On May 30, 2013, at 5:31 PM, Phoebe A. Rice <[email protected]<mailto:[email protected]>> wrote:
In the olden days, when dinosaurs did roam, Ribbons had a nice fix-up feature that would gently move the alpha carbon end of the stick so that it met the ribbon. Looked MUCH better than the current wavy ribbon one gets with side chain helper, and I haven't been able to find a trick like that in pymol. So pymol developers, please consider yourselves wheedled ... Well, there is another program, which is probably (no flames please!) more powerful, feature-rich than pymol and at the same time much easier to use called… drumroll… UCSF Chimera. One can display wavy and smooth secondary structure cartoons with it. The Chimera engine takes care of connecting side chains to the secondary structure cartoons in both representations. The command to control the cartoon representation is in the Ribbon Style Editor menu: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html The name of the command (can be run from the command line prompt in Chimera or chosen from the above menu) is ribspline: https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html Best wishes, Petr ------------------ Petr Leiman EPFL BSP 415 CH-1015 Lausanne Switzerland Office: +41 21 69 30 441 Mobile: +41 79 538 7647 Fax: +41 21 69 30 422 From: CCP4 bulletin board [[email protected]<mailto:[email protected]>] on behalf of Jason Vertrees [[email protected]<mailto:[email protected]>] Sent: Thursday, May 30, 2013 10:17 AM To: [email protected]<mailto:[email protected]> Subject: Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted. Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller <[email protected]<mailto:[email protected]>> wrote: Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees <[email protected]<mailto:[email protected]>> wrote: Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing: # disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui <[email protected]<mailto:[email protected]>> wrote: Dear all, I found a problem when I use pymol to prepare structure interface. Strand is distorted when residue from the strand is connected to the strand by turning on "side_chain_helper on". However when side_chain_helper is off, the strand turns to normal shape but the residue from it is disconnected to the strand. I attached the picture for your help. I know there must be some tricks for this. Welcome for any input. Thanks a lot. Best, Donghui -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) [email protected]<mailto:[email protected]> (o) +1 (603) 374-7120<tel:%2B1%20%28603%29%20374-7120> -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: [email protected]<mailto:[email protected]> ******************************************* -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) [email protected]<mailto:[email protected]> (o) +1 (603) 374-7120
