Mark, Sorry, but the current C code appears to be broken. For future reference, you should be able to do the following: load $TUT/1hpv.pdb # absolute linear scaling from the B factor set cartoon_putty_transform, 7 # set a base radius of 1.0 (will be scaled based on B factors) set cartoon_putty_radius, 1.0 # no limits on the scaling set cartoon_putty_scale_min, -1 set cartoon_putty_scale_max, -1 # set the B factors alter all, b=0.2 # display the cartoons appropriately unset cartoon_smooth_loops unset cartoon_flat_sheets as cartoon cartoon putty # unfortunately, the above does not in fact work because there is a bug in the code when all B factors are the same...you get a radius of 1 instead. # regardless, setting non-identical B factors should currently work: alter chain A, b=0.2 alter chain B, b=0.4 rebuild Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:supp...@delsci.com
_____ From: Mark A. White [mailto:mawh...@utmb.edu] Sent: Monday, December 15, 2008 3:34 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] B-factor putty tube representation Hi, I would like to define the radius of the cartoon putty on absolute, rather than a relative scale. Is there any way to do this? If I am comparing rmsd, for example, I would like every image to be representative of the true RMSD differences, rather than being a unique relative scale for each comparison. I notice that others have also asked about this in the past, but I did not see a response on the Pymol-Users Email Archive. Maybe there are new features in 1.1 that address this? [PyMOL] putty tube representation From: Evan Kantrowitz <evan.kantrow...@bc...> - 2007-08-09 21:37 Attachments: HTML-Email.html <http://sourceforge.net/mailarchive/attachment.php?list_name=pymol-users&mes sage_id=5845f13b-ca26-4932-b0d2-a1131591d...@bc.edu&counter=1> I am making tube representations as a comparison between two structures. I have the rmsd in the b-factor field. 1) If I do a putty representation it works. How does the program decide on the width variation of the tube? 2) How can this be reset? I want to do this so when I compare two different rmsd plots the width of lets say 1 rms is the same in both figures. Any help would be apprecipated. ------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz Boston College Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
