- ChimeraX-users - RBVI Mailing Lists

Identifying symmetry of a model
by Y. Mutum 06 Feb '21

06 Feb '21

Hi I am working with pdb id: 3cx5. This model is roughly C2 symmetric. Is there a way to identify the symmetry (or rough symmetry of a not-so symmetric model) of a pdb/ mmcif model and orient the symmetry axis to the axis perpendicular to the screen? On a similar note, say we select a 4 somewhat symmetry-related residues in this model and make 2 intersecting lines, is there a way to align these lines perpendicular to the perpendicular screen axis? Thanks Yaikhomba

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error when using Blast Protein
by Elghobashi-Meinhardt, Nadia 05 Feb '21

05 Feb '21

Dear ChimeraX forum, I am trying to do a sequence search with the Blast Protein tool (MacOS). I have tried using various pdb structures/chains but am repeatedly getting the following error: "ValueError: not enough values to unpack (expected 2, got 1)" from ".../blastprotein/pdbinfo.py", line 206, in fetch_info entry, auth_cid = pcid.split('_') What is the correct usage of Blast Protein? Thank you! Nadia

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ChimeraX tool installationg
by Yongcheng MU 04 Feb '21

04 Feb '21

Hello, Hope you are doing well. This is Yongcheng. I am writing this email because I am trying to install a Deep learning tool in ChimeraX, but I have some issues about it. I built and installed my code following the steps on the Chimera Guide website. I installed my code successfully, but when I run using command that I created, it hold some errors: *"RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:* *cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register* *raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))"* *"During handling of the above exception, another exception occurred:* *Traceback (most recent call last): File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 275, in execute cmd.run(cmd_text) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2746, in run self._find_command_name(final, used_aliases=_used_aliases) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2489, in _find_command_name what.lazy_register(cmd_name) File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))RuntimeError: delayed command registration for 'CL_Tensorflow' failed (register_command() failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2142, in lazy_register* *raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e))"* I wonder if you know what's going on here, and how to fix it. Thank you so much for your time. Best regards, Yongcheng

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Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by Elaine Meng 03 Feb '21

03 Feb '21

Hi Yeping, **Please send ChimeraX questions to the chimerax-users(a)cgl.ucsf.edu address, *not* to chimera-users(a)cgl.ucsf.edu, because that makes people confused about which program we are talking about. Two more thoughts about your file: (1) you need to make sure the residue numbers in the file all match to your structure. I don't know which structure you are using so when I test it on some other structure that doesn't have all the same residue numbers, it does not work unless I change the match mode from "1-to-1" to "any". You might want to try using match mode "any". (2) looks like one residue has a high value 0.788 and all the others are very close to zero, so when I color the whole range the structure is all the same color (used for the low end) except for the one high-value residue. E.g. coloring by attribute entropy using palette blue-white-red makes the whole structure blue except for one residue red. Elaine > On Jan 27, 2021, at 8:25 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Sun Yeping, > To use the "open" command to open defattr format you need ChimeraX daily build from Oct 30, 2020 or newer. Or if you are using ChimeraX 1.1, you can use the "defattr" command to open the file. Older ChimeraX than version 1.1 cannot read this file type at all. Changes and approximate dates are given in the Change Log: > > <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> > > The format is described here: > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jan 27, 2021, at 1:04 AM, sunyeping <sunyeping(a)aliyun.com> wrote: >> >> Dear Elaine, >> >> Thank you for your reply. The attribute file entropy.txt is available at >> >> https://drive.google.com/file/d/1oG0O4zKqw-uD5SeLTrAu16c3Jh8m3LG5/view?usp=… >> >> Could you please help check whether the format is correct"? >> >> I cannot figure out how to open this attribure file in chimera. When I input "open entropy.txt format defattr" in chimerax, I get the following error message: >> >> Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc' >> >> Could you tell me what is the correct way to open the file? >> >> Thank you, >> Best, >> Yeping >> ------------------------------------------------------------------ >> From:孙业平 <sunyeping(a)aliyun.com> >> Send Time:2021年1月26日(星期二) 11:53 >> To:chimera-users <chimera-users(a)cgl.ucsf.edu> >> Subject:[Chimera-users] how to color an model by an attribute in chimerax >> >> Dear all, >> >> I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: >> >> attribute: entropy >> match mode: 1-to-1 >> recipient: residues >> :1 0.0 >> :2 0.0014948 >> :3 0.0090952 >> :4 0.0004805 >> :5 0.1102497 >> :6 0.0095258 >> :7 0.0008226 >> :8 0.0042205 >> :9 0.0037255 >> :10 0.0006678 >> :11 0.0027988 >> :12 0.0193925 >> :13 0.0153925 >> :14 0.0052115 >> :15 0.0020136 >> .......... >> >> However, when I input the command "color byattr attr.txt", I get the following error information: >> "No known/Registered attribute attr.txt" >> >> Could anyone tell me what is the correct way to do this? >> >> With many thanks. >> >> Best regards >> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Reading cube file from Quantum Espresso pp.x
by Zack Gainsforth 02 Feb '21

02 Feb '21

Hi, I produced some projected wavefunctions in a crystal that I'm working with using Quantum Espresso (DFT). I output these projections to a gaussian cube file using the pp.x program (built into Quantum Espresso). I'm able to read these into ChimeraX but I'm unable to see the atoms -- only the volumetric data. I tried Actions - Atoms/Bonds - Show, but I still don't see the atoms. Is there another step I should take to make them visible? I see something like this: (very nice!) I'm attaching a link to the cube file below -- I can't include it because it is 600 MB. Thanks, Zack https://www.dropbox.com/s/ehhli8h3qr7vd4y/wfc_k001_b329wfc.cube?dl=0

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mapping out water channels in chimerax
by Noor Agip 29 Jan '21

29 Jan '21

Hi, I am working on a membrane protein, and I am trying to map out water channels (responsible for proton conduction from one side of the membrane to another). I am currently doing this manually from one connecting water molecule to the next using the structural analysis/H-bond function. Is there an easier way to do this with 14 linked water/residues? Best wishes, Noor

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Labeling canine Apolipoprotein A-I
by Moradkhan, Tiglath A 29 Jan '21

29 Jan '21

Hi I'm trying to model the N-terminus of mature canine Apolipoprotein A-I using Chimera. However the actual sequence in uniprot is not that of the mature protein. Here is the sequence: MKAALLTLAVLFLTGSQARHFWQQDEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG LLPVLESFKVSLLAAIDEATKKLNAQ The sequence of the mature form is: DEPQSPWDRVKDLATVYVDAVKDSGRDYVAQFEASA LGKQLNLKLLDNWDSLSSTVTKLREQIGPVTQEFWDNLEKETEVLRQEMSKDLEEVKQKV QPYLDDFQKKWQEEVELYRQKVAPLGSELREGARQKLQELQEKLSPLAEELRDRARTHVD ALRAQLAPYSDDLRERLAARLEALKEGGGASLAEYHARASEQLSALGEKARPALEDLRQG LLPVLESFKVSLLAAIDEATKKLNAQ According to how the sequence is labeled in uniprot the first aspartate residue of mature canine Apolipoprotein A-I starts at position 25, and this what Chimera uses. However, for the mature protein this should start at position 1. How can I change the numbering system so the first aspartate residue starts at position 1? I would be very glad for your advice. Thank you. Tiglath

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Copy/combine function in ChimeraX
by Zhang, Rui 26 Jan '21

26 Jan '21

Hi, Is Copy/combine function still not available in ChimeraX? This is the command that I use on daily basis in Chimera. Thanks! Rui Zhang Washington University in St. Louis

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Re: [chimerax-users] [Chimera-users] how to color an model by an attribute in chimerax
by Elaine Meng 26 Jan '21

26 Jan '21

On Jan 25, 2021, at 7:47 PM, sunyeping <sunyeping(a)aliyun.com> wrote: > > Dear all, > I wish to color an model by an attribute in chimerax. The attribute is the entropy which is calculted by an external software. I wrote the entropy values of each residue in a text file (attr.txt) like the following: > > attribute: entropy > match mode: 1-to-1 > recipient: residues > :1 0.0 > :2 0.0014948 > :3 0.0090952 > :4 0.0004805 > :5 0.1102497 > :6 0.0095258 > :7 0.0008226 > :8 0.0042205 > :9 0.0037255 > :10 0.0006678 > :11 0.0027988 > :12 0.0193925 > :13 0.0153925 > :14 0.0052115 > :15 0.0020136 > .......... > However, when I input the command "color byattr attr.txt", I get the following error information: > "No known/Registered attribute attr.txt" > > Could anyone tell me what is the correct way to do this? > With many thanks. > Best regards Hello, Since this is a ChimeraX question, better to send to the chimerax-users(a)cgl.ucsf.edu address CC'd here instead of the chimera-users list. (1) First you need to make sure the text file is the right format. It should be tabs (not just a space) before the residue number and between the residue number and the value, e.g. as described here: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html> (2) Then (after the atomic structure is open), open the attribute file with the "open" command, e.g. with pathname of your file, or if you want use a file browser window to find the file, "open browse". It is easiest to first name the file ending in .defattr so that ChimeraX will know what kind of file it is supposed to be. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#defattr> (3) then the Log should report that the attribute named entropy is assigned and you are ready to do the coloring. The coloring command could be something like color byattribute entropy palette rainbow ...there are several other options, see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: [chimerax-users] windows 10 GPU acceleration?
by Tom Goddard 24 Jan '21

24 Jan '21

Hi Chuck, Glad you figured it out. I wonder what that graphics scheduling option is doing. Tom > On Jan 24, 2021, at 3:36 PM, Sindelar, Charles <charles.sindelar(a)yale.edu> wrote: > > Hey, I figured it out! There is some kind of new windows option called hardware-accelerated graphics scheduling, in the graphics settings->change default graphics settings control panel. I turned it off, and boom- ChimeraX started using the Nvidia. Thanks for the pointers- definitely helped me guess the solution. Maybe this will help someone else… cheers! > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Sunday, January 24, 2021 2:38 PM > To: Sindelar, Charles <charles.sindelar(a)yale.edu> > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] windows 10 GPU acceleration? > > Hi Chuck! > > Yes ChimeraX and Chimera should both be using your laptop Nvidia 2080 GPU and not the Intel graphics. Chimera(X) does not choose the GPU and does not even know that there is more than one -- nothing in the OpenGL graphics library gives that information. It is up to the Windows operating system to decide what GPU used, and it usually makes the right choice. There is in fact a flag in ChimeraX that tells Windows it should use the Nvidia GPU if available. > > You can see for certain which GPU is being used in Chimera with the command > > graphics driver > > Here's what it reports in the log on my laptop > > OpenGL version: 4.1 ATI-3.10.18 > OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine > OpenGL vendor: ATI Technologies Inc. > > Yours should either save Nvidia or Intel in the output. It may say Nvidia but your 2080 GPU use does not seem to get much use. The GPU will only be used when the graphics are changing -- for instance, use the command "roll" to set the models in motion (and command "stop" to halt them). Even when the graphics is constantly changing if your model is small and lighting mode is simple, it will probably show the GPU is hardly working. Use "full" or "soft" lighting to get ambient shadows and that should load the GPU some ("lighting full", or "lighting soft"). > > The high performance graphics mode you set in Windows should certainly make the Nvidia GPU get chosen. > > If ChimeraX "graphics driver" says the Intel GPU is being used then something is clearly messed up. But it must have something to do with your Windows and graphics driver configuration. In fact are you sure you have a working Niovida graphics driver installed? Are there any other apps you use where you see the Nvidia GPU in use? > > Tom > > > > > On Jan 24, 2021, at 10:09 AM, Sindelar, Charles <charles.sindelar(a)yale.edu <mailto:charles.sindelar@yale.edu>> wrote: > > Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. > > I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows “Graphics Settings” control panel for “high performance”, which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. > > Thanks and cheers! - Chuck > _______________________________________________ > ChimeraX-users mailing list > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > Manage subscription: > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl…>

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windows 10 GPU acceleration?
by Sindelar, Charles 24 Jan '21

24 Jan '21

Dear Tom, Elain, Eric et al, happy new year to you and I hope all is well. I was wondering how much GPU acceleration I can hope for with my new Dell XPS 17, for either ChimeraX or Chimera? Right now I am noticing that when I use the programs, all the graphics load goes to my integrated Intel graphics GPU, and frame rates are not impressive. The Nvidia 2080, which should be awesome, sits idling. This is on Windows 10. I tried setting the Windows "Graphics Settings" control panel for "high performance", which should try to make Chimera(X) use the NVidia, as far as I know, but nothing happens. Thanks and cheers! - Chuck

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CastP surfaces in ChimeraX/ Chimera
by Y. Mutum 20 Jan '21

20 Jan '21

Hi Is there a way to open the results from CastP results in 'ChimeraX' and visualise the surfaces calculated using CastP? In this case, the pdb is 3cx5, and the surfaces are calculated from CastP webserver. Just on using Chimera (version 1.15c) - I have also tried to open the CastP results using 'Chimera', but the molecular surfaces display are failing (picture attached). I followed up the abberant surface-calculation problems in https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html. However, the display surfaces are all still failing - I tried the first 2 suggestions relevant to mine, but they are still failing. The first - which involves splitting the chain using the command 'split', shuts down the Castp: surfaces-window in Chimera and I can't see of a way to retrieve this CastP window with the list of surfaces. As, I do not want to split the model, I tried the second suggestion of 'surfcat one' (as CastP server selects atoms from multiple chains to create surfaces). I am not sure if I want to mess up with the Vanderwaal radii (the third suggestion) either, as these surfaces were calculated in CastP with a specific probe radius. Would you have any suggestions of how to use ChimeraX to open and analyse molecular surfaces calculated by CastP? Last, but not the least, if suppose you have to end up using Chimera if ChimeraX doesn't support .poc files, could you please suggest this work-around for opening these problematic CastP-calculated-surfaces in Chimera? Thanks Yaikhomba [cid:8c139fcc-51aa-496c-9f20-9c01badbbe12]

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Re: [chimerax-users] video of digestion kinetics
by Elaine Meng 18 Jan '21

18 Jan '21

Hi Tynan, Besides abruptly hiding atoms and bonds, you could fade them in or out over time (spread hiding across multiple movie frames), or don't hide them but select them (shown as green outline), or color them differently, or show them with different styling like fatter or thinner sticks, etc. These are all things you can do with the commands of either program, normal stuff that people frequently do when making figures or movies. Or instead of (or in addition to) changing how the peptide is shown, you could show a 2D label that is an arrow pointing to the cleavage point (see 2dlabels command of either program). Elaine > On Jan 18, 2021, at 12:04 PM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: > > Hi Elaine, > Thank you for the very quick response. The info does help. I was thinking that I might be able to take this approach. And I don't mind learning the command line > > However, I was also wondering if there was a way to highlight the peptide bonds between residues to show the actual cleavage points and what gets added as time goes on. This would be a more accurate representation of my data because some peptides are "lost" due to limitations in mass spec rather than the digestion (a very short peptide might not have been digested, but also wasn't IDed by the instrument). > Thank you! > Tynan > > -------- Forwarded Message -------- > Subject: Re: [chimerax-users] video of digestion kinetics > Date: Mon, 18 Jan 2021 11:47:07 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > To: Tynan A. Becker <tabecker(a)alaska.edu> > CC: chimerax-users(a)cgl.ucsf.edu > > > Hi Tynan, > I'm not sure if you meant to send this to the chimera-users(a)cgl.ucsf.edu list or the chimerax-users(a)cgl.ucsf.edu list. Anyway, using either program, UCSF Chimera or UCSF ChimeraX, in general you would need to make a command file for what happens during the movie. The command file could include hide successive parts of the peptide, i.e. if residues 10-12 get cut off first, hide them, then several steps (movie frames) later hide the next set of residues to get cut off, etc. > > In either program, making a command script would require learning the commands, so you would need to invest some time. In Chimera, however, there is also a graphical interface to movie recording, so if you are able to use the menus instead of commands to get to various states you want in your movie (e.g. with more and more of the peptide hidden), with this Movie Recorder interface you can save them as scenes and place them on a timeline. Still, however, at a minimum it will require learning how to use the menus of Chimera to do all the coloring, styles, 2D labels etc. that you want in your movie. > ChimeraX "making movies" page: > <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> > > Chimera "making movies" page: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> > Chimera Movie Recorder tool: > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On Jan 18, 2021, at 10:32 AM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: >> >> Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the cleavage sites that develop sequentially over time in a specific protein as it is digested? >> Thanks, Tynan >

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video of digestion kinetics
by Tynan A. Becker 18 Jan '21

18 Jan '21

Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the */cleavage sites/* that develop sequentially over time in a specific protein as it is digested? Thanks, Tynan

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Black/Dark Theme
by Petrychenko, Valentyn 13 Jan '21

13 Jan '21

Dear ChimeraX Developers Team, Do you have in your features list an dark or black GUI theme? I understand that stylistic features have lover priority than a really useful ones, but during many hours of work every day in ChimeraX white GUI eyes getting tired especially at late hours and especially when it contrasts with dark interface of the rest of the system and other dark themed software. I really looking forward to see a dark theme feature in future updates. Respectfully yours, Valentyn Petrychenko

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Question about the comparative homology modelling tool
by Moradkhan, Tiglath A 12 Jan '21

12 Jan '21

Hi I have two questions about the homology modelling tool: 1. Why is the default number of models to be built five? Does having five models provide a better choice for choosing the best model? 2. In evaluating a protein model which of the following parameters plays a much more dominating role: zDOPE, predicted RMSD or the predicted native overlap? Or do all three measures contribute the same effect on model evaluation? For instance a model might have a low zDOPE score but have a higher RMSD while another model might have a much more positive zDOPE score but a lower RMSD. Based on this, would the first model be the better one to pick or do both models have equal weight in terms of overall model quality? I would be very glad for advice. Thanks Tiglath

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high results tiff
by Fabian Glaser 10 Jan '21

10 Jan '21

Dear experts, I am sorry to bug with this issue again, but I dont’ find a good tutorial or clear instructions about the right way to prepare figures with high quality for publication with chimeraX, and I find myself again and again making them with chimera, since it seems I am able to produce 300 dpi with chimera on tiff for example using the save image dialogue, but on chimeraX I am only able to produce them with 72 dpi using the save command. I have tried all kind of sizes but… well for me it does not work yet. Again, may this is trivial, but I am not an expert in graphics, and if somebody could guide me would be really thankful. Thanks in advance, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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Re: [chimerax-users] Stereo mode error
by Tom Goddard 07 Jan '21

07 Jan '21

Hi J.C., Since Chimera works in stereo and ChimeraX does not I think the problem is almost surely that ChimeraX requires a "core" OpenGL context (ie using modern OpenGL) while Chimera requires a "legacy" OpenGL context. I assume ChimeraX is working for you not in stereo. So it can get a core context, but apparently not a core stereo context. It looks like the Nvidia driver is not providing a core OpenGL stereo context. But Nvidia has clearly stated that it does support this in their 3D Vision FAQ https://nvidia.custhelp.com/app/answers/detail/a_id/4845 "Without 3D Vision, will NVIDIA Quadro GPUs still support OpenGL Quad-buffered Stereo? Absolutely YES. OpenGL Quad-buffered Stereo is not affected by changes to the 3D Vision driver." ChimeraX is asking for quad-buffered stereo core context and "core" contexts are the standard of current OpenGL. So if we believe Nvidia's statement then their driver will give this kind of context. And that suggests that you have a driver configuration setting that prevents it. It is certainly also possible that the Nvidia driver you are using is simply broken in its ability to provide core stereo contexts. But I think it is more likely you have it configured to not give such a context, possibly your X server "Option "Stereo" "10"" setting is the cause. When the Nvidia driver provides a core OpenGL stereo context this does not mean your 3D Vision glasses will work. In fact the above 3D Vision FAQ very clearly says it will not work with a current Nvidia driver unless a separate 3D Vision USB driver is installed. "NVIDIA announced it is no longer supporting 3D Vision. What does this mean? Hardware: NVIDIA is no longer selling the 3D Vision emitters and glasses. Drivers: R418 graphics drivers will be the last driver to contain the 3D Vision driver package. The R418 branch will be supported until January 2020. In addition, NVIDIA will decouple the 3D Vision USB driver from the graphics driver. NVIDIA will provide the 3D Vision USB driver package as a separate installer on NVIDIA.com moving forward - see Quadro Advance Options <https://www.nvidia.com/object/quadro-advance-options.html>. This will allow users to upgrade the graphics driver while continuing to use the standalone 3D Vision USB driver." If this statement from Nvidia is true then the 3D Vision emitter on your computer can only work if you have installed a separate 3D Vision USB driver. If the emitter does not work the screen will show a double image and stereo software like ChimeraX, Chimera and Coot will not complain but you will not see it in stereo through the glasses because the glasses cannot synchronize to the interleaved in time left and right eye images without the infrared emitter. It is possible that that separate 3D Vision USB driver does not work with a core OpenGL context. Kenneth Satyshur has several legacy Nvidia stereo systems and may know how to make ChimeraX work in stereo with 3D Vision. Ultimately, you are trying to use no longer supported hardware. Honestly Nvidia never supported 3D Vision well, and Windows is much more likely to work than Linux. It probably can be made to work with ChimeraX if enough hours are sunk into it, and will certainly be easier if you use old graphics software such as Chimera or Coot which was written based on the legacy OpenGL that 3D Vision originally worked with. Tom > On Jan 7, 2021, at 5:53 AM, Jean-Christophe HAESSIG <haessigj(a)igbmc.fr> wrote: > > Le mardi 05 janvier 2021 à 10:31 -0800, Tom Goddard a écrit : >> Hi Jean-Christophe, > Hi, > > That was a *very* insightful answer, thank you vey much. But at the > same time it's a bit saddening because it sounds like there will be no > way to use ChimeraX fully on this setup. > > My tests indicate that for the time being, 3D Vision still works with > the latest Nvidia driver on Linux. Despite nvidias decision to retire > 3D Vision, it only means they will stop producing shutter glasses. The > following FAQ entry makes that a little clearer : > https://nvidia.custhelp.com/app/answers/detail/a_id/4845 > Still, that doesn't explain how standard OpenGL calls would not be > supported on a recent driver. Maybe using 'Option "Stereo" "10"' in X > selects an alternate code path where only legacy contexts are > available. On the other hand, it seems this is the only way to get the > glasses to work. In fact, I tried every single stereo mode of the > nvidia driver, and all of them except one gave the same results : the > programs using the legacy contexts worked and ChimeraX crashed. > I also tried Chimera and indeed, it works as you suggested. > > In mode 14 (dubbed "Generic Stereo for DP") however, I couldn't get any > of the programs to work. Stereo is reported as disabled in nvidia- > settings but that could simply be beacuse there is no DP screen > attached. Anyway, it sounds more like this mode could support one of > the more recent GL calls. > > I guess I will keep the older 3D vision sets to run coot and chimera, > and seek more recent hardware for chimeraX. > > J.C. Haessig -- systems administrator, IGBMC > >

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Stereo mode error
by Jean-Christophe HAESSIG 05 Jan '21

05 Jan '21

Hi, I'm in charge of software packaging for our users at IGBMC. I'm trying to make stereo mode work since we still have several 3D vision sets. Even if that hardware has been retired, it seems that there isn't a more practical solution to 3D visualization ATM. We are going to test how it goes with a VR headset, but it already seems that not being able to look at anything else while using it will be a hindrance. I found a message on that subject dating back to June 2017, but I get the same errors even with the 0.1alpha2 version which seems to match what would have been current at that time : 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 "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 73, in draw_new_frame view.draw(check_for_changes = False) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/view.py", line 165, in draw self._draw_scene(camera, drawings) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/view.py", line 205, in _draw_scene camera.set_render_target(vnum, r) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/camera.py", line 442, in set_render_target render.set_stereo_buffer(view_num) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/opengl.py", line 1206, in set_stereo_buffer GL.glDrawBuffer(b) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK_RIGHT,) ) The host computer runs ubuntu 20.04 with the latest nvidia drivers (455). ChimeraX is deployed through a singularity container based on ubuntu 18.04. I got glxgears and coot running on the same setup (in 0.8.2 since latest coot also has a known bug in hardware stereo rendering as of now) Can anyone make sense of the error above ? I have a programming background so I can have a look but I have no idea where to start. Thanks, J.C. Haessig -- systems administrator, IGBMC

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VR for DICOM images
by Tom Goddard 04 Jan '21

04 Jan '21

H Gabriel, I am glad you were able to get ChimeraX to work with the Oculus Rift to look at DICOM images. I think this could be a useful feature but it has a long ways to go. ChimeraX is primarily used for molecular visualization, electron microscopy, and 3d light microscopy. The DICOM medical imaging capabilities have had very little development. As you found out the "volume appearance" settings are almost all useless. That was a first try to borrow some image rendering settings from other software that is designed for medical imaging data, but as you saw it does not look good at all. The trouble is that the ChimeraX volumetric rendering is different than other medical imaging software and I have not had enough time to figure out the differences. I have not looked at Invesalius -- thanks for that suggestion. Although some of the volume appearance presets have the brightness curve as a horizontal line, they use different transparencies and colors along that horizontal line. Still I am not surprised that they don't work right. They probably should not have been added to ChimeraX because they are not working correctly. If you can figure out useful presets in Hounsfield units by manually adjusting the curve in ChimeraX Volume Viewer and setting colors for each node, I could add your specific presets to ChimeraX (and probably take out those old broken presets that were translated from other software). You can add vertices to the brightness curve on the histogram in Volume Viewer by right clicking and choosing menu entry "New Threshold". The color button above the histogram changes the color of the last vertex on the curve that you clicked on. This is easiest not using VR. If you get a useful setting you can use the command "volume settings #1" (if your DICOM model is #1) and it will report all the settings including "image levels" and "image colors" which describe the brightness curve. Those are the values I would need to add a volume appearance preset. Did you see this ChimeraX VR DICOM tutorial? Maybe it has some useful info for understanding the current limited capabilities. https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html> And this documentation page on ChimeraX DICOM page summarizes the features (not specific to VR). https://www.rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html I agree with you that there is great potential for VR for medical imaging. It will take years of software improvement to make it work reasonably well, and since it is far from our primary audience for ChimeraX I cannot promise it will ever get those improvements. Tom > On Jan 4, 2021, at 12:31 PM, Biomodelos 3D <unidadbiomodelos3d(a)gmail.com> wrote: > > Tom, thanks for your answer, I finally was able to use ChimeraX with Oculus Rift and it's absolutely amazing!. (I may have issues with some USB contacts in my notebook, don't know really). > My first concern is about DICOM images, as we produce Biomodels (VR, AR and 3D printed). I've been playing with ChimeraX Volume Viewer and Oculus. I found a lot of advantages to accelerate and improve our workflow for VR Biomodels and online demonstrations, I'd like to share: > -We can enter a VR environment immediately, no need of complex segmentation and post processing. This is really fast! and allows us to face emergency cases (usually our job can't face emergencies). > -We can directly measure in 3D and see those measures in real time. > -Doctors can have a much more realistic sense of the problem, in a much faster way, and relate it to different tissue densities. > -Working in VR over original dicom images, many dimensional errors are avoided (any segmentation process implies dimensional errors). > -Also, interpretation errors (biomodelist's most important problems) are avoided, as doctors can see the study in VR by themselves, over an unaltered set of dicom images. > So I think ChimeraX VR capabilities are a complete game changer for doctors and surgeons. > > Beside, I have some questions: > I created a .txt to load a buttonpanel having Volume Appearances Presets (file attached). It works really fine, but I noticed some issues: > Black & White does not work > Glossy II and Glossy have all points over an horizontal line > High Contrast and Low Contrast have no difference (and have all points over an horizontal line) > Pencil does not work > Soft Skin II and Soft Skin III are the same > Soft on Blue and Soft on White have no difference (and all points over an horizontal line) > Appearances Presets look pretty different in ChimeraX compared to other Dicom Viewer software, can it be improved? > We use Invesalius, an open source brazilian software, as our mainstream workflow to produce volumetric renderings and .stl or .obj surfaces from dicom images. Unfortunately, it has no real time VR or AR tools. But is really good in Volumetric Rendering and segmentation of surfaces based in Hounsfield scale thresholds. So I wonder if some kind of knowledge-interchange may be useful for both developments? Please let me know if you think so. > > Thanks again! > > Gabriel Massano > Biomodelos 3D, Hospital de Ninos, Córdoba, Argentina > www.biomodelos3d.com.ar <http://www.biomodelos3d.com.ar/> > <ChimeraX Volume_Presets.txt>

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Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi Elaine Thank you for the help. I figured out what I was doing wrong. I wasn't using the proper syntax to delete the lipid molecules. Thanks Tiglath

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Bottleneck Large Surfaces
by Anderson, Jacob 04 Jan '21

04 Jan '21

With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay? ~jacob

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Sequence viewer Background color
by Y. Mutum 02 Jan '21

02 Jan '21

Hi This is a quick question, which I couldn't find online. I'm using ChimeraX-0.93 and was looking at the sequence of a protein chain. The background of the sequence viewer is black (picture attached) - is there any way to change it to some light color, as I can barely see the letters? I tried background color -but that changes for the molecule in display not the sequence. I also checked settings for the sequence viewer but there doesn't seem to be a setting specifically for the background sequence viewer either. Thanks Yaikhomba

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Computing protein cavities
by Y. Mutum 29 Dec '20

29 Dec '20

Hi This question is on calculating empty cavities of large protein complexes (~2 MDa) For example, the pdb-id: 6J5K. I have tried a few webservers and they are ignoring to calculate such large protein-pdb files as a whole. Does ChimeraX have tools that can be installed from the 'More-Tools' or an inbuilt one to calculate protein cavities in ChimeraX? If you could suggest external programs for computing cavities, that are reliable for such large protein-inputs, it would be also of a great help. The cavities need not be sealed by proteins all around - they can still be open to the bulk solvent. Thanks Yaikhomba

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ChimeraX "color by conservation" tutorial
by Elaine Meng 29 Dec '20

29 Dec '20

In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser. <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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