November 2017 - Chimera-users - RBVI Mailing Lists

Axes/Planes/Centroids for the OPM membrane visualization
by James Starlight 22 Nov '17

22 Nov '17

Dear Chimera Users, I have a question regarding Axes/Planes/Centroids for the visualization of the membrane plane predicted by OPM. Firstly, I have uploaded my structure with DUM atoms. Than, I selected the DUM atoms in both layers and try to show the membrane plane via defining of a plane for it. As the result, a cylindrical surface oriented perpendicular to the imaginative membrane has been emerged. What should I change in options to obtain it aligned along the membrane normal in a correct way? Is it possible to make more flexible selection of the DUM atoms only in the selected layer? Thank you for the help! Gleb

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TERs in PDB ?
by Marek Maly 21 Nov '17

21 Nov '17

Hello, is it possible to save the given molecular model (which is open in Chimera) in PDB format but with the TER string between consequent residues ? example: --------------------------- ATOM 1 Si1 CEN A 1 56.395 15.633 50.147 1.00 0.00 Si TER ATOM 2 C1 RE1 A 2 54.892 16.772 50.453 1.00 0.00 C ATOM 3 H1 RE1 A 2 54.289 16.821 49.538 1.00 0.00 H ATOM 4 H2 RE1 A 2 54.219 16.552 51.290 1.00 0.00 H ATOM 5 C2 RE1 A 2 55.394 18.185 50.780 1.00 0.00 C ATOM 6 H3 RE1 A 2 55.896 18.665 49.932 1.00 0.00 H ATOM 7 H4 RE1 A 2 56.038 18.053 51.659 1.00 0.00 H ATOM 8 C3 RE1 A 2 54.181 19.075 51.202 1.00 0.00 C ATOM 9 H6 RE1 A 2 53.674 18.496 51.984 1.00 0.00 H ATOM 10 H5 RE1 A 2 53.589 19.325 50.313 1.00 0.00 H ATOM 11 Si3 RE1 A 2 54.714 20.646 51.949 1.00 0.00 Si ATOM 12 C4 RE1 A 2 53.140 21.420 52.746 1.00 0.00 C ATOM 13 H8 RE1 A 2 53.430 22.271 53.376 1.00 0.00 H ATOM 14 H7 RE1 A 2 52.690 20.675 53.413 1.00 0.00 H ATOM 15 H9 RE1 A 2 52.466 21.649 51.911 1.00 0.00 H ATOM 16 C5 RE1 A 2 55.491 21.841 50.620 1.00 0.00 C ATOM 17 H12 RE1 A 2 56.423 21.426 50.217 1.00 0.00 H ATOM 18 H10 RE1 A 2 55.768 22.733 51.196 1.00 0.00 H ATOM 19 H11 RE1 A 2 54.875 22.300 49.836 1.00 0.00 H TER ATOM 20 C1 RE1 A 3 57.436 16.272 48.673 1.00 0.00 C ATOM 21 H1 RE1 A 3 58.039 17.117 49.028 1.00 0.00 H ATOM 22 H2 RE1 A 3 58.209 15.633 48.228 1.00 0.00 H ATOM 23 C2 RE1 A 3 56.488 16.820 47.464 1.00 0.00 C ATOM 24 H3 RE1 A 3 55.675 17.467 47.819 1.00 0.00 H ATOM 25 H4 RE1 A 3 55.960 16.034 46.910 1.00 0.00 H ATOM 26 C3 RE1 A 3 57.354 17.603 46.475 1.00 0.00 C ATOM 27 H6 RE1 A 3 58.241 17.015 46.210 1.00 0.00 H ATOM 28 H5 RE1 A 3 57.812 18.464 46.978 1.00 0.00 H ATOM 29 Si3 RE1 A 3 56.645 18.300 44.851 1.00 0.00 Si ATOM 30 C4 RE1 A 3 55.474 17.030 44.146 1.00 0.00 C ATOM 31 H8 RE1 A 3 54.666 17.578 43.646 1.00 0.00 H ATOM 32 H7 RE1 A 3 54.864 16.542 44.918 1.00 0.00 H ATOM 33 H9 RE1 A 3 55.893 16.349 43.396 1.00 0.00 H ATOM 34 C5 RE1 A 3 58.034 18.987 43.812 1.00 0.00 C ATOM 35 H12 RE1 A 3 59.000 18.584 44.141 1.00 0.00 H ATOM 36 H10 RE1 A 3 58.180 20.062 43.974 1.00 0.00 H ATOM 37 H11 RE1 A 3 58.009 18.601 42.786 1.00 0.00 H TER ATOM 38 C1 RE1 A 4 57.426 15.522 51.783 1.00 0.00 C ATOM 39 H1 RE1 A 4 58.370 14.991 51.606 1.00 0.00 H ATOM 40 H2 RE1 A 4 57.769 16.539 52.007 1.00 0.00 H ATOM 41 C2 RE1 A 4 56.787 14.966 52.995 1.00 0.00 C ATOM 42 H3 RE1 A 4 57.587 14.881 53.741 1.00 0.00 H ATOM 43 H4 RE1 A 4 56.321 13.982 52.869 1.00 0.00 H ATOM 44 C3 RE1 A 4 55.776 15.938 53.682 1.00 0.00 C ATOM 45 H6 RE1 A 4 54.722 15.759 53.439 1.00 0.00 H ATOM 46 H5 RE1 A 4 55.920 17.004 53.467 1.00 0.00 H ATOM 47 Si3 RE1 A 4 55.756 16.172 55.603 1.00 0.00 Si ATOM 48 C4 RE1 A 4 57.359 16.942 56.191 1.00 0.00 C ATOM 49 H8 RE1 A 4 57.601 17.853 55.629 1.00 0.00 H ATOM 50 H7 RE1 A 4 58.242 16.306 56.061 1.00 0.00 H ATOM 51 H9 RE1 A 4 57.248 17.148 57.263 1.00 0.00 H ATOM 52 C5 RE1 A 4 55.827 14.369 56.251 1.00 0.00 C ATOM 53 H12 RE1 A 4 56.581 13.702 55.818 1.00 0.00 H ATOM 54 H10 RE1 A 4 54.854 13.866 56.186 1.00 0.00 H ATOM 55 H11 RE1 A 4 56.205 14.393 57.280 1.00 0.00 H TER . . . --------------------------- If yes, how to do it ? Thank you in advance for your advice. Best wishes, Marek -- Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/

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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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