June 2012 - Chimera-users - RBVI Mailing Lists

Question about animated Ramachandran plot
by Trina Manalo 05 Jun '12

05 Jun '12

Hello, I would like to create an animated Ramachandran plot using an MD trajectory. One approach I've considered is using a per-frame script to save Ramachandran plot images (i.e., using the model panel, its possible to create a plot and then save the image as a png) Is there a way to do this using commands? Or is there an easier way to animate a plot of phi and psi angles over time? Thank you very much, Trina

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triggering events when findhbond finds a bond
by Anne Bowen 04 Jun '12

04 Jun '12

Hi, I currently have a "Per-Frame Command" set up (in the MD Movie dialog) that finds the H bonds (findhbond makePseudobonds true lineWidth 2.0 color green intramodel true intermodel false selRestrict any) every frame of a trajectory. Whenever a hbond is detected, I would like to turn the entire structure a different color just for that frame, and then have it go back to being colored by heteroatom. Is there an easy way to accomplish this? I tried to look through the documentation to determine if "findhbond" could return true or false if an h bond was found and it did not seem like it was possible. Is the only way to do this to change the findhbond script itself? Any help or suggestions is greatly appreciated! Thank you, Anne

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bond transparency as a function of length?
by Kersey Black 04 Jun '12

04 Jun '12

Hi, Very recent to Chimera. Trying to set the transparency of a bond to be a function of bond length in each frame of a trajectory. I have figured out how to define a transparent color, and now I am imaging the solution might use something like range color to vary the blending of the opaque version of the color and the fully transparent version based on distance, with the distance being determined as a per frame attribute of those atoms, but someplace around here I am lost. Any hints, links or suggestions would be very much appreciated. Cheers, KB

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Re: [Chimera-users] [chimera-dev] Rotating about an axis with mouse
by Elaine Meng 04 Jun '12

04 Jun '12

Hi Patrick, If I understand correctly, you can do what you want with "Constrained Move" (in menu under Tools... Movement): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/constrained/constr…> (The purpose of "Movement Mouse Mode" is different, mainly to allow moving subparts of a model. By default, mouse manipulation moves whole models.) You can also specify center and axis of rotation if using commands (turn, roll). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.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 Jun 4, 2012, at 6:28 AM, ladam wrote: > Hi all, > I have a python script that allows me to rotate a residue in a molecule > of a desired angle around a predefined vector. > Now I'd like to be able to do this graphically with the mouse on a selected > residue. > I have almost found what I want if I use the 'Move selection' option in the > 'Movement Mouse mode' but this does rotate around the center of Mass or > geometric center, not around a vector. > What I plan to do is derive the code from the corresponding /share/MoveSelection/move.py > module and try to insert a vector instead of the center_of_rotation(self.movable_groups) > but there is maybe a better, simpler idea. > Any suggestion? > Thanks a lot > -------------------------------- > Patrick Ladam > Maître de Conférence > Université Paris 13 - UFR SMBH > CSPBAT - Service RMN > 74, rue Marcel Cachin > 93017 Bobigny Cedex > Tel: 01 48 38 73 25 > Fax: 01 48 38 77 77 > mail: ladam(a)smbh.univ-paris13.fr > -------------------------------

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make selection disappear smoothly
by Thomas Evangelidis 01 Jun '12

01 Jun '12

Dear Chimera developers, Simple question: is there any way to make a selection disappear smoothly during a movie? Thanks, Thomas

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copy & paste multiple commands
by Thomas Evangelidis 01 Jun '12

01 Jun '12

Dear Chimera developers, This is an elementary question, but after searching a while in the mailing list and the documentation, I couldn't find the answer. So the question is if it is possible to copy & paste multiple commands in a single line into the Chimera command line interface. Alternatively, is the any "end of line" character that designates the end a of one command and the start of the next one? Thanks in advance, Thomas

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pH based conformational change
by Nikolay Igorovich Rodionov 01 Jun '12

01 Jun '12

Hi all, Is there any way in Chimera to model protein denaturation across various pH values? Thanks Nikolay Rodionv

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Re: [Chimera-users] Interpreting field / force direction in Coulombic Surface Coloring
by Elaine Meng 01 Jun '12

01 Jun '12

Hi Sumitro, The interaction energy of a "test" charge at some point would be the charge multiplied by the electrostatic potential. So if the test charge is -1 e (like one electron) its interaction energy at a point with potential +10 kcal/(mol.e) would be favorable, -10 kcal/mol. Positive potential favors interaction with negative charges and vice versa. I hope this clarifies, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco P.S. better to send questions to chimera-users(a)cgl.ucsf.edu because if you send to me and I'm on vacation, you might not get answered On May 18, 2012, at 12:36 AM, Sumitro Harjanto wrote: > Hi Elaine, > I have a simple question regarding the Coulombic Surface Coloring. I understand that the potential are generated by assuming a charged probe that moves along the surface of the model and as it traverses the surface the potential is picked up as the calculated electrostatic force the probe should experience (that's my understanding, correct me if I'm wrong please). > > I am just, however, a little confused about the interpretation of the value. say if I got a blue patch on the surface, which means I'm getting values in the range of ~10 (positive) kcal/(mol·e) at 298 K; does that mean the region indicated by the blue patch should potential attract or repel electron? > Thanks! > Cheers, > Sumitro

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