
>> 
>> 3) (less important) How to hide the pseudoatom?
>> I wish not have the pseudoatom listed among models in the GUI
>> panel.
>> 
>> 4) (less important) I need to execute all these operations by script
>> (mdo
>> commands during a movie)
>> To simplify the movie I wish use only one mdo command
>> 
>> def doAll()
>> .. all my script here ..
>> 
>> extending the cmd just before the movie start
>> 
>> cmd.extend('doAll', doAll)
>> 
>> and clearing the cmd just at the end of the movie but I don't
>> know
>> how.
>> Is there a way to clear a command?
>> 
>> 
>> Thanks,
>> Roberto
>> 
>> 
>>
>-----------------------------------------------------------------------
>> -------
>> Free Software Download: Index, Search & Analyze Logs and other IT data
>> in
>> Real-Time with Splunk. Collect, index and harness all the fast moving
>> IT data
>> generated by your applications, servers and devices whether physical,
>> virtual
>> or in the cloud. Deliver compliance at lower cost and gain new
>business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> PyMOL-users mailing list (PyM...@li...)
>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> Archives:
>http://www.mail-archive.com/pym...@li...
>
>

Roberto, 
partial answer to point 3. Adding a "_" before an object name hides it
from the panel.
For points 1 or 2. Could you please expand on your question? Is this for
interactive
or scripted mode? 
For scripted mode you could modify the coordinates of the pseudoatom to
be closer to the target atom or not? Otherwise look up the commands in
"Edit" mode. BTW in Edit mode you can actually mode regular labels with
the mouse as well (Edit Mode: CTRL Middle click)
Hope it helps somewhat
Carsten
> -----Original Message-----
> From: rv...@li... [mailto:rv...@li...]
> Sent: Friday, February 25, 2011 5:00 PM
> To: pym...@li...
> Subject: [PyMOL] labeling by a pseudoatom
> 
> Hello everyone,
> 
> trying to use a pseudoatom as label I met several problems:
> 
> 1) How to move the label (pseudoatom) to a target residue?
> Is there a simple command to do?
> 
> 2) How to change the label without messaging the user?
> The 'label' command appears not have a 'quiet' option.
> 
> 3) (less important) How to hide the pseudoatom?
> I wish not have the pseudoatom listed among models in the GUI
> panel.
> 
> 4) (less important) I need to execute all these operations by script
> (mdo
> commands during a movie)
> To simplify the movie I wish use only one mdo command
> 
> def doAll()
> .. all my script here ..
> 
> extending the cmd just before the movie start
> 
> cmd.extend('doAll', doAll)
> 
> and clearing the cmd just at the end of the movie but I don't
> know
> how.
> Is there a way to clear a command?
> 
> 
> Thanks,
> Roberto
> 
> 
>
-----------------------------------------------------------------------
> -------
> Free Software Download: Index, Search & Analyze Logs and other IT data
> in
> Real-Time with Splunk. Collect, index and harness all the fast moving
> IT data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new
business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives:
http://www.mail-archive.com/pym...@li...

Hi Kanika,
You're right about the columns for translation and rotation. But since in
your case it's an identity matrix, it's not going to help you achieve your
goal.
Cheers,
Tsjerk
On Feb 26, 2011 8:14 AM, "kanika sharma" <ksh...@gm...> wrote:
Does anyone know how to apply these biometric constraints to generate a
dimer of my molecule????
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK
350 APPLY THE FOLLOWING TO CHAINS: A, B
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
i think first 3 cols represent rotation and last 3 rep translation...But how
to do it??
Regards,
kanika
------------------------------------------------------------------------------
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data
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_______________________________________________
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Archives: http://www.mail-archive.com/pym...@li...

Does anyone know how to apply these biometric constraints to generate a
dimer of my molecule????
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK
350 APPLY THE FOLLOWING TO CHAINS: A, B
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
i think first 3 cols represent rotation and last 3 rep translation...But how
to do it??
Regards,
kanika

Hello everyone,
trying to use a pseudoatom as label I met several problems:
1) How to move the label (pseudoatom) to a target residue?
 Is there a simple command to do?
2) How to change the label without messaging the user?
 The 'label' command appears not have a 'quiet' option.
3) (less important) How to hide the pseudoatom? 
 I wish not have the pseudoatom listed among models in the GUI panel.
4) (less important) I need to execute all these operations by script (mdo 
commands during a movie)
 To simplify the movie I wish use only one mdo command
def doAll()
 .. all my script here ..
 extending the cmd just before the movie start 
cmd.extend('doAll', doAll)
 and clearing the cmd just at the end of the movie but I don't know 
how.
 Is there a way to clear a command? 
Thanks,
 Roberto

Tsjerk Wassenaar wrote:
>
> Hi Johannes,
>
> It's not that hard. The clipping planes are defined by the z 
> coordinate (in the viewing matrix). So you can get the atoms for a 
> selection, transform to get the new z coordinate only, and check 
> whether it's in between the planes:
>
> m = cmd.get_model(selection).atom
> v = cmd.get_view()
> m = [ i for i in m if clipped(i,v) ]
>
Fine, it's that simple! (First I didn't realize that it is sufficient to 
transform the atom coordinates of the pdb file).
>
> So clipped should do the transform and check whether the atom is 
> clipped. The trick then is to turn m back into a selection.
>
That would be nice, but isn't absolutely necessary. At present, it is 
sufficient to have the indices of the clipped atoms.
Thanks
Johannes
> Hope it helps,
>
> Tsjerk
>
>> On Feb 25, 2011 5:18 PM, "Johannes Wollbold" <jwo...@gm... 
>> <mailto:jwo...@gm...>> wrote:
>>
>> Jason Vertrees wrote: > Having said this, you can however, can get 
>> the clipping information > from P...
>>
>> Hi Jason,
>>
>> thank you again for the hint. First I looked if I can select atoms
>> according to their coordinates, or store new coordinates after a
>> rotation / shift. But implicitly you already said that such
>> functionalities are not yet implemented. If clipping is performed with
>> the original camera view, the task is simple. get_view gives the output
>> (see above link to the help page):
>>
>> set_view (\
>> 1.000000000, 0.000000000, 0.000000000,\
>> 0.000000000, 1.000000000, 0.000000000,\
>> 0.000000000, 0.000000000, 1.000000000,\
>> 0.000000000, 0.000000000, -320.337890625,\
>> 74.147140503, 74.174217224, 74.123344421,\
>> 317.145324707, 323.530487061, -20.000000000 )
>>
>> According to (4,3), the camera is shifted by -320 A in z direction only.
>> Since (6,1) and (6,2) indicate the camera distances of the slab planes,
>> I can select, in the pdb file, the atoms with (74 - 320 + 317 ) <= z <=
>> (74 - 320 + 323).
>>
>> For different views, coordinate transformations with the rotation matrix
>> of the first 3 lines are needed. This should not be very difficult, but
>> perhaps somebody has already a solution?
>>
>> Best regards
>> Johannes
>>
>> > On Thu, Feb 24, 2011 at 3:50 AM, Johannes Wollbold 
>> <jwo...@gm... <mailto:jwo...@gm...>> wrote: > >> Hello, >> >>...
>>

Hi Johannes,
It's not that hard. The clipping planes are defined by the z coordinate (in
the viewing matrix). So you can get the atoms for a selection, transform to
get the new z coordinate only, and check whether it's in between the planes:
m = cmd.get_model(selection).atom
v = cmd.get_view()
m = [ i for i in m if clipped(i,v) ]
So clipped should do the transform and check whether the atom is clipped.
The trick then is to turn m back into a selection.
Hope it helps,
Tsjerk
On Feb 25, 2011 5:18 PM, "Johannes Wollbold" <jwo...@gm...> wrote:
Jason Vertrees wrote: > Having said this, you can however, can get the
clipping information > from P...
Hi Jason,
thank you again for the hint. First I looked if I can select atoms
according to their coordinates, or store new coordinates after a
rotation / shift. But implicitly you already said that such
functionalities are not yet implemented. If clipping is performed with
the original camera view, the task is simple. get_view gives the output
(see above link to the help page):
set_view (\
 1.000000000, 0.000000000, 0.000000000,\
 0.000000000, 1.000000000, 0.000000000,\
 0.000000000, 0.000000000, 1.000000000,\
 0.000000000, 0.000000000, -320.337890625,\
 74.147140503, 74.174217224, 74.123344421,\
 317.145324707, 323.530487061, -20.000000000 )
According to (4,3), the camera is shifted by -320 A in z direction only.
Since (6,1) and (6,2) indicate the camera distances of the slab planes,
I can select, in the pdb file, the atoms with (74 - 320 + 317 ) <= z <=
(74 - 320 + 323).
For different views, coordinate transformations with the rotation matrix
of the first 3 lines are needed. This should not be very difficult, but
perhaps somebody has already a solution?
Best regards
Johannes
> On Thu, Feb 24, 2011 at 3:50 AM, Johannes Wollbold <jwo...@gm...>
wrote: > >> Hello, >> >>...

Jason Vertrees wrote:
> Having said this, you can however, can get the clipping information
> from PyMOL and write scripts against that yourself to determine atom
> inclusion. See get_view (http://www.pymolwiki.org/index.php/Get_View)
> for more help.
> 
Hi Jason,
thank you again for the hint. First I looked if I can select atoms 
according to their coordinates, or store new coordinates after a 
rotation / shift. But implicitly you already said that such 
functionalities are not yet implemented. If clipping is performed with 
the original camera view, the task is simple. get_view gives the output 
(see above link to the help page):
set_view (\
 1.000000000, 0.000000000, 0.000000000,\
 0.000000000, 1.000000000, 0.000000000,\
 0.000000000, 0.000000000, 1.000000000,\
 0.000000000, 0.000000000, -320.337890625,\
 74.147140503, 74.174217224, 74.123344421,\
 317.145324707, 323.530487061, -20.000000000 )
According to (4,3), the camera is shifted by -320 A in z direction only. 
Since (6,1) and (6,2) indicate the camera distances of the slab planes, 
I can select, in the pdb file, the atoms with (74 - 320 + 317 ) <= z <= 
(74 - 320 + 323).
For different views, coordinate transformations with the rotation matrix 
of the first 3 lines are needed. This should not be very difficult, but 
perhaps somebody has already a solution?
Best regards
Johannes
> On Thu, Feb 24, 2011 at 3:50 AM, Johannes Wollbold <jwo...@gm...> wrote:
> 
>> Hello,
>>
>> I clipped a part of a protein by a slab, by manual, graphical
>> inspection. Now I want to select the slab and store the clipped atoms as
>> new molecule (pdb file), in order to sum up the accessible surface area
>> previously computed by an external program. Unfortunately I didn't find
>> hints, e.g. in the selection algebra
>> (http://www.pymolwiki.org/index.php/Selection_Algebra).
>>
>> Thanks for your advice.
>> Johannes
>>
>> 

Hi, Kanika,
are you looking for biological units of proteins when you say stable 
dimer? If this is the case, I recommend the page:
http://pdbwiki.org/index.php/Biological_unit
at the bottom of the page you can find four very useful servers for the 
determination of biological units of proteins (PQS is not updated anymore):
 The Protein Quaternary Structure Server (PQS) [2] or [3]
 The Macro-Molecular Structure Database (MSD) [4] or [5]
 The Protein Interfaces, Surfaces and Assemblies server (Pisa) [6]
 Protein quaternary structure investigation (PiQSi) [7]
As a matter of fact, the PDB also provides the biological assembly of 
each PDB entry for download. More information can be found at:
http://www.rcsb.org/pdb/static.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
If your protein is not from the PDB, you can still try pisa ( 
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html ), which accepts 
protein coordinate files uploaded by the users and determines the 
"stable dimer" or else-mer of your protein.
hope these help!
hongbo
On 02/25/2011 01:46 PM, kanika sharma wrote:
> Hi,
> i am working to generate a dimer of my protein..I have made a duplicate
> of my protein....Can any one tell me how to rotate my molecule to get
> maximum stability..???
>
>
> Regards..
> Kanika
>
>
>
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-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hon...@bi...-dresden
Webpage: www.biotec.tu-dresden.de

Hi,
i am working to generate a dimer of my protein..I have made a duplicate of
my protein....Can any one tell me how to rotate my molecule to get maximum
stability..???
Regards..
Kanika

I forgot to mention that the msms shipped with your VASCo (v1.0.2) is 
installed at:
VASCo_1.0.2/unix/VASCo-Modules-1.0.2/ppix_modules/cprogr/unix/msms
cheers,
hongbo
On 02/24/2011 05:18 PM, Yarrow Madrona wrote:
>
> Hello pymol users,
>
> I apologize if this posting is not appropriate for the pymol user list.
> If there is a better place to direct these questions please let me know.
>
> I have installed the vasco plugin into pymol on my mac by:
>
> "python setup_vasco_x.py install" in the Vasco modules directory. I have
> also installed the plugin into pymol.
>
>
> "python VASCo.py -testrun
>
> 1. However instead of making a test_out directory it makes an input.ppix
> to use on the next run.
>
> 2. When I add my pdb and run I get an error message. Here is the log file:
> (Is this a problem with PDB format?)
>
> Write ./CIN4sfA.pdb_atoms.csv file (for HydroCalc)
> Write ./CIN4sfA.pdb_c2fmtx.csv file (for PatchCalc)
> ________________________________________________________________________________
> Run MSMS...
> -no_header
> -probe_radius 1.4
> -density 1
> -all_components
> Delete Inner MSMS Surface files...
> MSMS Warnings: 0
> ERROR: msms calculation error
> MSMS surface calculating error, try to skip file and continue run.
> CODE ;TIME SEC ;DATE ;RUN_ID;STATUS
> ;REASON;PROPERTIES ;CHAINS ;UNITS ;ATOMS
> ;SURFPNT ; PATCHPNT
> CIN4sfA ;0.000 ;Wed Feb 23 20:57:24 2011 ;0 ;ERROR
> ;MSMS:ERROR: msms calculation error; ;1
> ;1 ;3152 ; ;
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> Finish: time:16 sec
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> Thank you for your help.
>
> -Yarrow
>
>
>
>
>
-- 
Hongbo ZHU
Postdoctoral Researcher
Structural Bioinformatics
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
Tel.: +49 (0) 351 463-40083
Fax: +49 (0) 351 463-40087
E-Mail: hon...@bi...-dresden
Webpage: www.biotec.tu-dresden.de