[PyMOL] symmetry operation to generate the whole virus particle
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
Re: [PyMOL] symmetry operation to generate the whole virus particle
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 -- 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
Re: [PyMOL] symmetry operation to generate the whole virus particle
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 Emtekær 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 Emtekær Linnet Ved kløvermarken 9, 1.th http://1.th 2300 København 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 Schrödinger 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) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] symmetry operation to generate the whole virus particle
Hi Yeping - Try using: fetch 2buk, type=pdb1, multiplex=1, async=0 This will fetch the biological assembly (type=pdb1) from the pdb, split the 60 states into separate objects (multiplex=1), and tell PyMOL to wait for all this to be completed before moving to the next command in a .pml script (async=0). Cheers, Jared -- Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center Old Public Health Building, Room 610 341 East 25th Street New York, NY 10016 212-263-7898 http://kong.med.nyu.edu/ On Feb 28, 2013, at 4:30 AM, yp sun sunyep...@yahoo.com.cnmailto:sunyep...@yahoo.com.cn wrote: 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 -- 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
