Dear Jaim, After dislaying a protein in FirstGlance in Jmol: click "More Views", then "Disulfide Bonds: Show All". This also shows cysteines (not in SS bonds) and labels all cys residues. To see met sulfurs, use "Find" and enter "sulfur and met".
Please recall that scenes generated in FirstGlance can be installed in Proteopedia: http://www.proteopedia.org/wiki/index.php/Help:Copying_FirstGlance_Scenes_into_Proteopedia Reminder: "cystine" means a pair of ssbonded cys residues. "cysteine" strictly speaking means cys residues not engaged in ssbonding (I think -- maybe someone can correct me?) but is sometimes used loosely to include all cys residues regardless of whether ssbonded. "cys" in Jmol selection includes both cystine and cysteine. A convenient example with cysteines, cystines, and methionines is 3kwb. Consider the following script options: select cys select cystine select sulfur and cystine select sulfur and cys select sulfur and cys and not cystine (Hbonds seem complicated to me and I can't help with them.) Regards, -Eric At 4/14/11, jaime.prilu...@weizmann.ac.il wrote: >A question just came out from a chemistry teachers workshop: >"Can you place a label pointing to an ssbond?" They wanted to >make it evident for students where hbonds and ssbonds are. > >My question: how do I select a particular (or all) ssbond/hbond ? >The idea is not to select neither of the atoms that the >bond is connecting to, but to the bond line itself. >If possible, then, can I attach a label to the selection? > >Thanks in advance, >Jaim >-- > Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il > Head Bioinformatics | > R&D Bioinformatics and Data Management | > Department of Biological Services | > Weizmann Institute of Science | fax: 972-8-9344113 > 76100 Rehovot - Israel | tel: 972-8-9344959 > > OCA, http://oca.weizmann.ac.il (the protein structure/function database) > Proteopedia, http://proteopedia.org (because life has more than 2D) > ------------------------------------------------------------------------ > >------------------------------------------------------------------------------ >Benefiting from Server Virtualization: Beyond Initial Workload >Consolidation -- Increasing the use of server virtualization is a top >priority.Virtualization can reduce costs, simplify management, and improve >application availability and disaster protection. Learn more about boosting >the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
