Hi Thomas, Thanks for input - the 'bug' was because the misbehaving PDB had ACs for residues in the helices that were not being drawn correctly. Stripping out the alternative conformations fixed problem, and dss forces cylinder to match dssp header, so I'm good.
Mark >Hi Mark, > >cylindrical helices just connect start and end of continous helix >annotations. Could it be that those "misplaced" helices just have a >strong bend to one or both ends, pulling the cylinder from the major >axis of the helix? Same with the fused helices, are you sure there is at >least one none-helix residue between them? > >Does it look better if you type "dss" into the PyMOL command line? This >will reassign secondary structure more strict than dssp does. > >http://pymolwiki.org/index.php/Dss > >Cheers, > Thomas > >On 05/14/2012 05:39 PM, nih\mayerm wrote: >> I've run into a problem not encountered before: drawing a cartoon >> with cylindrical helices does not accurately follow secondary >> structure (a couple of helices are badly misplace and another 2 >> helices fused into 1) even though pdb has secondary structure >> defined by dssp in header. >> >> A cartoon with the same coords, but drawn as round or fancy helices >> is accurate. >> >> Are their settings I can use to control how the cylindrical helices >> are drawn? My backup plan at this point is to go back to >> molscript/raster3d, if I can remember how !!! >> >> Thanks >> >> Mark Mayer > >-- >Thomas Holder >MPI for Developmental Biology >Spemannstr. 35 >D-72076 Tübingen -- +++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892 3712 Phone: 301-496-9346 (office); 301-496-9347 (lab); FAX 301-496-2396 Lab web site: http://snb.nichd.nih.gov/index.htm Send packages, Fedex and anything requiring a signature to: Bldg 35, Room 3B 1004 35 Lincoln Drive Bethesda MD 20892 ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ 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
