- Chimera-users - RBVI Mailing Lists

NMRCLUST
by Austin B. Yongye 04 May '09

04 May '09

Dear chimera users, Does the NMRCLUST algorithm in the Ensemble Cluster tool use Kelley penalty values (Kelley et al. Protein Engineering, 1996, 9(11), 1063-1065) to determine the optimum number of clusters during a clustering procedure? Thanks, Austin-

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Merging models
by Elaine Meng 04 May '09

04 May '09

On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > Hi everybody, > > I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz > ) made of two models. I need to merge this two models into one. How > can I do that? > > Thanks in advance, > > Maziar S. Ardejani > Lab 9, The Orner Lab > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > 21 Nanyang Link > Nanyang Technological University > Singapore 637371 > Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? <http://www.rcsb.org/pdb/explore/explore.do?structureId=2VXI> There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols. Please send Chimera questions to chimera-users(a)cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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Coulombic Surface Coloring
by Francesco Pietra 03 May '09

03 May '09

Hi: I would like to simply color the surface of a protein by the Coulombic Surface Coloring method. I can show the surface, have a file with calculated charges if useful, but i am unable to implement the indications below "There are several ways to start Coulombic Surface Coloring, a tool in the Surface/Binding Analysis category. The molecular surface(s) should first be displayed (using Actions... Surface... show or the command surface) and then chosen from the list of Surfaces to color by ESP. " which tool should be opened from Surface/Binding Analysis? Of those related, I can only see Electrostatic Surface Coloring and that - in my hands - does not bring to the simple Coulombic method. Thanks for clearing francesco pietra

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recording operations
by Fajer 03 May '09

03 May '09

Dear All, Does Chimera record the "menu" selected operations that can be played back in a manner analogous to storing "command" entered operations ? I'd rather avoid having to modify python script of the stored session. Peter Fajer

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My Chimera 1.4 build 27395 is not keeping 2D Labels when saving images except if Pov-Ray tracing is turned on
by Victor Alves 01 May '09

01 May '09

Hi When I save a picture with 2D Labels, they don't show up in the saved image. I tried with different image types (jpg, tiff, png) and even a new image just with some 2D Labels in it. I don't know if this is important but all of them have a white background. The only way I managed to see the labels was to turn on Pov-Ray tracing! Any ideas? Thank you in advance Victor Alves

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Re: [Chimera-users] pivot point
by Elaine Meng 30 Apr '09

30 Apr '09

On Apr 30, 2009, at 10:51 AM, Tatyana Fedotova wrote: > Dear Mrs. Meng, > I have a question about pivot point. > Could you explain howfor example I can rotate part of a helix from a > chosen pivot point. > I fount how I can selet and move atoms. But that's not what I need. > Thanks, > Tanya Dear Tanya, I can think of two ways to move only part of a structure rather than a whole model: (a) by rotating bonds, see Adjust Torsions, where the bonds define the pivots <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/stru… > (b) with Movement Mouse Mode, which is probably what you were talking about <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.… > Although method (b) does not include control over the center of rotation (pivot point), you can set the center of rotation before using that tool. You can set the center of rotation to an atom or centroid of a set of atoms by selecting the atom(s) and using "Actions... Set Pivot" in the menu. Or, you can use the "cofr" command to do the same thing, or if you have a fairly recent version of Chimera (1.4, so a daily build), specify particular X,Y,Z coordinates as the center. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/cofr.html> The center of rotation set as described above also applies when you are rotating whole models. In newer versions of Chimera (1.4), the rotation commands "roll" and "turn" also allow specifying the center to use when executing that command. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html> Please send Chimera questions to chimera-users(a)cgl.ucsf.edu rather than my personal address, unless you are describing private data. Even though I answer a lot of those messages, I might be sick, or on vacation, or not know the answer! Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html

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creating volume maps
by Nils Becker 29 Apr '09

29 Apr '09

Hi, I would like to use chimera for measuring the steric accessibility of particular atoms in a structure to reactive species in solution. To do that I had the following idea: 1. create a volume map which represents a solid sphere centered on the atom in question (alternatively, a Gaussian blob), with some chosen radius. 2. mask this sphere using the solvent accessible surface of the protein (for example, if the atom is at the surface and the surface is flat, half of the sphere would be cut away) 3. measure the volume of the remaining piece of the sphere. So now my question is: can this work, and how can I generate the sphere in step 1. ? thanks for any advice! Nils

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color by element
by Eric Pettersen 28 Apr '09

28 Apr '09

On Apr 28, 2009, at 3:31 PM, Thiruvarangan Ramaraj wrote: > Hi Eric, > > I have a question regarding the colouring by element option. > > If I select a surface and I go to colour and choose by element, does > it colour in any order, if so what is the order, how do i find out > what element is given what colour. > > Thanks for your time > > Thiru Hi Thiru, I'm not sure what you mean by "does it colour in any order", but the colors assigned to each element are described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortables.html#by… and how you can change them is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/colordef.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Problem recording raytraced movie
by Tom Goddard 28 Apr '09

28 Apr '09

maya shcushan wrote: > Dear Tom, > Thanks, this was very helpful... > I have a new question: I want to make a simple movie in which the molecule > rotates. Using the commands script I found on the internet, the movie is of > very low quality (attached). Moreover, running it with windows media player > shows the opening in the script, embedded in the movie. This were the > commands: > > "movie record > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > > I want to record the same movie in good quality, like the pictures I get > with pov-raying. I tried running: > "movie record raytrace true > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > But it falls all the time. > > I looked in the internet for scripts but didn't find an answer. Can you > please help me to create a simple script in which the molecule rotates and > presented in ray-tracing and high quality? > > Thanksm > Maya > > Hi Maya, In Chimera 1.3 before the movie encode command you need the command "movie stop". movie record raytrace true turn y 3 150 wait 150 movie stop movie encode mformat avi output spin.avi bitrate 4000 Otherwise it keeps on recording frames forever. In Chimera 1.4 (daily builds) this is unnecessary and your original script works correctly because in 1.4 movie encode does a movie stop implicitly. Tom

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measure
by julien(GWDG) 28 Apr '09

28 Apr '09

Dear all, I have the last vesion of chimera 1.4 (27371) under a linux machine. I want to use the measure function. I have two models. The difference between this 2 models is a 5 degree rotation around the x axis. >> matrix rotation #1 #0 >>reply in the log Position of test.pdb (#0) relative to test1.pdb (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 I think the command does not work in this version (if I misunderstood the command please tell me as well). It always give me the same answer for any different models I did try. Since I have to ask my admin each time I want to install something, could you just tell me in which version of chimera this command will work. Many many thanks. best Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 Göttingen

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