December 2009 - Chimera-users - RBVI Mailing Lists

volume planes tool
by Jeff Triffo 22 Jun '16

22 Jun '16

hi folks, anyone know if the volume plane tool will support arbitrary orientation of the plane any time soon? -Jeff

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Silhouette edges around dashed wire-style bonds
by Dipl.-Ing. Thomas Mitterfellner 05 Jan '11

05 Jan '11

Hello! In some of my structures, I need dashed bonds to indicate hydrogen bonding or metal complexation. As I understand it, in order for bonds to be displayed as dashed, they need to be wire-style. I wondered if silhouette edges could also be extended to these wire-style bonds? Alternatively, could stick-style bonds possibly be displayed in a dashed fashion? Maybe as a series of cylinders, each separated by a certain distance, or eg. as a series of equally spaced small spheres. Thank you, Thomas

4 3

lighting in Chimera
by Dan Gurnon 27 Jan '10

27 Jan '10

I wanted to tell you all that I love the new "glossy lighting" feature- now its easy to see the difference between the inside and outside of a surface when you use the per-model clipping tool. Without it, I had a hard time getting a sense of depth when a surface was clipped. But with the improvement glossy lighting brings, I have begun to wonder if other improvements in coloring and lighting are in the works or are possible. For instance, I use radial coloring with a grey palette to help my students pick out tunnels and pockets in a surface, but a better method would ambient occlusion on-the-fly. I've seen it in the molvis program "Qutemol", though the program does little else. Alternatively, is it possible to change the quality of shadows enabled in the effects window? And on a separate note, is it possible to change the inside color of a surface (something like "ribinsidecolor" for surfaces?) Thanks Dan -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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lost focus wile rotating molecules after zoom-in
by Sheng-Hung Wang 05 Jan '10

05 Jan '10

I notice that chimera lost focus while rotating molecules after zoom-in operation. Will this problem be solved in the future version? Shawn ___________________________________________________ 您的生活即時通－溝通、娛樂、生活、工作一次搞定！ http://messenger.yahoo.com.tw/

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matching peptides with altenate locations
by Sumitro Harjanto 31 Dec '09

31 Dec '09

Hi, I would like to match two peptides; one with alternate conformations in residue 4 and 5. I have tried: match #0:1-9.c@ca #1:1-9.c@ca.a match #0:1-5.c@ca #1:1-3.c@ca | #1:4-5.c@ca.a but both don't work and give me the "unequal number of atom chosen" error message. I tried changing match to sel in the latter case and I can get 10 atoms; 5 from each model, which is what I intended. How should I deal with this? Thanks, Sumitro

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distance measurement
by Farhana F Syed 30 Dec '09

30 Dec '09

Hello, I have been using Chimera for some months but suddenly my distance measurement is not working. I pick one atom and then shift-double pick the other atom, the hand shows, it blinks a couple times but no distance menu pops up. Any idea what could be wrong?! I just uninstalled and reinstalled the chimera software again, still the same trouble. [I use a laptop whose mouse works great (except when I need to move the molecules, then I use a real mouse instead of the laptop's finger mouse)]. Any help is greatly appreciated. Thank you for your time. Farhana

2 1

binding energy calculation?
by r n 29 Dec '09

29 Dec '09

hi I wanted to do energy minimization for the pdb file with two chains by keeping their backbone fixed , tried chimera energy minimization but did not give me any energy after the minization or binding energy for the complex. Is it anyway that I could do simulation of side chains and obtain the energy values such as lowest minima or the binding energy for two chains, using chimera? thanks ram

2 1

hello !every one!
by gytjyb 27 Dec '09

27 Dec '09

can i load a file about force field into chimera. if it is ture,i could chose other force field in chimera! how can i do? i just come from china and am poor in english and knowledge. thank for you help!

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hello!every one!
by gytjyb 27 Dec '09

27 Dec '09

can i load a file about into chimera how can i do? i just come from china and am poor in english and knowledge

1 0

perframe script
by Bala subramanian 23 Dec '09

23 Dec '09

Friends, I loaded a amber trajectory in chimera. I simply want to calculate the distance between two atom in each frame in the traj. and write it to a text file. I used the per-frame utility in MD movie tool. I chose interpret script as 'chimera commands' substitute text 001-200 (frame 1 to 200) In the script section i gave distance :163@CA :166@CA It reports to me the following in the reply log. Distance between GLY 163 CA and ARG 166 CA: 5.083 Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists Problem in per-frame script: Distance monitor already exists How should i actually use the perframe option so that the analysis will be done in each frame and reported output file will hve the distance values for every frame. Thanks, Bala

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Chimera-users December 2009