- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] chimerax mesh commands doesn't work
by Elaine Meng 20 Sep '18

20 Sep '18

Hi Yehuda, I don’t think you are doing anything wrong; in ChimeraX, the lineThickness option doesn’t work for me either, although it works fine in Chimera on the same computer — we will look into it. Sorry for the inconvenience and thanks for reporting, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there is a chimerax-users(a)cgl.ucsf.edu mailing list too <http://rbvi.ucsf.edu/chimerax/docs/contact.html> > On Sep 20, 2018, at 4:56 AM, Yehuda Halfon <yehuda.halfon(a)weizmann.ac.il> wrote: > > Hi all, > I wanted to use chimeraX to use some commands on mesh display. > Some works like meshLightning but others like lineThickness doesn't > I use volume #1 lineThickness 10 (or any other integer) but nothing seems to change. What am I doing wrong? > Yehuda Halfon

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Ca trace
by v.kalienkova＠bioc.uzh.ch 19 Sep '18

19 Sep '18

Dear all, I was wondering, is there an option to just show a Ca trace in ChimeraX? If yes, can one modify the width of it? Thanks a lot in advance, Valeria

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Forward of moderated message
by chimera-users-bounces＠cgl.ucsf.edu 17 Sep '18

17 Sep '18

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ChimeraX - Color by Electrostatic Potential
by Maurício Menegatti Rigo 14 Sep '18

14 Sep '18

Hi, is there a way to color the protein surface according to Electrostatic Potential, just like we do with Chimera ("Electrostatic Surface coloring" under "Tools"). The input potential file was calculated with Delphi. Thanks in advance, Maurício Menegatti Rigo, *Ph.D.* Brazil

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Saving obj file
by Donghyun Park 13 Sep '18

13 Sep '18

Dear ChimeraX-users, I have a question about saving the scene as obj file. In the traditional Chimera, I was able to generate obj file with texture by simply clicking 'save' button. I tried to save obj file simply by typing *save ~/Desktop/file.obj . *I generated obj file but it does not show texture - basically black &white. I was hoping to find some more information on the user guide but I did not find much. Could somebody please help me with this problem? Thank you, Raphael

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Thank you for your free vector icons.
by Moira Ames 11 Sep '18

11 Sep '18

Hi, I hope this email finds you well. Thank you for making this page: https://www.cgl.ucsf.edu/chimerax/docs/embedded.html I recently passed my thesis with a lot of aid from that resource page. It has helped us tremendously. May I ask if you are still updating the page? If you are, I would like to repay you by way of recommending an additional resource which could be a good addition to it. Here it is: https://www.webhostingsecretrevealed.net/free-icons/. <https://www.webhostingsecretrevealed.net/free-icons/> I hope you find it useful and helpful as well. Best Regards, Moira Ames *Graduating student from University of St. Thomas*

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Apply dust command to entire timeseries
by Scott, Brandon L. 10 Sep '18

10 Sep '18

I am attempting to remove small connected components from my timeseries volumes. The surface dust command works well for this, but it only works on one time point at a time, is there a way to script this, or use in conjunction with the vseries play command to apply this to each timepoint? Thanks, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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Re: [chimerax-users] invert selection in ChimeraX
by Yashar Sadian 10 Sep '18

10 Sep '18

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Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Tom Goddard 04 Sep '18

04 Sep '18

Hi Pascal, I enhanced the ChimeraX select command so you can select the crosslinks in a length range. Then you can color the selected ones. For example, select #1.1 minimumLength 30 color sel red select #1.1 minimumLength 5 maximumLength 10 color sel yellow sel #1.1 min 10 max 15 color sel blue The minimumLength and maximumLength options will be in tonight’s ChimeraX builds (available around 5 AM Pacific time). Tom > On Sep 1, 2018, at 2:57 AM, Pascal Albanese wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal > > -- > Pascal Albanese, PhD > Post-doc, Politecnico di Torino > Dipartimento DISAT, > BioSolar Lab@Environment Park > > Via Livorno 60 > > 10144 Torino > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Elaine Meng 04 Sep '18

04 Sep '18

Hi Pascal, Many features are are still in development, so although we can easily imagine useful features (and we welcome your suggestions), many are not yet implemented. Yes, you can load different sets of crosslinks. The “pseudobond” input format is just plain text specifiying pairs of atoms. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> Then you can specify the different models (input file -> model) in the “crosslinks histogram” command by their numbers as shown in the Models panel, e.g. crosslinks hist #1.3 crosslinks hist #3 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram> Currently there isn’t color-by-length or selection-by-length, sorry. The interaction with the histogram that you may already have seen is that passing the cursor over the columns of the histogram temporarily enlarges the corresponding-length pseudobonds and hides the others. There isn’t control over how wide the histogram bars are. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there’s a chimerax-users mailing list CC’d on this message which you can send to and/or join > On Sep 1, 2018, at 2:57 AM, Pascal Albanese <pascal.albanese(a)polito.it> wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal

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FYI: Model.id_string API change
by Eric Pettersen 22 Aug '18

22 Aug '18

For those of you writing code in ChimeraX, in case you’re using Model.id_string you should know that as of tomorrow’s build, Model.id_string is a property instead of a function. —Eric Eric Pettersen UCSF Computer Graphics Lab

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question about chimerax
by Fang, Fei 14 Aug '18

14 Aug '18

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

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Export a scene from Chimera and into ChimeraX?
by Oliver Clarke 06 Aug '18

06 Aug '18

Hi, I love the new visualization features in ChimeraX, but I also really like the depth of functionality available in the original Chimera. I understand that ChimeraX has been rebuilt from the ground up and therefore can’t be expected to support importing sessions from Chimera1. However, Chimera1 is also able to export static scenes - e.g. as COLLADA or VTK format. Would it be possible to add an import function for these scenes in ChimeraX, so we can create a static scene just the way we like it in Chimera1, and then render it with e.g. ambient occlusion etc in ChimeraX? Alternatively/additionally, would it be possible to add an export function for molecular surfaces to ChimeraX? One of the major improvements in ChimeraX (at least for my work) is that it has a robust and fast surface calculation function that works on large, multi chain structures. Would it be possible to export these surfaces (e.g as MRC format) so they could be imported into Chimera1? Cheers Oli

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Setting the bgColor transparent in ChimeraX
by bertrand beckert 03 Aug '18

03 Aug '18

Dear all, I have now been trying to use ChimeraX as a replacement for Chimera for making really nice images for publication. So far I have to say I really liked the rendering! definitely a really nice work! However I was really wondering how to get the background transparent... In Chimera we were able to set the background transparent as preference which is actually really useful... any idea how we can to do it in ChimeraX? Any help would be highly appreciated! Best Bertrand

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Transparency and Scaling factor in ChimeraX
by Christoph Bachmann 31 Jul '18

31 Jul '18

Dear ChimeraX team First of all, great piece of software. It's a lot more userfriendly than pyMol or VMD. But it is hard to find information, since most is still for the old Chimera. I'm struggeling to get transparency in saved pngs to work. I've tried it on a PC and a Mac with no luck. This is strange since both computers support transparency and I regularly work with that feature so it can't be a hardware problem. My main question is how to get absolute sizes of the molecules. I'm currently making an illustration with different molecules, from small to large and I want their size to be displayed as accurate as possible (so a carbon atom in one molecule is exactly as big as the one in another molecule). I'm sure there is an easy way but I haven't found anything so far. If I would load them all into ChimeraX their sizes are represented correctly, but that's just too much for the computer. So, thanks in advance for your help. Best wishes Christoph Bachmann University Basel - Switzerland

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How to not build bundles/use wheel?
by Yuri 25 Jul '18

25 Jul '18

I am trying to build on FreeBSD. It calls the module 'bundle_builder', which calls 'wheel'. How to only do a regular python build, and not call 'wheel'? Thanks, Yuri

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Volume isosurface transparency
by Zack Gainsforth 24 Jul '18

24 Jul '18

Hi, I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question. I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface. When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it: I’m setting the transparency using the colors dialog box: For comparison, if I make the isosurface invisible to show the objects inside: If instead I use the transparency command: volume #5 transparency 50 The isosurface turns black: My question is: am I doing this incorrectly? Thanks, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 zackg(a)ssl.berkeley.edu

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Re: [chimerax-users] I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by Eric Pettersen 20 Jul '18

20 Jul '18

Hi Jean-Yves, The latest builds of ChimeraX have a “Presets” menu with an entry (“Original Look”) which allows you to easily return to the initial depiction of a model. —Eric Eric Pettersen UCSF Computer Graphics Lab > Greetings, > > > thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. > > > As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". > > > I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> which are useful and one can reconstruct the initial display. > > > As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. > > Simply pressing the "Show atoms" button will display all water molecules as small spheres. > > But now if I click "Hide atoms" only the ribbon is left. > > > Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html>> but that was not the best solution. > > > Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: > > > show ions > > show ligand > > select ligand:<3.8 & protein > > show selAtoms > > > For novices this is a bit complicated to understand. > > > Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. > > > I firmly believe that this would avoid lots of frustration for many new users! > > > P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? > > > Sincerely, > > Jean-Yves Sgro

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Hardware for VR of volume data
by Tom Goddard 11 Jul '18

11 Jul '18

Hi Bernard, VR is not going to handle large volumes no matter what hardware you buy. To avoid causing nausea current VR headsets use 90 frames/second graphics updating. That is in two eyes, so the effective graphics frame rate needed is 180 frames/second. By comparison on a flat panel display it is routine to show a very large volume at 10 frames per second and this causes no problem. So VR requires about 20 times the rendering speed of visualization on a conventional display. So here are some ideas of what you can expect. Some recent 3d light microscopy I was looking at in VR is 4K by 2K by 31 z planes with 3 channels — and it rendered fast enough with VR on a GTX 1080 and also on a Quadro P6000. Comparing to your 2K cubed example my data was equivalent to about 2k x 2k x 186, or about 1/10th the size. I haven’t benchmarked volume rendering so I don’t actually know at what size graphics is too slow — I should test this. But I suspect this is close to the limit. For molecular structure display, 100,000 atoms with very coarsely triangulated spheres works in VR but is near the limit. For surface and triangle rendering the limit is about 2-5 million triangles depending on which high-end graphics card before frame drops start causing flicker. For molecules showing 2.4 million atoms of HIV capsid 3j3q is fine on a desktop display but is not going to work in VR. With that in mind I would recommend a GTX 1080 Ti graphics card with a high-end CPU, maybe 64 Gbytes of memory, definitely get a high-end SSD drive or two as the data transfer rates of about 3 Gbytes/second are very handy for large data compared to the 100 Mbytes/second of spinning drives — the whole system would be about $4-5k. You could spend more but you won’t get any better performance. The main VR performance bottleneck is going to be in the software if you use ChimeraX. Unfortunately it does color blending and mapping data values to colors and cropping on the CPU instead of the GPU which is painfully slow, tens of seconds to adjust brightness on the above-mentioned 3-channel light microscopy. I expect to put the blending and color lookup on the GPU in ChimeraX over the next 12 months. Tom > On Jul 10, 2018, at 12:48 PM, Heymann, Bernard (NIH/NIAMS) [E] wrote: > > Hi > > I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? > > Bernard > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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pdb and map colors
by Andrey Feklistov 25 Jun '18

25 Jun '18

My question is about ChimeraX 0.6: is it possible to highlight different parts of a pdb (based on the protein sequence) with different colors and then color a corresponding map accordingly. I can't find an option 'Sequence' like in the old Chimera, is it possible to do this from a command line? Thanks!

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Re: [chimerax-users] [Chimera-users] ChimeraX won't start on Ubuntu 16.04
by Greg Couch 22 Jun '18

22 Jun '18

(This is really a question for the chimerax-users mailing list, not the chimera-users one.) If you can wait a week or so, I'll have a ChimeraX .deb package for Ubuntu 16.04 (and another for 18.04). But to answer your question, you do not need a system-wide replacement of Qt5. libQt5core.so.5 is in CHIMERAX/lib/python3.6/site-packages/PyQt5/Qt/lib/libQt5Core.so.5, where CHIMERAX is where ChimeraX was installed. So add that directory to the LD_LIBRARY_PATH environment variable and rerun ldd on libqxcb.so. And please let me know what you find out so I can make sure the .deb package avoids that problem. Regards, Greg On 06/21/2018 10:34 AM, Petr Leiman wrote: > Dear ChimeraX users and Developers, > > ChimeraX v. 0.5 or 0.6 would not start on our stock Ubuntu 16.04 > machines. The error message is as follows: > > This application failed to start because it could not find or load the > Qt platform plugin "xcb" > in "". > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, > offscreen, vnc, xcb. > > Reinstalling the application may fix this problem. > Fatal Python error: Aborted > > Current thread 0x000014f406ce7740 (most recent call first): > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/chimerax/ui/gui.py", > line 93 in __init__ > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 485 in init > File > "/usr/local/lbbs/chimerax/current/lib/python3.6/site-packages/ChimeraX_main.py", > line 788 in <module> > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 85 in _run_code > File "/usr/local/lbbs/chimerax/current/lib/python3.6/runpy.py", line > 193 in _run_module_as_main > Aborted (core dumped) > > A few more errors while checking for missing libraries (ldd) of > ChimeraX-supplied libqxcb.so, libqxcb-glx-integration.so > or libqxcb-egl-integration.so > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5.9' not found > /usr/lib/x86_64-linux-gnu/libQt5Core.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5XcbQpa.so.5: version > `Qt_5_PRIVATE_API' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5: version `Qt_5' not found > /usr/lib/x86_64-linux-gnu/libQt5Gui.so.5 > > Do I need to do a system-wide replacement of Qt5 for a different > flavor (OpenGLES)? > > Thanks, > > Petr > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Questions about ChimeraX and problems re-downloading Chimera
by Steven Douglas Aird 21 Jun '18

21 Jun '18

Dear Elaine, Is there a way in ChimeraX to specify colors for individual species of amino acids? I would like to color cysteine residues to illustrate disulfide bonds. There appears to be no ‘byresidue' or ‘byaminoacid’ command. Since I had formerly done this in Chimera, I sought to re-download that from: https://www.cgl.ucsf.edu/chimera/download.html This page has been unresponsive for hours and the download cannot be completed. Thanks for your help, as always. Sincerely yours, Steve Aird Steven D. Aird Technical Editor Faculty Affairs Office Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son Kunigami-gun, Okinawa-ken Japan 904-0495 Phone: 098-982-3584 Cell: 080-4154-9504 Email: steven.aird(a)oist.jp<mailto:steven.aird@oist.jp>

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Color clip plane
by Reza Khayat 15 Jun '18

15 Jun '18

Hi, I'm coloring a cryo-EM image reconstruction based on its local resolution. Thus, the image reconstruction will contain multiple colors. Is it possible to color the clipping plane the same as the underlying image reconstruction? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

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Deactivate model
by Reza Khayat 12 Jun '18

12 Jun '18

?Hi, Is it possible to deactivate a model like in Chimera? I wan to manually align a cryo-EM image reconstruction to another before using the fit command. The orientations are too different for fit to work. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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naming chain ids
by Andrew Macrae 06 Jun '18

06 Jun '18

To whom it concerns I am wondering if it is possible to change the names of the models in chimera X in a similar manner that was possible in chimera. When I split a large complex such as the ribosome it is nice to rename them so I don't need to memorize or reference the PDB what all the numbers and or letters mean. Thanks Cheers, Andrew MacRae

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can now bundle user documentation with ChimeraX bundles
by Greg Couch 30 May '18

30 May '18

Starting with the next daily build, it is possible to have documentation for the tools and commands in the bundle automatically integrated into the User's Manual index. In the bundle_info.xml file, add the documentation to the DataFiles section, e.g.: <DataFiles> <DataFile>docs/user/commands/tutorial.html</DataFile> <DataFile>docs/user/tools/Tutorial_GUI.html</DataFile> </DataFiles> As you can see above, the documentation is in a directory hierarchy that matches the hierarchy of the builtin documentation. The file name for the tool should be the tool's name with underscore's replacing any spaces followed by .html. The file name for commands should be the the first word in the command name followed by .html. If help is asked for a subcommand, then a named reference is made to the subcommand, i.e., /command/.html#/subcommand/. -- Greg

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Re: [chimerax-users] Question about Space navigator and ChimeraX
by Tom Goddard 29 May '18

29 May '18

Hi Rod, I just tried SpaceNavigator with the May 29, 2018 ChimeraX build on macOS 10.13.4 and it worked. Are you still getting the error that it cannot load _spacenavigator? Are you trying to use it on Mac or Windows or Linux? And does space navigator work with Chimera on that same machine? Tom > On May 29, 2018, at 12:17 PM, Tweten, Rodney K. (HSC) wrote: > > Hi Tom, > I downloaded the latest ChimeraX daily build (2018-05-29 02:45:16 PDT), but the space navigator still does not appear not work. Was it included in this build? Thanks! > > From: Tom Goddard <goddard(a)sonic.net> > Date: Friday, May 25, 2018 at 4:33 PM > To: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Cc: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > Subject: [EXTERNAL] Re: [chimerax-users] Question about Space navigator and ChimeraX > > Hi Rod, > > Our Mac ChimeraX build machine did not have the Space Navigator library installed so it did not compile the module to use Space Navigator with ChimeraX. I've installed it on the build machine so hopefully tonight's build will have Space Navigator support. It works on my development machine. Thanks for reporting the problem. > > Tom > > > >> On May 25, 2018, at 11:02 AM, Tweten, Rodney K. (HSC) wrote: >> >> I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! >> >> <image001.png> >> >> Cheers, >> Rod Tweten, Ph.D. >> George Lynn Cross Professor >> "It's a great life if you don't weaken" >> >> Microbiology & Immunology >> BMSB-1053 >> 940 Stanton L. Young Blvd. >> The University of Oklahoma Health Sciences Center >> Oklahoma City OK 73104 >> USA >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mail…>

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Question about Space navigator and ChimeraX
by Tweten, Rodney K. (HSC) 25 May '18

25 May '18

I have been using Chimera for some time and like it very much so I thought I would try ChimeraX, which has an undo button! However, I am unable to get the Space navigator to work with chimeraX. I keep getting that it can’t load space navigator (see attached screenshot). Can you tell me if I am doing something wrong here (likely) or if the use of the Space Navigator is not implemented yet. Thanks! [cid:image001.png@01D3F428.99CAA4A0] Cheers, Rod Tweten, Ph.D. George Lynn Cross Professor "It's a great life if you don't weaken" Microbiology & Immunology BMSB-1053 940 Stanton L. Young Blvd. The University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA Work phone: 405 271-1205 FAX: 405 271-3117 Skype: toxlab1 Email: rod-tweten(a)ouhsc.edu

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info selection
by Wei Wang 14 May '18

14 May '18

Hello, After using ctrl-left click to select an atom, I use “info selection” as instructed in the manual. However I received the following error message: TypeError: 'str' object is not callable File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/list_info/util.py", line 50, in spec return o.atomspec() See log for complete Python traceback. If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. If I use “info selection atom” then: info selection <help:user/commands/info.html#selection> atom Expected a keyword What am I doing wrong with? Please advice. Best, Wei

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setattr m stickScale
by Wei Wang 14 May '18

14 May '18

Hello, I’m switching from Chimera1. I used to have “setattr m stickScale 0.6” to make whole stick representation “thinner”. Now in ChimeraX “stickScale” seems not available. Using “size stickRadius” looks similar to “setattr b radius” in Chimera1, but in this case the solvents radius are not changed. Is there a method to set all stick representation in the same arbitrary scale? Many thanks Wei

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How to import chimera session to chimeraX
by Liz Kellogg 03 May '18

03 May '18

Hi all I love the graphics in chimera X, and I would like to render a scene I've set up in chimera. However, chimeraX doesn't seem to be able to open chimera session files. I tried exporting the chimera scene to different file format, such as vtk or wrl, but chimeraX can't seem to open those files either. Is there any way to open chimera sessions in chimeraX? Thanks a lot Liz

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Re: [chimerax-users] spin movie error
by Sven Lange (PG Research) 02 May '18

02 May '18

Hi, I ran into the same error (related to _clock_gettime) today on macos 10.11, but found a workaround. I build ffmpeg using homebrew (brew -v install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265) and then replaced the ChimeraX.app/Contents/bin/ffmpeg with the homebrew ffmpeg. Movies encoding now works in ChimeraX on my macos 10.11. Best wishes Sven The University of Dundee is a registered Scottish Charity, No: SC015096

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mutitouch mac
by Edoardo Gianni 01 May '18

01 May '18

Hello, I was wondering if multitouch was available on chimerax for mac, or if you had plans to implement it in the future. Thanks and best wishes, Edoardo

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Change the size of the model
by Shuto Araki 01 May '18

01 May '18

Dear Chimera X developers, I am trying to create a VR protein tour video by using the movie command. There is no problem and it works perfectly fine, but I was wondering if I could change the size of molecule models themselves so that, when the camera is inside a model, I can look around the inner structure of the model with the surface further placed. Right now, the model is so small that the surface feels too close to the camera when it is inside the model. Is it possible to change the size of a model with the coordinate being fixed? Thanks, Shuto

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Equivalent of surface colour by radius in tools/Volume viewer of Chimera
by Shabih Shakeel 17 Apr '18

17 Apr '18

Hi, In ChimeraX, is there an equivalent of surface colour by radius in tools/Volume viewer of Chimera? I would like to colour an EM density map of a virus from its centre to the outside of the capsid with direct colour range in ChimeraX. Thanks. Regards, Shabih

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Re: [chimerax-users] [Chimera-users] ConSurf script on ChimeraX
by Eric Pettersen 10 Apr '18

10 Apr '18

Hi Fabian, As a stopgap, you can color by bfactor by using a script I’ve attached. I’m attaching two scripts, one a generic color-by-bfactor that can be used for anything in the bfactor column. You would edit the values at the top of the script to choose low-high coloring or low-mid-high coloring, and what values to associate to what colors. The other script is tailored to ConSurf output in that it knows the nine ConSurf colors and colors only those residues whose bfactors are all equal and are integers in the range 1-9. You just open the ConSurf-generated PDB and then open the script (which runs it). I’ve attached an example output image (2gbp). —Eric > On Apr 10, 2018, at 12:26 AM, Fabian Glaser <fabian.glaser(a)gmail.com> wrote: > > Dear Eric, > > Thanks for your detail answer, so maybe the only thing it will be really useful now is to be able to color the residues with consurf colors in ChimeraX, with that I will be able to make figures for a paper, which is what I am after at this point. > > Of course we would be very happy to get a script for ChimeraX at some point that could be included in our output pages. > > Best, > > Fabian > > Fabian Glaser PhD > > Head of the Structural Bioinformatics section > Bioinformatics Knowledge Unit - BKU > The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering > Technion - Israel Institute of Technology, Haifa, Israel > Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> > Tel +972 (0) 4 8293701 > > >> On 10 Apr 2018, at 1:59, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> >> Hi Fabian, >> ChimeraX is not backwards compatible with Chimera, so a Chimera session file cannot be opened in ChimeraX — such as what you tried to do below. We want to add a tool to Chimera that will write out a file that ChimeraX can read to restore the Chimera session as best it can, but we haven’t gotten there yet. >> Furthermore, although ChimeraX can display sequence alignments, its capabilities in that regard are currently much less than what Chimera offers. The features it lacks that ConSurf uses are: >> >> 1) Read Clustal ALN alignments >> 2) Show alignment headers >> 2b) Make header values available as residue attributes >> 3) Show Phylogeny trees >> 4) Color alignment/structures from coloring file >> >> To show ConSurf results in even bare bones form would require #1 and #4, and obviously #2 and #3 add a lot of value. So I’d say ChimeraX is not “ConSurf ready” yet. What I will do is open an “enhancement request” ticket in our bug database with you on the recipient list. As the above features get added I will update the ticket and at whatever point you feel it’s worthwhile you could work on getting ConSurf to deliver ChimeraX results. I would help with any questions or issues that popped up. Sorry I don’t have better news. >> >> —Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >>> On Apr 8, 2018, at 7:56 AM, Fabian Glaser <fabian.glaser(a)gmail.com <mailto:fabian.glaser@gmail.com>> wrote: >>> >>> Hi, >>> >>> I would like to use Chimera ConSurf scripts in ChimeraX, but I get the following error when I try to run the script on ChimeraX >>> >>> ModuleNotFoundError: No module named 'cPickle' >>> >>> File "consurf_final_zn.py", line 1, in >>> >>> See log for complete Python traceback. >>> >>> If you wish to report this error, send mail to chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created. >>> >>> Is this something that can be fixed or updated? >>> >>> More generally I would like to update ConSurf with a version of the script for ChimeraX, can you help me with that? >>> >>> Here is the beginning of the original chimera script >>> >>> import cPickle, base64 >>> try: >>> from SimpleSession.versions.v65 import beginRestore,\ >>> registerAfterModelsCB, reportRestoreError, checkVersion >>> except ImportError: >>> from chimera import UserError >>> raise UserError('Cannot open session that was saved in a' >>> ' newer version of Chimera; update your version') >>> checkVersion([1, 12, 41623]) >>> import chimera >>> from chimera import replyobj >>> replyobj.status('Restoring session...', \ >>> blankAfter=0) >>> replyobj.status('Beginning session restore...', \ >>> blankAfter=0, secondary=True) >>> beginRestore() >>> >>> def restoreCoreModels(): >>> from SimpleSession.versions.v65 import init, restoreViewer, \ >>> restoreMolecules, restoreColors, restoreSurfaces, \ >>> restoreVRML, restorePseudoBondGroups, restoreModelAssociations >>> molInfo = >>> >>> Thanks a lot, >>> >>> Best, >>> >>> Fabian >>> >>> Fabian Glaser PhD >>> >>> Head of the Structural Bioinformatics section >>> Bioinformatics Knowledge Unit - BKU >>> The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering >>> Technion - Israel Institute of Technology, Haifa, Israel >>> Web http://bku.technion.ac.il/ <http://bku.technion.ac.il/> >>> Tel +972 (0) 4 8293701 >>> _______________________________________________ >>> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> >>> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> >> >

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Re: [chimerax-users] [Chimera-users] CjimeraX PDB save
by Eric Pettersen 02 Apr '18

02 Apr '18

Hi John, The PDB format only supports single-character chain IDs (one of the reasons for mmCIF format), so it is impossible to save structures with more than 36 chains in PDB format without losing chain information. A semi-workaround is to: 1) In ChimeraX: split the structure into multiple structures, one per chain (“split #1”) 2) Save those models into a multi-MODEL PDB file (“save ~/rib.pdb models #1”) 3) Read them into Chimera. 4) If there are <= 36 models, combine them into a single model (“combine” button of the Model Panel), otherwise you just have to work with them as separate models. —Eric Eric Pettersen UCSF Computer Graphics Lab > On Apr 2, 2018, at 2:29 PM, John Mercer, Ph.D. <jmercer(a)duke.edu> wrote: > > Hi Elaine, > > I load a ribosome mmcif file in ChimeraX and save it at as a PDB file. It loads and works fine in Chimera but all the chain identifiers have disappeared. Is there away to save a PDB file from ChimeraX that retains the identifiers? I am wanting to use the larger set of tools in Chimera when only mmcif files are available. > > Best, > -John > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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morph and surfaces
by Giorgio Luciano 02 Apr '18

02 Apr '18

Hello ! I was looking at the script for morphing among structures that can be found here http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html (*coordset #1 1,161). * I've tried to use the surfacecat command in the script in order to obtain a morph through volumes since my idea was to create the movie and then export all the surface perframe in order to use them in another 3d software. I've seen that surfcat can actually create volumes for all the surfaces included in the 1r7w but morph start does not seems to work among the surface created. I've seen also that it could be a solution to create density maps from the surface and them morph them using volume viewer but it seem quite an awkard solution (at least for me that I'm no expert :) I've tried to find the limitation of morph command but it does not report anything regarding surfaces. Any help is very appreciated. Sorry for the cross-posting

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I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by JEAN-YVES SGRO 29 Mar '18

29 Mar '18

Greetings, thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html which are useful and one can reconstruct the initial display. As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. Simply pressing the "Show atoms" button will display all water molecules as small spheres. But now if I click "Hide atoms" only the ribbon is left. Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html> but that was not the best solution. Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: show ions show ligand select ligand:<3.8 & protein show selAtoms For novices this is a bit complicated to understand. Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. I firmly believe that this would avoid lots of frustration for many new users! P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? Sincerely, Jean-Yves Sgro

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Export as .obj
by Boris Chaumette 28 Mar '18

28 Mar '18

Dear colleagues, I am currently using ChimeraX and would like to save my file as a .obj I tried the following command line: save "ATPtest.obj" obj But model is expected. I don't understand how I can specify it to incorporate the whole figure. Thank you, Best, Boris Chaumette MD/PhD - postdoctoral researcher Laboratory of Guy A. Rouleau Montreal Neurological Institute McGill University Irving Ludmer Building 1033, Pine av. Room: 327 Montréal, Québec, H3A 1A1 Phone: +1 514-398-6821

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Matrixset equivalent
by Reza Khayat 15 Mar '18

15 Mar '18

Hi, Is there a matrixset (from Chimera) equivalent for ChimeraX? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

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VR mode not working
by Sebastian Poelsterl 13 Mar '18

13 Mar '18

Hi, I'm trying to view a PDB structure (2fha) in vr mode, but get the following error after executing 'vr on': An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\updateloop.py", line 61, in draw_new_frame view.draw(check_for_changes = False) File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\view.py", line 178, in draw r.draw_background() File "C:\Program Files\ChimeraX-0.5\bin\lib\site-packages\chimerax\core\graphics\opengl.py", line 677, in draw_background GL.glClear(flags) File "zr\accelerate\src\errorchecker.pyx", line 53, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError (src\errorchecker.c:1270) OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glClear, cArguments = (16640,) ) I'm using ChimeraX 0.5 with an Oculus Rift (1.24.0.545657), NVIDIA GeForce GTX 1060 (driver version 391.01) and SteamVR Version 2018-02-10 (1518226924) under Windows 10 (10.0.0.14393). Any suggestions would be appreciated. Thank you. Sebastian The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

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Some core modules moving
by Eric Pettersen 07 Mar '18

07 Mar '18

Hi all, In the interest of making ChimeraX’s core smaller and less likely to need frequent updating (since it can’t be updated incrementally via the ToolShed), we will be moving some modules out of the core and into bundles, so those at least will be individually updatable via the ToolShed. Those core modules are atomic, map, surface, and ui. As of tomorrow’s daily build, you can and should use the the new import paths for these modules (e.g. from chimera.atomic import Atom rather than from chimerax.core.atomic import Atom). Old-style imports will continue to work for several months at least, at which time a warning will be raised if the import is still in use (but the import will work). Probably several months after that we will disable the old-style imports. One further note is that the MainToolWindow class can now be imported directly from the ui module, rather than from its gui submodule, so: from chimerax.ui import MainToolWindow is preferred over: from chimerax.ui.gui import MainToolWindow —Eric Eric Pettersen UCSF Computer Graphics Lab

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Surfaces & color by attribute
by Hernando J Sosa 06 Mar '18

06 Mar '18

Dear ChimeraX Is it possible to color a surface by atom/residue attribute (hydrohobicity, charge)? I know it is possible to do it in ucsf-chimera but unfortunately surface calculation does not work in chimera for the files I am working on. Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa(a)einstein.yu.edu<mailto:hernando.sosa@einstein.yu.edu>

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Cororing by B-factor
by Rajiv G Govindaraj 23 Feb '18

23 Feb '18

Hello, I am NOT able find the coloring atoms by bfactor in ChimeraX. I have a b-factor values range from negative to positive, and wants to color them from min to max(blue to red) as normal bfactor colors. Appreciated if you could tell me how it can be done in ribbons and surface using ChimeraX? Thank you. Regards, RJ

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ChimeraX user guide display issue
by Jerry Honts 19 Feb '18

19 Feb '18

Unlinked and linked text is *invisible* in user guide (and elsewhere in interface) because font color is *white* on white background. The apparently invisible text can be selected and displayed after copy and paste to another text field. Hyperlink underlines remain visible. Is this a CSS style sheet problem? Jerry E. Honts -- Jerry E. Honts, Ph. D. Associate Professor of Biology Drake University 2507 University Avenue Olin Hall 324 (office)

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open local pdb files "containing no atoms and bonds"
by Fekete Attila 15 Feb '18

15 Feb '18

Dear Colleagues, I have tried to open several local *.pdb files, but in each case I got the error: "Opened PDB data containing 0 atoms, 0 bonds and 0 coordinate sets", and a series of warnings (for each lines of the files) and ChimeraX doesn't show the structure. I have also tried different versions of ChimeraX (0.1/0.5 and even alpha releases, recently I'm using 0.5 under Ubuntu 16.04). I can open any online files (*pdb,*mmCIF) from the RCSB database, however if I download the same file, I got the above mentioned error message, so I have absolutely no clue to resolve the problem because I suppose this isn't related to pdb format issues but a bug can be somewhere in the softwere. I am really impressed by the visualization capabilities of ChimeraX so please help me if you can. Yours, Attila

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ChimeraX surface coloring
by Nadishka Jayawardena 14 Feb '18

14 Feb '18

Hi there, I recently installed ChimeraX and been trying to figure out a way to colour a cryo-EM map by radius- however, I couldn't find a way to get this done? Is this feature not implemented on ChimeraX as yet? Is there a way to colour the map by using a python script? Many thanks Nadishka P.S. Must say that this new version is a huge improvement!

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spin movie error
by Andrey Feklistov 05 Feb '18

05 Feb '18

Dear chimera X developers, upon trying to record a spin movie with a corresponding button I get an error: dyld: Symbol not found: _clock_gettime,Referenced from: /Volumes/ChimeraXInstaller 2/ChimeraX.app/Contents/bin/ffmpeg,Expected in: /usr/lib/libSystem.B.dylib Typing the command manually results in the same error. I remember that the feature used to work when I first tested ChimeraX last year. Thanks for any advice.. Andrey

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2dimage?
by Emmott, Ed 31 Jan '18

31 Jan '18

Hi, Is there (or likely to be in future) a 2d image feature, allowing you to overlay 2d graphics (.tif, .png) in the same way as the 2dlabel command (e.g. Xpos Ypos )? My use case is wanting to add additional 2d graphics (e.g. color bar or graphs) over a pdb structure prior to rendering images/generating movies. Whilst I can get ChimeraX to open the images easily e.g. (open "...test.tif"), they are acquiring edges (white background image on white background scene -> grey borders) I assume as a result of being interpreted as a 3d object. Otherwise loving the software! Thanks a lot, Ed Using ChimeraX build v0.5 (2018-01-12) Dr Edward Emmott Research Associate Slavov Lab Northeastern University 332 Mugar, 360 Huntington Ave. Boston, MA.

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