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
