- ChimeraX-users - RBVI Mailing Lists

Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

Good morning, We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices? Thank you very much for your help. Kind regards, Ernesto. -- Ernesto Arias Palomo, PhD Group Leader Biological Research Center (CIB-CSIC) Ramiro de Maeztu, 9. 28040. Madrid. Spain earias(a)cib.csic.es +34 91 837 31 12 ext 4446

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Calculation of polar and apolar surface area
by Gorman, Scott Daniel 02 Oct '19

02 Oct '19

Hi All, I was wondering if anyone has a preferred way of calculating the polar and apolar surface areas for a macromolecule with ChimeraX? I've tried deleting all of the solvent and then using the command "measure sasa @N @O @S" for the polar surface area and then "measure sasa @C" for the apolar surface area, but the calculation for either comes up with a number too close to the total surface area, i.e. apolarSASA + polarSASA > totalSASA. So clearly I'm not approaching this problem correctly. Scott Gorman PhD Candidate Boehr Lab PSU Chemistry

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GUI not properly visualized
by Pascal Albanese UU 25 Sep '19

25 Sep '19

Hi Chimera staff, i just changed PC ad now i have huge visualization problems of the GUI, when opening is fine but when i open any pdb file or session all buttons and commands in the window disappear. Command line actually works but all i see is this: [image: image.png] do you have any explanation? i tried different releases (0.9 official, daily builds) I'm using W10 enterprise, 64bit, intel i9 9900, UHD graphics 630. Thanks for the support, best regards, -- Pascal Albanese Ph.D PostDoc Biomolecular Mass Spectrometry and Proteomics Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8 3584 CH, Utrecht The Netherlands Telephone: +31 30 253 6805 https://www.hecklab.com/

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ray tracing
by Ahel,Juraj 24 Sep '19

24 Sep '19

Dear all, pardon me if this has already been answered elsewhere, but I failed to find any information about this in the publication, webpage, or the mailing list archive. Is there a way to generate images of ray-traced maps in ChimeraX? I was often using it in Chimera but I can't find the option to do it in ChimeraX. Was it not included as a feature? Many thanks! Juraj

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Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

Hello I am having difficulty in manually imposing symmetry on a map (*.mrc file) and then extracting the unit cell for the subsequent fitting of PDB structures with fitmap. (1) When I use the command "Volume symmetry #1, C33 axis z centerIndex 107.5" I get the error message "No placements for #1" that I do not understand. (2) I cannot figure out from the help documentation on how to save and display one of the created segments. Any ideas? Thanks Shahid -- Dr Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

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render buriedArea surface?
by Alexis Rohou 09 Sep '19

09 Sep '19

Hi all, I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. Is there a way to do this in ChimeraX? If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program? Thanks in advance! Cheers, Alexis

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vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

Hello, In chimera one can display dot van der Waals surfaces for atoms. *vdw* *atom-spec* <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> What would be the equivalent command in ChimeraX? Thank you, Elena

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Open days EPFL - ChimeraX VR
by Krapp Lucien Fabrice 05 Sep '19

05 Sep '19

Hello, We are creating some small VR demos in ChimeraX for the EPFL open days in a few weeks (https://www.epfl.ch/campus/events/celebration-en/portes-ouvertes/) It is an event to show to a broader audience what the university is doing. The demos consists of small proteins up to density maps of bacteriophage with a few simple animations and menus to interact with the structures. Everything is almost done, I'm currently trying to fix the last issue but I didn't find a solution in the documentation. For two of the demos we would like the user to move a selection in VR with one of the VR controller right out of the box without having to go in the VR menu and click on the "move selected" button. I was able to make it work on Linux by loading the session though the remote API with the right part selected but it doesn't seem to work on Windows. The log shows a status change when clicking on the button "move selected" in VR but not the actual command to change the mode. Do you know if there is a way to change the mode of the VR controller without having to manually go through the menu in VR ? In the mean time, I will try different saved sessions and (remote) commands to try and solve the issue. If the demos are a success we will most likely make them available online so that anybody can try and improve them. Thank you in advance for your help. best, Lucien

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semitransparent volumes with ambient occlusion
by Sindelar, Charles 03 Sep '19

03 Sep '19

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! Here is a little request. For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful. What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off! I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like. I sure would like to have this option! I guess there must be some reason it is disabled? Best, Chuck Sindelar Opaque map + PDB (ChimX v0.6) (pretty but the PDB is obscured) [cid:image001.png@01D55FF9.D8266CF0] After adjust to 80% map opacity (ChimX v0.6) (pretty!) [cid:image002.png@01D55FF9.D8266CF0] After unshow/show PDB model (ChimX v0.6) (argh!) [cid:image003.png@01D55FF9.D8266CF0]

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silhouette of transparent density
by YAO HE 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

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silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

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Chimera X and the Oculus Quest
by Thomas Gluick 28 Aug '19

28 Aug '19

HI First please excuse my computer language ignorance. My question is: Is the Oculus Quest compatible with Chimera X; if it is, is software available to link the program to the Quest. I am aware already that the Rift can be connected and also certain phones. Thank you for you time. Best Tom Dr. Thomas Gluick Assistant Professor of Chemistry School of Science and Technology 770-842-5532

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Question about Calphas and line between them
by Yazan Abbas 21 Aug '19

21 Aug '19

Hi, While looking through the user guide, I came across an option to draw a line between consecutive Calphas that are displayed. I made a mental note to use that option in my figure, but I failed to bookmark it or write down what the command was. I've been through the user guide several times again, but can't seem to find it. Would appreciate it if someone could jog my memory. Thanks, Yazan

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discontinuous helices in tube mode
by Yazan Abbas 19 Aug '19

19 Aug '19

Hi, Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success. Thanks, Yazan

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Question about "color sample" command
by Sean Connell 19 Aug '19

19 Aug '19

Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion) The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read? Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right? Finally is there a way to show a key for the coloring in chimerax? Many thanks for any advice you can provide. Sean

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Fly function in ChimeraX - 2
by Gabor PAPAI 16 Aug '19

16 Aug '19

Dear developers, I’ve seen that two years ago the fly command from Chimera was not implemented in ChimeraX. Is it implemented now? Or does ChimeraX have a similar function? I tried the view command inside the perframe function, unfortunately this didn’t result in a smooth transition between two named views. The only option I have now is to translate, zoom and rotate the scene with the individual commands, however this is quite tedious to set. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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RESMAP output superposition.
by chimerax-announce-owner＠cgl.ucsf.edu 15 Aug '19

15 Aug '19

From: Shahid Khan <outlook_CD0472DE47DC92D6(a)outlook.com <mailto:outlook_CD0472DE47DC92D6@outlook.com>> Subject: RESMAP output superposition. Date: August 14, 2019 at 7:33:59 PM PDT Hello The python script for mapping the RESMAP local resolution output does not work in ChimeraX. Has anybody modified it so that it does? Or written a new script with the same purpose for ChimeraX. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Understanding the output of the align command
by Yazan Abbas 14 Aug '19

14 Aug '19

Hi, I am trying to make a movie to rotate density in a manner that follows rotation between two atomic coordinates. To do that, I am aligning the two models and using the reportMatrix output to inform turn and move commands in order to transform the density. However, I am encountering some difficulty, and I'm not sure if this is related to bugs or my lack of understanding. For example, if I want to move from the position of model #1 to model #2, "align #1/b toAtoms #2/b move nothing reportMatrix true" produces the following: *Axis 0.11 -0.018 0.99Axis point 166 190 0Rotation angle (degrees) 108Shift along axis -0.24* I would think my turn command should be *turn 0.11,-0.018,0.99 108 models #1 center 166,190,0* But that doesn't work. I can get it to work if I assume that the reported axis is x,z,y instead of the expected x,y,z. Also, I have to use a rotation angle of -108 instead of 108. I'm not sure if I am using the axis point value correctly though, is it correct to use that as my center of rotation? It's location (166, 190, 0) places at the top of the box, which seems unusual to me. And finally, would I use this same information in a move command (i.e. move axis distance(shift), as reported by the align command? Many thanks in advance, I hope explained this clearly. Best, Yazan

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Morphing atomic models and volumes in a single movie
by Yazan Abbas 05 Aug '19

05 Aug '19

Hi, I am trying to create a movie that is morphing between 3 atomic models while simultaneously morphing between the 3 corresponding volumes. The following is my script for recording this movie: *set max 25windowsize 1080 1080view frame1movie record supersample 3wait 1volume morph #12,13,14,15 frames 181 playStep 0.005524861878453038 constantVolume true modelId #16perframe "surface dust #16 size 40" frames 181coordset #10 1,181wait 181movie stopmovie encode test_full.mp4 quality high* There are 4 maps in my morph, but the fourth map is simply a copy of the first in order to mimic the *wrap true* option of the atomic model morph. I am encountering the following issue during the volume morph step: somewhere in between the morph between volume #14 and #15, the map disappears for a fraction of a second in the movie. I suspect its because of a calculation/waiting issue, because if I record the movie using filtered versions of the volumes (*volume guassian sDev 2*), I don't have the same issue. Am I correct in my interpretation of the issue? Is there a way to modify my recording script to avoid this? Thanks, Yazan

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pixel size
by Yazan Abbas 31 Jul '19

31 Jul '19

Hi, I am trying to create a scale bar using the following method: 1. camera is set to ortho 2. save image image.png width 4000 height 4000 transparentBackground true 3. check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178) 4. in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å 5. Show scale bar of desired in length in ImageJ However, the resulting scale bar looks unusually small given the dimensions of my particle. Have I misunderstood something about the pixelSize settings? The user guide doesn't say anything about pixelSize when one of or both of width and height are specified in the same image command, so I assumed the pixel size of the saved image would be the same as in the graphics window. Thanks, Yazan

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Runing multiple command lines in ChimeraX
by Marie Locard-Paulet 26 Jul '19

26 Jul '19

Hello, I am running ChimeraX version 0.9 (2019-02-16) on a Mac (macOS Mojave version 10.14.6). It works fine, and I can work by adding commandes in the command “box” in the bottom. But I would like to open a text file with multiple ChimeraX command lines (for reproducibility and gain of time). I saw the command “open” that should open a document with the suffix “.com” or “.cmd”. It doesn’t work in my hands. It says it does not recognise the suffix. Is there something I am missing? Could you please help? Kind regards, Marie. --------------------------- Marie Locard-Paulet NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Denmark

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ChimeraX Side View
by Elaine Meng 19 Jul '19

19 Jul '19

In response to a question about Side View... From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Side View Date: July 19, 2019 at 10:34:44 AM PDT Hi Zhijie, Thanks for your registration comments! You will be happy to know that ChimeraX does have Side View. You can choose it from the menu: Tools… General. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html> To make a tool (Side View, etc.) start automatically every time you start ChimeraX, right-click in that tool (or Ctrl-click on some systems) to show the context menu, and from that menu choose “Start at ChimeraX Startup” <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#tool-context>

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Zalman 3D monitor support
by Tom Goddard 19 Jul '19

19 Jul '19

Hi Zhijie, We are not likely to support Zalman 3D monitors (row interleaved stereo mode) in ChimeraX. Those monitors were made 2009-2011 and then discontinued. We don't have the funding to support technology from long ago. Tom

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Fw: Genentech ChimeraX source code inquiry
by Williams, Joanne 18 Jul '19

18 Jul '19

________________________________ From: Slaton Lipscomb <lipscomb.slaton(a)gene.com> Sent: Thursday, July 18, 2019 10:00 AM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Genentech ChimeraX source code inquiry Hi, Genentech has a commercial license for ChimeraX. However we have run into challenges installing it for our high performance computing cluster because of the binary-only distribution model. We automate the build and deployment of applications for our HPC cluster using the tool EasyBuild. It's far easier to do this when working from source code. Is the source code for ChimeraX available to license holders? thanks slaton -- Slaton Lipscomb gRED IT Scientific Computing Support for gRED IT Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…> FAQs for gRED Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…>

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Molecular Dynamics Viewer
by James Starlight 16 Jul '19

16 Jul '19

Dear ChimeraX users! I would like to make a movie of molecular dynamics trajectory that has been pre-converted to pdb format (totally 250 frames). 1) Firstly, I have a problem with the recognition of the SS elements of that ensemble in ChimeraX, where each snapshot looks just like a mixture of points ( i tried to use dssp but it did not solve the issue). At the same time the snapshots looks fine in another viewers including UCSF Chimera (not X) 2) If I have a pdb of the same protein with mapped B-factors and then I colored it using color byattribute bfactor palette rainbow range 2,100 2) would it be possible to map the trajectory to that pdb in order to see the motions (observed in MD) mapped onto the structure that has been coloured by b-factors? Thanks for help!

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session files do not save "color zone" command actions
by Rasmus Kock Flygaard 15 Jul '19

15 Jul '19

Hi all, I'm using chimerax-daily-build (downloaded two weeks ago, Chimerax-0.91). I am using a model to color EM density maps per subunit using the "color zone ..." command, but when I save Chimerax session files these colored zones are not saved and I have to redo all of them to fully restore a session. Is there any way to include these colored zones in the saved sessions files? Kind regards, Rasmus ------------------------------------ Rasmus Kock Flygaard, Ph.D Postdoc, Amunts' Lab SciLifeLab, Stockholms University Sweden

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MLP value of the ASP and GLU carboxylate
by Zhijie Li 12 Jul '19

12 Jul '19

Hello, I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: 'ASP': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CG': 0.54, 'N': -0.44, 'O': -0.68, 'OD1': -0.68, 'OD2': 0.53} 'GLU': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CD': -0.54, 'CG': 0.45, 'N': -0.44, 'O': -0.68, 'OE1': -0.68, 'OE2': 0.53}, As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me. Is there a justification for this setting? In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance? Zhijie

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mesh lineThickness
by Yazan Abbas 12 Jul '19

12 Jul '19

Hi, In chimera the volume mesh lineThickness option could be changed. I can't seem to find the equivalent option in chimeraX. Is it possible to change the thickness of mesh lines? Thanks, Yazan PS apologies if you received this message twice, there was an error in my browser when first sent...

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WebGL apps still in the pipeline?
by Oliver Clarke 11 Jul '19

11 Jul '19

Hi, Loving the regular improvements to ChimeraX! Just wondering regarding a web viewer - the original roadmap for chimeraX mentioned “WebGL apps” (http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html <http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html>), and original Chimera had a limited capacity to export scenes as interactive html files. Is this still something that is in the pipeline for ChimeraX? I would really love to be able to export ChimeraX scenes in a format that I can share on the web, without the need for users to download and know how to use ChimeraX. Ideally the user would be able to rotate, zoom and slab, but perhaps not translate - that is, the center of rotation would be fixed. The idea would be to enable sharing of “interactive figure” kind of views of the molecule/map (perhaps allowing switching between multiple scenes/views within one session). Cheers Oli

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Appearance of thick edges
by Yazan Abbas 11 Jul '19

11 Jul '19

Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug? I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan

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feature request / suggestion
by Alexis Rohou 09 Jul '19

09 Jul '19

Hello, Apologies if this already exists, but I'd like to suggest a new option to the show/hide command: show /spec/ toggle which would behave like the toggle option of volume (one of my favorite chimeraX features by far), but would work on atomic models. Within the spec, anything currently shown would become hidden, and vice versa. Cheers, Alexis

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by James Starlight 08 Jul '19

08 Jul '19

Hi Greg, sorry for some delay :-) Actually I just checked and indeed, there is still problem with rendering of the images with chimera-X using here is the detailed output if it would help chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc" INFO: Offscreen rendering is not available. INFO: module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS' INFO: UCSF ChimeraX version: 0.9 (2019-04-03) INFO: © 2016-2019 Regents of the University of California. All rights reserved. INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb INFO: Summary of feedback from opening /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb --- _warning_ | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX INFO: _B-factors_0476.pdb_ title: **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon** [[more info...]](cxcmd:log metadata #1) INFO: Chain information for B-factors_0476.pdb #1 --- Chain | Description [ ](cxcmd:select :1-219 "Select chain") | [No description available](cxcmd:sequence chain #1/ "Show sequence") INFO: Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb INFO: Chain information for florence.pdb #2 --- Chain | Description [ ](cxcmd:select #2:1-219 "Select chain") | [No description available](cxcmd:sequence chain #2/ "Show sequence") INFO: Executing: mmaker #1 to #2 INFO: Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 INFO: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: INFO: Executing: hide #2 models INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: dssp #1 INFO: Executing: zoom 1.3 ERROR: turn x 15 y 15 z -40 ERROR: ..........^ ERROR: Expected an integer >= 1 or a keyword ERROR: Expected an integer >= 1 or a keyword INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: preset "'overall look'" publication INFO: Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_ INFO: Executing: set silhouettes true INFO: Executing: set silhouetteColor indigo INFO: Executing: set silhouetteDepthJump 0.02 INFO: Executing: color byattribute bfactor palette rainbow range 2,100 INFO: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 STATUS: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 INFO: Executing: cartoon style width 2.4 thickness 0.50 xsection barbell INFO: Executing: 2dlabels create title text '"Cluster 0476"' color red font gothic xpos .01 ypos .90 size 36 INFO: Executing: lighting depthCueStart .4 depthCueEnd .8 INFO: Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer INFO: Executing: save image /home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png width 600 height 600 supersample 4 transparentBackground false and this is my script open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb open /home_pers/novikov/Bureau/test/test/florence.pdb mm #1 to #2 hide #2 models wait dssp #1 #view zoom 1.3 turn x 15 y 15 z -40 wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 color byattribute bfactor palette rainbow range 2,100 cartoon style width 2.4 thickness 0.50 xsection barbell # make info of the screen 2dlab create title text "Cluster 0472" color red font gothic xpos .01 ypos .90 size 36 # options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png format png width 600 height 600 supersample 4 transparentBackground false exit пн, 22 апр. 2019 г. в 23:38, Greg Couch <gregc(a)cgl.ucsf.edu>: > > Salut, > > Does ChimeraX work in offscreen mode for you now? I believe it is fixed. > > -- Greg >

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Re: [chimerax-users] [Chimera-users] Cylinder coloring extension
by Elaine Meng 03 Jul '19

03 Jul '19

Hi Thomas, Chimera “pipes” are always a single color each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pi…> However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color. Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs. <http://www.rbvi.ucsf.edu/chimerax/index.html> In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this: ... and then command “color by bfactor palette rainbow” gives this: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom(a)gmail.com> wrote: > > Dear Chimera Team, > > I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? > > Looking forward to an answer, > Thank you for your time reading my suggestion. > > Thomas M

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mclip - surface clipping per-model
by bertrand beckert 03 Jul '19

03 Jul '19

Hi Elaine, I just wonder if the option clipping per-model has also been introduced in ChimeraX like it is in chimera ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod…) ? Apparently the command mclip doesn't seem to exist... Has it been replaced? Best Bertrand

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MacOS two-finger swipe on help window
by Alexis Rohou 02 Jul '19

02 Jul '19

Hi all, Not sure this is a bug, but on my MacOS laptop when I use two finger swipe motion while hovering over the help window (to browse up and down the page), the help page is scrolled as expected, but simultaneously the view in the main window is rotated. Is this expected behavior? It seems a bit counter productive to me. Cheers, Alexis

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color a surface by volume data
by bertrand beckert 02 Jul '19

02 Jul '19

Dear all, I have been searching in the documentation for quite a while and I haven t yet found the solution of how we can in chimeraX color a surface/volume by a volume data like in chimera ... i.e: local resolution map in cryo-em... in chimera: volume viewer/Tools/Surface color/color suface by is it possible to do so in ChimeraX? Any Help would be really appreciated! Thanks also for the amazing software ! Best Bertrand

2 1

An error opening chimerax seesion
by Yehuda Halfon 02 Jul '19

02 Jul '19

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

2 4

Placing markers using the VR wands
by Schmid, Michael F. 01 Jul '19

01 Jul '19

Hi- I don’t seem to be able to activate the Marker Placement functions in the menu that it called up by pushing the menu button (above the trackpad of the wand) to display a floating menu. It doesn’t seem to work with “vr off” either, using the mouse. I’d like to place markers in a tomogram, either in a density, or (preferably) at a specific 3D position with the wand. Thanks, Mike Schmid

3 4

suggestion for ChimeraX on MacOS
by Alexis Rohou 01 Jul '19

01 Jul '19

Hi there, I noticed that when I do "open browse", the native MacOS file browser is started, but when I click on File > Save..., a file browser from some other toolkit is used. I find this inconvenient because that file browser does not know about my recent history, bookmarks, etc. Any chance the File > Save... dialog could use the native OS file browser? Cheers, Alexis

2 1

Restoring views and how to use clip
by Yazan Abbas 01 Jul '19

01 Jul '19

Hi, Instead of using chimera sessions (which can get very big) to save my work when preparing figures for publications, I save all my commands in a .cxc file to be read by chimeraX later. Is there a single command that outputs all the necessary information in an appropriate format needed to restore a view? Currently what I have done is *alias myview view matrix; zoom *to output the information into the log, but the output needs to be re-formatted whenever I want to use that information with the view matrix and zoom commands. Is there a command that outputs that information in a format ready for copying and pasting? I know name view can partially fulfil what I am looking for, but it is only session specific. On a related note, I want to also restore the clipping for each figure/panel I create, but I don't seem to be using the clip command appropriately. For example, if I enter the command clip list, and the output is Using 2 clip planes: far -34.697, near -45.723, executing the command clip far -34.697 near -45.723 does not restore the same view. Am I missing something? Thanks, Yazan

3 2

Orientation and pre-superimposition of the PDB
by James Starlight 28 Jun '19

28 Jun '19

Dear Chimera Users! I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation). The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!) Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX! Thanks in advance!

2 4

Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, Apologies if this has been posted before, still new to chimerax and the mailing list. Was wondering if there are plans to add support for modifying mouse keys with ctrl (similar to what is in chimera). I am also wondering if there are plans to create a recenter + change pivot button/function that is also part of chimera. Thanks, Yazan

3 4

Map issue after using color zone
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, I already submitted a bug report for this issue, but was wondering if there was a quick fix. After applying color zone to my map, parts of it appear broken where density is forming protrusion. An image example is attached. Using the latest daily build (jun 25). Thanks, Yazan

2 2

volume splitbyzone and color zone issues
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, I executed 'color zone #2 near #1 distance 5 sharpEdges true' to colour a map I loaded, followed by "volume splitbyzone #2', but repeatedly would get an error that the volume specified is not coloured by zone. Eventually after trying multiple times, it worked, however the log outputted the following: Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", > line 130, in invoke > return self._func(self._name, data) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 3557, in _update_drawings > v.update_drawings() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 701, in update_drawings > self._update_surfaces() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 724, in _update_surfaces > s.update_surface(ro) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 1953, in update_surface > va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, > level, rendering_options) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2048, in _calculate_contour_surface > rendering_options, level) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) > ValueError: not enough values to unpack (expected 3, got 2) > Error processing trigger "graphics update": not enough values to unpack > (expected 3, got 2): > ValueError: not enough values to unpack (expected 3, got 2) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails) Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", > line 254, in execute > cmd.run(cmd_text) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", > line 2641, in run > result = ci.function(session, **kw_args) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", > line 1248, in color_zone > color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, > auto_update = update) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 14, in color_zone > zc.set_vertex_colors() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 84, in set_vertex_colors > replace = True) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 123, in color_zone_sharp_edges > ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 147, in _edge_cuts > f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, > distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f) > ValueError: Cut fraction 1.8061 is out of range (0,1) > ValueError: Cut fraction 1.8061 is out of range (0,1) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)

3 2

Distinguishing between upper and lower case chain IDs before and after splitting chains
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, My model (cif format) contains 34 chains, and so I've been using upper case and lower case letters for chain IDs. When I read in my model, the select command distinguishes between upper case and lower case, but after applying the split command on my model ('split #1 chains'), the select command no longer distinguishes between upper and lower case. I.e. 'select #1/D' will select both chains D and d. The split command works correctly, producing models 1.1-1.34. Also, is it possible to create a model from a selection? I can't find such a command anywhere, and the only thing I can figure out is to do the following: 'save *name* format mmcif models *selecion_name*; open test.cif' Thanks, Yazan

2 1

measure blob - persistent color?
by Alexis Rohou 25 Jun '19

25 Jun '19

Hi there, I absolutely love the new measure blob UI in the daily builds. Very useful. Thank you so much for putting it together. Is there a way to get the blob surface color to persist beyond hiding/showing the volume object? Obviously, in a script I could just re-measure the blob and re-color it, but is there another way to make the color "stick"? (Note, I don't plan to change the isocontour level) Cheers, Alexis

2 4

#2013: Trouble pip-installing Pyyaml prereq for bundle
by Andrés Giner Antón 20 Jun '19

20 Jun '19

Hello, two weeks ago we reported a problem regarding the installation of Pyyaml as a prereq of a bundle that we created, do you have any forecast of when we will get an answer? Here is the URL of the ticket: https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013 Thanks for your attention. Greetings, Andrés Giner Antón

2 1

ISOLDE 1.0b3 now released for ChimeraX 0.9
by Tristan Croll 17 Jun '19

17 Jun '19

Dear ChimeraX users, Just letting you know that I've released ISOLDE 1.0b3 on the ChimeraX Tool Shed for use with ChimeraX 0.9. If you're not familiar with ISOLDE, you can get an overview at https://isolde.cimr.cam.ac.uk/. In brief, ISOLDE is designed to allow the high-fidelity, interactive remodelling/refinement of atomic models into low-medium resolution cryo-EM or crystallographic electron density maps. In designing ISOLDE, I've always had two groups in mind. The first is, of course, the experimental structural biologists whose job it is to solve the structures of new macromolecules and their complexes. The second (and, to my mind, equally important) group is the downstream *users* of such models. Like every other human endeavour, macromolecular model building is an imperfect field, and (particularly in the worse-than-2-Angstrom resolution range targeted by ISOLDE) many deposited models contain serious errors that are eminently fixable with modern tools. My hope is that ISOLDE will become a useful tool allowing you to directly inspect your model of interest in the context of its original data, providing you with a feasible pathway towards fixing any issues you find (or, failing that, moving to a new target) prior to committing serious resources to its study. Please enjoy. Constructive feedback is always welcome. Best regards, Tristan

1 0

Transparent background movie
by Norberto Escudero 14 Jun '19

14 Jun '19

Hi, I have succesfully created images with transparent background, but it seems is an impossible task for a movie. Is there any way around this? Thanks and regards, -- Dr Norberto Escudero Urquijo Prof. A. Warren's group Cambridge Institute for Medical Research (CIMR) Hills Road, Cambridge, CB2 0XY

3 2

Saving stereo pairs
by Gyunghoon Kang 14 Jun '19

14 Jun '19

?Hi, apologies if this information is available somewhere but all my searches returned information for the original Chimera. Is there a way to generate stereo pairs either in the command line or GUI? Best, Gyunghoon Kang

2 1