- Chimera-users - RBVI Mailing Lists

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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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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Re: [Chimera-users] the matrix reported in 'fit in map'
by Tom Goddard 14 Nov '17

14 Nov '17

Hi Qiang, Glad you figured this out. Chimera uses whatever map origin is specified in the map file, and this may not follow the EMAN2 convention of putting the origin at the center of the map. You can change the map origin in Chimera using Volume Viewer panel menu entry Features / Coordinates, and you could save a new map with that origin with Volume Viewer menu File / Save Map As…. Tom > On Nov 13, 2017, at 8:10 PM, 周强 wrote: > > Hi Tom, > Thank you very much for your kind reply. > I have tested the Chimera matrix in EMAN2 Transform class as you described. The rotation part is consistent between Chimera and EMAN2. The translation part is also consistent if the origin index is set to the center of the map. ( For even images, the center is at (nx/2,ny/2) where the first pixel is at (0,0). For odd sized images, the center is at ((nx-1)/2,(ny-1)/2). The same concept extends to 3-D. http://blake.bcm.edu/emanwikiEman2TransformInPython ). > > Qiang > > >> -----原始邮件----- >> 发件人: "Tom Goddard" <goddard(a)sonic.net> >> 发送时间: 2017-11-14 02:13:27 (星期二) >> 收件人: "周强" <zhouq2015(a)mail.tsinghua.edu.cn> >> 抄送: >> 主题: Re: [Chimera-users] the matrix reported in 'fit in map' >> >> Hi Qiang, >> >> The 3x4 matrix reported by Chimera has the 3x3 rotation in the first 3 columns and the translation in the last column. I do not know EMAN2 conventions. Chimera does not use or convert to Euler angles. Keep in mind that the rotation is about the origin of the map coordinates which is set by the “Origin index” value (shown with Chimera Volume Viewer menu entry Features / Coordinates). If you rotate your map about a different origin, then that becomes a non-zero translation and a rotation about the map origin. >> >> Tom >> >> >>> On Nov 10, 2017, at 8:36 PM, 周强 <zhouq2015(a)mail.tsinghua.edu.cn> wrote: >>> >>> Dear Chimera developer group, >>> I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. >>> Thank you very much. >>> Qiang >>> _______________________________________________ >>> 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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Help using Chimera with SFLD - I cannot 'view in chimera'
by Anne-Frances Miller 14 Nov '17

14 Nov '17

Dear Elaine, or other Chimera Guru, I would like to start using the wonderful tools in SFLD, and watched the tutorials, however when I try to do any of the things that is supposed to send something to Chimera, it crashes. I cannot open enzyme active sites in Chimera, or HMM alignments. I have updated by chimera. I am running Mac OS X 10.10.5, and firefox 56.0.2 Anne-Frances Miller Professor of Chemistry University of Kentucky

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cap clipping plane
by René Frank 13 Nov '17

13 Nov '17

Hi, I have a problem that the cap of my clipping plane is capping only some of the electron density. See screenshot attached. Any tips on how to ensure all electron densities, including smaller structures, are capped would be gratefully received. Many thanks, René ============================= Dr R. Frank, PhD MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH United Kingdom Lab: +44 1223 267487 Mobile: +44 7870 208280 ============================

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question
by 等儿会儿 13 Nov '17

13 Nov '17

dear editor： i am a noob with using Chimera. Now, i want to find and select all amino acid surrounding my ligand within a particular range（eg. 10Å）,how should i do? thanks for your help ! from a user

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the matrix reported in 'fit in map'
by 周强 13 Nov '17

13 Nov '17

Dear Chimera developer group, I am Dr. Qiang Zhou from Tsinghua university in Beijing China. Recently I'm going to calculate relative position between two maps with 'fit in map' in chimera. The 'fit in map' feature reported a matrix of 3 x 4. Can I convert this matrix to Euler angle with transform class of EMAN2 directly? Is the matrix of chimera same to that of EMAN2? BTW, The translation column in chimera matrix maybe contains a bug. I just manually rotated a map and then fit it into the original map. The matrix reported by Chimera should contain zero translation column. However, it reported a non-zero value (about 6-7 pixel) in translation column. Thank you very much. Qiang

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working with PDB files from XplorNIH
by Miriam Gochin 13 Nov '17

13 Nov '17

I am wondering if it is possible in Chimera to select between different chains in a multimer that are defined by the SEGID parameter in XPLOR. This appears on columns 77-80 of the PDB file, e.g. in this homotrimer: ATOM 1 N GLN 1 -2.276 -27.488 29.307 1.00 0.00 A ... ATOM 684 N GLY 1 4.365 -26.465 20.200 1.00 0.00 C --- ATOM 1357 N GLN 1 13.798 -26.207 29.441 1.00 0.00 E ... Atom selection results in picking up 3 atoms instead of 1, since Chimera expects the chain designation after the residue name. The XPLOR output is therefore not compatible with Chimera input requirements and I am wondering if there is a workaround. Many thanks for any suggestions. --------------------------------- Miriam Gochin Touro University California miriam.gochin(a)tu.edu 707-638-5463

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help！
by 余汉文 12 Nov '17

12 Nov '17

Good afternoon! Can you give me a favor? I have a serious problem in the process of studying application cytoscape. I can't open protein structure formate file in cytoscape via RINalyzer. However UCSF Chimera does not start. SO I check the path to UCSF Chimera. The Chimera is installed at D:\Chimera. Finally, i open the dialog Cytoscape Preferences Editor to modify the path "D:\Chimera\bin". But i can't open the protein structure formate file in cytoscape via RINalyzer as same as early. I Heartfelt thank you to help me solve this problem. From the student in china

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Help with chimera / sfld compatibility
by Anne-Frances Miller 11 Nov '17

11 Nov '17

Hello experts, I have tried reloading many things and switched browsers. When I am in SFLD and want to view my aligned sequences of the subgroup identified by my enzyme, in chimera, I get the error message: Error while processing /Users/afm/Desktop/sfld-3.chimerax: '/var/folders/zg/vzx644v88xl59y001s75rw2h0000gp/T/hmmer_align_fsgWHiJp.sto' is not a Stockholm file Also Any ideas? IOError at /ajax/download_temp/hmmer_align_mZdHMnpU.sto/ [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Request Method: GET Request URL: http://sfld.rbvi.ucsf.edu/django/ajax/download_temp/hmmer_align_mZdHMnpU.st… Django Version: 1.6.8 Exception Type: IOError Exception Value: [Errno 2] No such file or directory: u'/tmp/sfld/hmmer_align_mZdHMnpU.sto' Exception Location: /usr/local/projects/sfld/production/www/sflddjango/apache/../../sflddjango/sfldajax/views.py in download_tempfile, line 61 Python Executable: /usr/bin/python Python Version: 2.7.5 Python Path: ['/usr/local/projects/netgen/production/lib/python/netgen/interface', '/usr/local/projects/sfld/production/lib/python/sqlparse-0.1.13-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/MySQL_python-1.2.3-py2.7-linux-x86_64.egg', '/usr/local/projects/sfld/production/lib/python/django_debug_toolbar-1.2.2-py2.7.egg', '/usr/local/projects/sfld/production/lib/python/pycharm-debug.egg', '/usr/local/projects/sfld/production/lib/python/Sphinx-1.0.7-py2.7.egg', '/usr/local/projects/sfld/production/www/sflddjango/apache/../../../lib/python', '/usr/local/projects/sfld/production/www/sflddjango/apache/../..', '/usr/lib/python2.7/site-packages/PEAK_Rules-0.5a1.dev_r2713-py2.7.egg', '/usr/lib/python2.7/site-packages/Extremes-1.1.1-py2.7.egg', '/usr/lib/python2.7/site-packages/AddOns-0.7-py2.7.egg', '/usr/lib/python2.7/site-packages/DecoratorTools-1.8-py2.7.egg', '/usr/lib/python2.7/site-packages/BytecodeAssembler-0.6-py2.7.egg', '/usr/lib/python2.7/site-packages/SymbolType-1.0-py2.7.egg', '/usr/lib/python2.7/site-packages/PrivateWikis-1.0.0-py2.7.egg', '/usr/lib64/python27.zip', '/usr/lib64/python2.7', '/usr/lib64/python2.7/plat-linux2', '/usr/lib64/python2.7/lib-tk', '/usr/lib64/python2.7/lib-old', '/usr/lib64/python2.7/lib-dynload', '/usr/lib64/python2.7/site-packages', '/usr/local/lib64/python2.7/site-packages', '/usr/lib64/python2.7/site-packages/gtk-2.0', '/usr/lib/python2.7/site-packages', '/usr/local/lib/python2.7/site-packages', '/usr/local/projects/netgen/production/lib/python'] Server time: Sat, 11 Nov 2017 08:54:00 -0800 Anne-Frances Miller Professor of Chemistry University of Kentucky

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labels turned white
by Oleksiy Kovtun 09 Nov '17

09 Nov '17

Dear community, I encountered a problem with 2D labels turning white disregards what colour presets I give. The script reads title presets from a file (2dlabel path) and then display the title with these commnads: 2dlabels change * bgColor 1,1,1,0.75; 2dlabels change title visibility show The 'title' label should appear as opaque black font as defined in the label file: Label title (x,y): (0.18,0.5) text: u'Title' shown: False font size(s): 40 font style(s): bold font typeface(s): sans serif color(s): (0, 0, 0, 1) But it appears in white. Bizarrely all other presets in the label file translate into the title appearance as they should except for the colour. I run Chimera 1.11.12 (build 41280) on Unix. Script and label file are attached. Thank you. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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All PDB ca atom pairwise distance
by Kyle Morris 03 Nov '17

03 Nov '17

Dear chimera dev and users, Is there a way to calculate (using the GUI, commands or using a python script) the pairwise distances for every single c-alpha atom in a set of loaded PDB coordinates and spit this out to a file for further analysis? There are 142,800 atoms in the current loaded assembly. Thanks! Kyle

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rmsd graph
by SEFA ÇELİK 02 Nov '17

02 Nov '17

Dear Dr. I am using Chimera software(windows platform). I tried to get rmsd graph. And I got the result. But, graph's x-axis "*frame*" and y-axis "*rmsd*" value. I want the x axis to be the "*time*". Briefly, I want to see how the value of rmsd changes with time. Can you help with this? Could you explain in detail? Best regard Dr. Sefa Celik

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error during MPEGM enconding
by Edoardo D'Imprima 02 Nov '17

02 Nov '17

Dear Chimera team, I ma trying to record a simple movie using the following command #!/bin/csh -f # # windowsize 900 1094 movie record supersample 4 volume #0 style solid; wait volume #0 planes z,0,0; wait volume #0 planes z,0,115; wait movie stop ###bitrate 5000 movie encode output my_movie.mp4 quality highest framerate 25 mformat mp4 however I keep on getting this error message: /Applications/Chimera/Chimera.app/Contents/Resources/bin/ffmpeg -r 25.0 -i /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm -vf crop=floor(in_w/2)*2:floor(in_h/2)*2:0:0 -y -f mp4 -pix_fmt yuv420p -qscale 1 /Users/user/Desktop/folder/my_movie.mp4 An error occurred during encoding. See Reply Log for details. Error during MPEG encoding: ----------------------------- Exit value: 1 Error message: libavutil 52. 48.100 / 52. 48.100 libavcodec 55. 39.100 / 55. 39.100 libavformat 55. 19.104 / 55. 19.104 libavdevice 55. 5.100 / 55. 5.100 libavfilter 3. 90.100 / 3. 90.100 libswscale 2. 5.101 / 2. 5.101 libswresample 0. 17.104 / 0. 17.104 libpostproc 52. 3.100 / 52. 3.100 [image2 @ 0x7fac00802000] Could find no file with path '/var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm' and index in the range 0-4 /var/folders/2h/r_flycl50hj8klh8w4t1xmw400030f/T/chimovie_Vcz6-%05d.ppm: No such file or directory Could you please let me know what am I doing wrong? I tried both on my laptop (MacBook Pro (Retina, 13-inch, Early 2015) with OS version 10.11.6 (15G1004)) and our linux terminals (Linux sbterm 3.10.0-514.16.1.el7.x86_64 GNU/Linux) It happens on both Chimera 1.12 and Chimera 1.11 Many thanks in advance, Edoardo --------------------------------------------------- Edoardo D'Imprima PhD Student Max Planck Institute of Biophysics Structural Biology Department Max-von-Laue Straße 3 60438 Frankfurt am Main Germany Tel: +49 (0) 69 6303 3015

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ChimeraX x Chimera feature comparison?
by Gustavo Seabra 02 Nov '17

02 Nov '17

Hi guys, I wonder if there is a ChimeraX x Chimera feature comparison anywhere. I’m aware of the “ChimeraX Advantages” page (http://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html) However, I’m actually looking for a comparison that can tell what features are currently on Chimera that are *not* in ChimeraX, to consider if there is any reason to keep both in the computer. Thanks, -- Gustavo Seabra Adjunct Professor Federal University in Pernambuco Recife - PE - Brazil +55-81-2126-7450 x5023 (goo.gl/ktsXSc)

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problem with showing broken peptide after residues with alternative conformation
by Wangshu Jiang 01 Nov '17

01 Nov '17

Dear Chimera Support, I am using Chimera to performing structural analysis for a manuscript. I have been struggling to show the protein structure with PDB entry 3LR2, the peptide bond between residue with alternative conformations and the next residue was shown broken, both in backbone and in ribbon presentation. I am not sure what went wrong here, I compared the PDB text file to other PDB entries with alternative conformations and I did not find obvious differences. It would be nice to show all the rotamers in the PDB instead of manually deleting by coot just from ‘eyeballing'. Could you please help me to solve this issue? Any suggestion is deeply appreciated! I attached an image illustrating the problem I described. I hope to hear from you soon! Best Regards, Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden [cid:0D42E809-5937-4AC1-83FB-07A00C355333] Wangshu Jiang PhD student Dept Cell and Molecular Biology BMC Box 596 Husargatan 3 751 24 Uppsala Sweden

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