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,
<pymol-users-requ...@lists.sourceforge.net>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 <sunyep...@yahoo.com.cn>
> Subject: [PyMOL] symmetry operation to generate the whole virus
> particle
> To: pymol-users@lists.sourceforge.net
> Message-ID:
> <1362043814.98368.yahoomailclas...@web15604.mail.cnb.yahoo.com>
> 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 <tlin...@gmail.com>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
> particle
> Cc: pymol-users@lists.sourceforge.net
> Message-ID:
> <
> ca+cbx2ovg1kp5cc4nbovybjsgtylebhv7kvs2dycheropwt...@mail.gmail.com>
> 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 <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
> >
> >
> >
> ------------------------------------------------------------------------------
> > 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
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Thu, 28 Feb 2013 11:43:03 +0100
> From: Folmer Fredslund <folm...@gmail.com>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
> particle
> To: yp sun <sunyep...@yahoo.com.cn>
> Cc: pymol <pymol-users@lists.sourceforge.net>
> Message-ID:
> <
> cae7rqxkk7rrjvzpbw5lfh6qkjm0xkancfz70cqtxjsxh-v1...@mail.gmail.com>
> 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 <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
> >
> >
> >
> ------------------------------------------------------------------------------
> > 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 4
> Date: Thu, 28 Feb 2013 16:56:04 +0100
> From: Thomas Holder <thomas.hol...@schrodinger.com>
> Subject: Re: [PyMOL] symmetry operation to generate the whole virus
> particle
> To: pymol-users@lists.sourceforge.net
> Message-ID: <512f7e14.2070...@schrodinger.com>
> 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 <sunyep...@yahoo.com.cn <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
> 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
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 82, Issue 1
> ******************************************
>
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