April 2011 - 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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Re: [Chimera-users] Display a spider volume data in a specific orientation
by Elaine Meng 08 May '14

08 May '14

Hi Zongli, This is not my area of expertise (our expert is currently out of town) -- at first I thought you could use "Transform Molecule Coordinates" (under Tools... Movement), but now I see that it works only on atomic structures rather than maps: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/transform/transfor… > It only works on molecular structures because it actually changes the atomic coordinates, without changing the model transformation. I've figured out one workaround, but it is both crazy and slightly tedious: (1) open your map (say as model 0). (2) open any atomic-resolution structure, it doesn't matter what, and open it twice -- now you have three models. Don't move them separately from the map (yet). Let's say the atomic structures are models 1 and 2. (3) use "Transform Molecule Coordinates" with desired Euler angles and shift on one copy of the atomic structure (say model 1). (4) use the match command to superimpose the other copy of the atomic structure on the one that was transformed: match #2 #1 (the command can use the whole models since they should have exactly the same atoms) (5) use the matrixcopy command to apply the transformation matrix of the second copy of the atomic structure to the map: matrixcopy 2 0 You might think "why do I need two copies of the atomic structure? can't I just transform one copy and then use matrixcopy?" ... in fact that's what I tried first, but after it didn't work, I realized it was because the Transform tool works by changing the coordinate values and not the stored matrix of the model. It is necessary to match the second copy to generate a corresponding matrix, and then matrixcopy can be used. I'm CC-ing the chimera-users(a)cgl.ucsf.edu list in case other Chimera users have suggestions. Our expert Tom G should be back next week and he might also have ideas. In general, it's better to send Chimera questions to that mailing list instead of just me, because I could be away from work or (like now) lacking a good answer! 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 Apr 7, 2010, at 11:51 AM, Li, Zongli wrote: > Hi Elaine, > I have a spider volume data (or mrc density map) from which I got a > serious 2D projections. I have the Euler angles for each projection. > Is there a way in Chimera that I can use those Euler angles to > display the 3D spider volume data (or mrc density map) in a specific > orientation that corresponding to that 2D projection? > Thank you very much in advance. > Best, > Zongli > > **************************************** > Zongli Li, Ph.D. > > Howard Hughes Medical Institute > Department of Cell Biology > Harvard Medical School > C Building, Room 420B > 240 Longwood Avenue > Boston, MA 02115 > > Tel: 617-432-4095 (Office) > 617-432-4708 (EM Suite) > 617-432-4091 (Computer room) > Fax: 617-432-1144 > Email: zongli_li(a)hms.harvard.edu > *************************************** >

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font size in pull-down menus
by Boaz Shaanan 09 Oct '13

09 Oct '13

Hi, Is there a way to change the font size of the pull-down menus? For some reason on the Windows (XP) v.1.5.1 they seem smaller to me. Nothing in terms of graphics (or my eyesight) has changed since I upgraded to 1.5.1 recently. Thanks, Boaz Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan‎

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color surface based on NMR Order parameters
by lalit.deshmukh＠huskymail.uconn.edu 08 Sep '11

08 Sep '11

Hello, I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on.. Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way? Thanks in advance, Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269

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square of density volume
by 仁田亮 12 May '11

12 May '11

Hi chimera users, I want to calculate the square value for the volume of the electron density because I want to calculate the variance map. Do anyone know whether we can calculate the square value of the volume by chimera? And if we can, could you teach me how to calculate? Thanks for your time and help, Ryo

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Information request
by Francesco Burresi 30 Apr '11

30 Apr '11

Hi, I've docked a ligand with a receptor and I get a pdb with1 chain (chain A) I'd like to separate recpetor-ligand in two different chians (chain A e chain B). How can I do that in Chimera? regards

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm trying to model a TM protein using a Fugue approach. This method involves to divide a transmembrane protein in fragment (Nter, TM1,LOOP1and so on) Each fragments is predicted separatly. I'd like to assembly and join fragment, superimposing the backbone of a fragment with that of the correspondent segment in the structure of my protein. How can I achieve this goal with Chimera? regards

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Re: [Chimera-users] Chimera: Myosin thick filament movie
by Tom Goddard 28 Apr '11

28 Apr '11

Hi Rogelio, The myosin thick filament movie in the Chimera animation gallery was made in 2006 using a 700 line python program I wrote. Fortunately Chimera animation capabilities are much better now, so I've made a Chimera command script that makes the same movie in Chimera 1.5.2 (Jan 2011), about 150 commands. I've attached the script. It of course requires the myosin data files to work. So I've put the script and data files in myomovie.zip and put a link to that in the animation gallery with the myosin animation (will appear after web site is rebuilt tonight). http://www.cgl.ucsf.edu/chimera/animations/animations.html To create the movie you open the myomovie.py Chimera session then open the myomovie.cmd command script. Rendering this movie takes about 15 minutes (for about 70 seconds of final video, 1760 frames) using the high quality supersample 3 option set in the script. The myosin movie is somewhat complex. There are about a half dozen simpler movie making command scripts with links on the animation gallery page. We don't have a separate movie scripts web page, although that is a nice idea. There is a movie making tutorial on the Chimera tutorials page http://www.cgl.ucsf.edu/chimera/tutorials/tutorials.html and there are details about all the commands in the Chimera User's Guide http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/movies.html Tom > Hi Tom, > > I have been recently looking at the animation gallery of Chimera and I > was wondering if I could get a copy of the script used to make the > Myosin movie, > Do you guys have a repository of scripts used for the displayed movies? > > I am working with a helical map and I would like to try to implement a > similar animation for my maps, > > thanks a lot for your help and consideration > > ROGELIO > > > -- > Rogelio A. Hernandez Lopez > Leschziner Lab > Harvard University > 305.G NWB > 52 Oxford Street, Room 305 > Cambridge, MA 02138 > > http://www.mcb.harvard.edu/Leschziner/

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Information request
by elisa carli 28 Apr '11

28 Apr '11

Hi, I'm working with a pdb file, that have two atoms in an ARG residue , not allowed by Charm H Polar force fields Is it possible to fix the problem with Chimera? Residues: ARG 251 1HH1 ARG 251 2HH2 Regards

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how to write log file in Chimera
by Rogelio A. Hernandez-Lopez 27 Apr '11

27 Apr '11

Hi, Is there any way to create a log file to store all the actions performed by the user during a chimera session, either using the menus or command line? I want to write a script for a movie and it would be very useful to copy and paste commands from such as file thanks, ROGELIO -- Rogelio A. Hernandez Lopez Leschziner Lab Harvard University 305.G NWB 52 Oxford Street, Room 305 Cambridge, MA 02138 rhernand(a)fas.harvard.edu (617)-872-5399 http://www.mcb.harvard.edu/Leschziner/

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Chimera-users April 2011