- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] will chimeraX support the BILD file format?
by Francois BERENGER 21 Nov '17

21 Nov '17

On 11/17/2017 09:53 AM, Greg Couch wrote: > We've been debating that. The bild format has many commands. Which ones > do you use? I ask because I have code that implements the transforms, > color, and shape commands, but not any of the line drawing, polygon or > marker commands. Does that work for you? I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent. The whole format is potentially useful to me. This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win. The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production). Regards, F. > -- Greg > > On 11/16/2017 04:35 PM, Francois BERENGER wrote: >> Hello, >> >> https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html >> >> I am a huge fan of this chimera feature, so I hope it will >> not disappear (trivial to create graphical annotations by hand >> or via a program). >> >> Regards, >> F. >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > >

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Fwd: Does volume outline is bigger than actual volume?
by Elaine Meng 21 Nov '17

21 Nov '17

> > From: Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> > Subject: Does volume outline is bigger than actual volume? > Date: November 21, 2017 at 6:00:17 AM PST > > Hello, > > I need to understand precisely what Chimera do. Please look at the attached screen shoot. The arrows are anchored in point (0,0,0), and they are point in direction [(1,0,0),(0,1,0),(0,0,1)] red, yellow and blue respectively. > > I set my volume to minimum (grey cube), I checked "Show outline box using color", and I noticed it does not cover the shape of my volume. > > There are "margins" in the top, and the bottom visible in the image and much smaller on the sides. > > Why they are there? What is its exact size? Where does volume actually begins in the (0,0,0), or slightly below that point? > > -- > best wishes, > Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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Match command question
by Yann STERCKX 21 Nov '17

21 Nov '17

Dear Chimera users, I've been struggling with the match command and was hoping you could help me out. I'm working a tetrameric enzyme. When the enzyme binds ligands, its domains rotate over a pivot point in the monomer. What I would like to do is superpose different liganded structures of the enzyme on the four monomer pivot points. Here's what I've done so far: * Each liganded state of the tetrameric enzyme is a single model * I use the match command to superpose the structures on the monomer pivot points (residues 430-433 in the structure). I used the following command match #model1:430-433 #model2:430-433 What is strange is that I obtain exactly what I want for 2 out of 4 models. Using this command I get an rmsd of 0.77A. But for the other 2 models, match does not seem to work as I obtain an RMSD of 27A and the superposition is clearly off. Including the iterate option does not alleviate the problem. I don't want to use matchmaker because this feature will, at least in my understanding, try to optimally fit two chains (or selections within two chains) on top of each other. If I do that, I do not get to see how the enzyme rotates around the monomer pivot points. How come match works really well for 2 out of 4 structures, but fails to perform the same task for the rest? Any pointers on what I might be doing wrong? Many thanks and kind regards, Yann PS: I've browsed through the archive, but could not really find a thread related to this problem (unless I overlooked it).

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Coordinates of atoms and volumes
by Michał Kadlof 20 Nov '17

20 Nov '17

Hi, 1. is there any way to get the exact Cartesian coordinates of any atom directly in Chimera? 2. Is there any way to get exact value from exact place inside density volumetric data? -- best wishes Michał Kadlof <m.kadlof(a)cent.uw.edu.pl>

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PipesAndPlanks coloring not accurate
by Andrew Hagen 17 Nov '17

17 Nov '17

Hello, I have a protein model that I colored according to region: N-terminal domain (green), a domain that I inserted (gray), and the flanking (GGS)2 linkers (tan). When I apply PipesAndPlanks, the tan regions are changed to either green or gray, which is not desired (and apparently, the PipesAndPlanks' color cannot be changed once rendered). Is this a bug or am I doing something wrong? To add a little more detail, I manually Frankensteined this model together. At the genetic level, it's just a domain insertion, flanked by linkers, but in Chimera I did this by: Opening my wt protein model (green), splitting the chain into two models at an internal site, generating GGSGGS linkers de novo in Chimera and joining these to the new models, and then finally joining those two fragments through a "bridge" of another model. There was lots of manual torsioning and minimizing using FoldIt in this process. I can imagine a work around is just to overlay two PipesAndPlanks renders and masking different regions, but this seems inelegant. Any assistance/advice is appreciated! --Andrew

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Re: [Chimera-users] visualisation of volumes
by Elaine Meng 16 Nov '17

16 Nov '17

Hello Michał, The answer is actually shown in the command line of your screenshot image! You would use the “volume” command to set levels and colors. Instead of a color name you could give r,g,b,a values (red, green, blue, alpha=opacity, each on a scale 0-1). Just like you can say “level” multiple times in the same command, you can also give “color” multiple times. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#general> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 16, 2017, at 6:22 AM, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl> wrote: > > Hello, > > how can I achieve the effect visible in attached image from command line? > > I need to add several semi transparent isosurfaces for a single volume. > > <Zaznaczenie_139.png>

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Command line for labelling specific residues in a zone
by Mark Rosenberg 16 Nov '17

16 Nov '17

I am not sure if this request was missed. I am having difficulty finding the syntax to write a line command in Chimera to label the non-polar or polar residues in say a 5 Angstroms zone. I would be grateful if you could advise me how to code the command line for labelling these residues with a 1-letter code please ? Once I see the format then I can readily adapt this to other situations. Thank you in advance. Mark

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Chimera/Modeller to add missing residues
by Daipayan Sarkar 16 Nov '17

16 Nov '17

Hello Elaine, I am using Chmiera-Modeller GUI to add the missing residues for my PDB file: (https://files.rcsb.org/view/1YPH.pdb) >From the mailing list, I am following the procedure listed in: http://www.cgl.ucsf.edu/pipermail/chimera-users/2013-September/009174.html However, once the missing residues for chains A and B are included, I save the new PDB file using File > Save PDB... > under save models selection "selected all three files" and clicked OK. The resulting PDB file includes the original header with additional 'MODEL 1', 'MODEL 2' and 'MODEL 3'. How to save the atom coordinates as a single PDB file after adding the missing residues? Any comments/suggestions is appreciated. Regards, Daipayan

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Chimera comands
by Michał Kadlof 16 Nov '17

16 Nov '17

Hello, I have some troubles with finding in documentation suitable commands. How do I should write script which: - open a trajectory in saved PDB or PSF/DCD in MD movie tool. - read pseudobonds from file, and change the color of all of them at once - change origin, voxel size and rotation angle of opened volumetric data Can you help me? -- best wishes, Michał Kadlof <m.kadlof(a)cent.uw.edu.pl <mailto:m.kadlof@cent.uw.edu.pl>>

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scripting: howto add IDATM labels
by Wiktor Pronobis 15 Nov '17

15 Nov '17

Hi all, I have a python script and want to know, how do I 1. add IDATM labels to the atoms 2. add a label in the upper right/left corner 3. make image nicer 4. save image as png I use the command "from chimera import runCommand as rc" and then "rc(COMMAND)" What should COMMAND be for my questions 1. - 4.? Thanks in advance, wpron

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