pymol-users

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Bachar C. <che...@gm...>]

 Dear pymol users,

I have wondered whether someone know how to know if a such structure in pdb
file is multi-mer or mono-mer biologically speaking? Somehow in the related
publication of structure this information is present in occurrence and  in
pdb also is not nonintuitive to catch without the BIOMT transformations. A
monomer could be deposited with multiple copies (or chains) of the same
protein, but strikingly a biological (in vivo) homo-tetrameter (ex.1xiu )
it seems to be represented as a dimeric (two chains) and missing the two
others in the pdb file

This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" does
not tell us if a structure is really multi or monomeric in the pdb file.

I would like just like to know how to conclude multimeric states
informations from the pdb file without doing transformations ? just this
information


Thanks a lot,

All the best


On Fri, Mar 1, 2013 at 4:12 AM,
<pym...@li...>wrote:

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> Today's Topics:
>
>    1. symmetry operation to generate the whole virus particle (yp sun)
>    2. Re: symmetry operation to generate the whole virus particle
>       (Troels Emtek?r Linnet)
>    3. Re: symmetry operation to generate the whole virus particle
>       (Folmer Fredslund)
>    4. Re: symmetry operation to generate the whole virus particle
>       (Thomas Holder)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 28 Feb 2013 17:30:14 +0800 (CST)
> From: yp sun <sun...@ya...>
> Subject: [PyMOL] symmetry operation to generate the whole virus
>         particle
> To: pym...@li...
> Message-ID:
>         <136...@we...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Thu, 28 Feb 2013 11:38:43 +0100
> From: Troels Emtek?r Linnet <tl...@gm...>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
>         particle
> Cc: pym...@li...
> Message-ID:
>         <
> CA+...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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 Emtek?r Linnet
> Ved kl?vermarken 9, 1.th
> 2300 K?benhavn S
> Mobil: +45 60210234
>
>
> 2013/2/28 yp sun <sun...@ya...>
>
> > 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 (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Feb 2013 11:43:03 +0100
> From: Folmer Fredslund <fo...@gm...>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
>         particle
> To: yp sun <sun...@ya...>
> Cc: pymol <pym...@li...>
> Message-ID:
>         <
> CAE...@ma...>
> Content-Type: text/plain; charset="gb2312"
>
> 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 <sun...@ya...>
>
> > 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 (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Folmer Fredslund
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 Feb 2013 16:56:04 +0100
> From: Thomas Holder <tho...@sc...>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
>         particle
> To: pym...@li...
> Message-ID: <512...@sc...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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 Emtek?r 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 Emtek?r Linnet
> > Ved kl?vermarken 9, 1.th <http://1.th>
> > 2300 K?benhavn S
> > Mobil: +45 60210234
> >
> >
> > 2013/2/28 yp sun <sun...@ya... <mailto:sun...@ya...
> >>
> >
> >     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
> Schr?dinger Contractor
>
>
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> 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
> PyM...@li...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 82, Issue 1
> ******************************************
>

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Robert C. <rob...@qu...>]

Hello Bachar,

On Fri, 2013-05-10 14:29  EDT,  Bachar Cheaib <che...@gm...>
wrote:

>  Dear pymol users,
> 
> I have wondered whether someone know how to know if a such structure in
> pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
> related publication of structure this information is present in
> occurrence and  in pdb also is not nonintuitive to catch without the
> BIOMT transformations. A monomer could be deposited with multiple copies
> (or chains) of the same protein, but strikingly a biological (in vivo)
> homo-tetrameter (ex.1xiu ) it seems to be represented as a dimeric (two
> chains) and missing the two others in the pdb file
> 
> This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC"
> does not tell us if a structure is really multi or monomeric in the pdb
> file.

This does tell you that the protein is thought to exist as a tetramer.
What is determined by crystallography and therefore what is present in a
PDB file is the structure that exists in the asymmetric unit, in other words
the unique part of the structure.  That could be a portion of the
structure if it has internal symmetry, but it could also be two or more
copies of the biological unit.  If the asymmetric unit is not a tetramer
(as in your case), then you do need to use the BIOMT information to generate
the tetramer. That is why that information is there.  Just in the answers
to a previous question that you included in your message, you could load the
structure with the "type=pdb1" option:

  fetch 1xiu, type=pdb1, async=0
  set all_states

which will fetch the biological assembly for that structure.  The extra
monomers that were generated by the crystallographic symmetry will be
visible when you set all_states.  Or you could split the states out into
separate objects.

> I would like just like to know how to conclude multimeric states
> informations from the pdb file without doing transformations ? just this
> information



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

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Robert C. <rob...@qu...>]

Hello Bachar,

On Fri, 2013-05-10 14:29  EDT,  Bachar Cheaib <che...@gm...>
wrote:

>  Dear pymol users,
> 
> I have wondered whether someone know how to know if a such structure in
> pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
> related publication of structure this information is present in
> occurrence and  in pdb also is not nonintuitive to catch without the
> BIOMT transformations. A monomer could be deposited with multiple copies
> (or chains) of the same protein, but strikingly a biological (in vivo)
> homo-tetrameter (ex.1xiu ) it seems to be represented as a dimeric (two
> chains) and missing the two others in the pdb file
> 
> This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC"
> does not tell us if a structure is really multi or monomeric in the pdb
> file.

This does tell you that the protein is thought to exist as a tetramer.
What is determined by crystallography and therefore what is present in a
PDB file is the structure that exists in the asymmetric unit, in other words
the unique part of the structure.  That could be a portion of the
structure if it has internal symmetry, but it could also be two or more
copies of the biological unit.  If the asymmetric unit is not a tetramer
(as in your case), then you do need to use the BIOMT information to generate
the tetramer. That is why that information is there.  Just in the answers
to a previous question that you included in your message, you could load the
structure with the "type=pdb1" option:

  fetch 1xiu, type=pdb1, async=0
  set all_states

which will fetch the biological assembly for that structure.  The extra
monomers that were generated by the crystallographic symmetry will be
visible when you set all_states.  Or you could split the states out into
separate objects.

> I would like just like to know how to conclude multimeric states
> informations from the pdb file without doing transformations ? just this
> information

<snip>

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

Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1

[Edward A. B. <Be...@up...>]

Bachar Cheaib wrote:
> This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" does not tell us if a structure is really multi
> or monomeric in the pdb file.
>
Right, that tells you what it is in vivo.
To see what it is in the pdb file, i.e. contents of the asymmetric unit,
look at the "compound" records near the top:

COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: RXR-LIKE PROTEIN;
COMPND   3 CHAIN: A, B;
COMPND   4 FRAGMENT: LIGAND-BINDING DOMAIN (LBD);
COMPND   5 SYNONYM: RETINOID X RECEPTOR LIGAND-BINDING DOMAIN, 9-CIS RETINOIC
COMPND   6 ACID;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1;
COMPND  10 CHAIN: E, F;
COMPND  11 SYNONYM: NCOA-1, STEROID RECEPTOR COACTIVATOR-1, SRC-1, RIP160, HIN-2
COMPND  12 PROTEIN;
COMPND  13 EC: 2.3.1.48;
COMPND  14 ENGINEERED: YES

You have an entry MOL_ID for each distinct protein. In this case there are two.
For each of these MOL_ID's there will be one or more chains, in this case
A,B are the receptor and E,F are the coactivator.
 From this you would conclude that the pdb contains a honmodimer of heterodimers,
or posibly a heterodimer of homodimers, if the distinction makes any sense.

In the simplest case there will be only one kind of subunit and the number of
chains for it is the nember of protomers in the ASU.

More complicted; the protomer could have non-integral ratios of subunits,
like F1 ATPase alpha(3) beta(3) gamma(1) and then multiple of these protomers
in the ASU. Then I guess the minimum number of chains in a subunit
would be the number of protomers in the ASU


Or going with a web browser to the page for that structure, select the link
"display files" then "FASTA fles" and see how many times each sequence is repeated.