Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1
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.netwrote: Send PyMOL-users mailing list submissions to pymol-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/pymol-users or, via email, send a message with subject or body 'help' to pymol-users-requ...@lists.sourceforge.net You can reach the person managing the list at pymol-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of PyMOL-users digest... 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
Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1
Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib cheaib.bac...@gmail.com 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 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1
Hello Bachar, On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib cheaib.bac...@gmail.com 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 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] PyMOL-users Digest, Vol 82, Issue 1
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: COMPNDMOL_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. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ 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
