Weird looking stretch in ribbon presentation
Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710
Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote:
Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, Boaz
Thanks Elaine, I'll try your suggestions. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Saturday, March 30, 2013 5:05 AM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Weird looking stretch in ribbon presentation Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote:
Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, Boaz
Hi Elaine, Yes, cardinal spline + smooth coil solves my problem. Thanks a lot. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Saturday, March 30, 2013 5:05 AM To: בעז שאנן Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Weird looking stretch in ribbon presentation Hi Boaz, The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions. You can use an unsmoothed ribbon if you want. The issue and possible solutions are explained here: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset> You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise. For example, commands: ribspline cardinal ribspline cardinal smooth strand <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote:
Hi , I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues 114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long. It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this? Thanks, Boaz
participants (2)
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Boaz Shaanan -
Elaine Meng