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

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 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
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> >
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> 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
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>
> End of PyMOL-users Digest, Vol 82, Issue 1
> ******************************************
>

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

PyMOL is an OpenGL based molecular visualization system

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