- ChimeraX-users - RBVI Mailing Lists

C-alphas rendered as dots
by Pranav Shah 03 Aug '21

03 Aug '21

Hi Team, I am working with a huge model (and a correspondingly huge map), which makes the handling on my GPU accelerated desktop an agonisingly frustrating experience. In order to speed up simple (rigid-body) fitting of the map and model, I decided to use the -C-alpha trace of the pdb. However, the pdb gets rendered as a bunch of disconnected dots whereas the same pdb in Chimera is rendered correctly with all things. Is this a normal behaviour for ChimeraX? I could use Chimera, but I prefer the way ChiemraX handles large maps as compared to Chimera. In the absence of a quick fix, would there be a way to increase the size of the atoms? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Showing C-alphas
by Casey 30 Jul '21

30 Jul '21

I am trying to show a single sphere at c-alpha carbons for some point mutants that i designed. When I use the command: show /a:473,476,477 atoms I can see all the atoms in chain A for residues 473, 476, 477. Using: show /a:473,476,477@cb atoms I can show "two spheres" for the c-alpha and c-beta carbon. When I use: show /a:473,476,477@ca atoms nothing happens and i don't see any spheres. If I show the full atom and then do: hide /a:473,476,477@ca* atoms Just the c-alpha sphere gets hidden. Why is it that i can't just show the c-alpha spheres? Unfortunately for my figure i make silhouettes of my model and so i can't just hide the other atoms by making them fully transparent

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Re: [chimerax-users] Automating Map segment
by Tom Goddard 30 Jul '21

30 Jul '21

To group by connectivity looks like you need to add d._group_con.value = True To figure out this stuff you would need to look at the Segger user interface code, it is in the ChimeraX distribution (under site-packages/chimerax/segger/segment_dialog.py) or on GitHub https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.… <https://github.com/tomgoddard/segger/blob/master/Segger/src/segment_dialog.…> Tom > On Jul 30, 2021, at 10:42 AM, Sam W Marchant <smarchant(a)UCSD.EDU> wrote: > > Thanks so much im trying to group by connectivity and I am having trouble finding the right line of code to add that ability. Any thoughts? > >> On Jul 29, 2021, at 3:56 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Sam, >> >> I did an initial port of Segger from Chimera to ChimeraX (also called Segment Map) but that code was written by Greg Pintilie and he has not worked the ChimeraX version so there is no new command to run it in a script. It would probably not be too hard to write some Python to run it. The Chimera script mentioned in the mailing list is attached to my message about it. >> >> https://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013979.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_pip…> >> >> That won't work in ChimeraX, but here I attach the equivalent for ChimeraX. >> >> Segger was developed to segment molecules in EM maps, so I have doubts that it will do much good for your light microscopy. But you can decide that by running it by hand on some time steps and see if you like the result. >> >> Here is a different approach we used to quantify protrusions of crawling neutrophils in light sheet microscopy by placing markers that might be of interest. >> >> https://www.cgl.ucsf.edu/chimera/data/protrusion-sep2015/protrusions.html <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.cgl.ucsf.edu_chime…> >> >> Tom >> >> >> >>> On Jul 29, 2021, at 3:24 PM, Sam W Marchant via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipe…> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me? >>> Thanks, >>> Sam Marchant. >>> _______________________________________________ >>> 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://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mai…> >> >> <segscript.py> >

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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Automating Map segment
by Sam W Marchant 29 Jul '21

29 Jul '21

Hi, I am looking to apply the Map Segmenting to multiple time series of light sheet imaging and so I was wondering if there is either a command or a python function to automate the process. It looks here<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-October/013980.html> that you said it was going to be added to ChimeraX but I cannot find any info on how to do it. If not you mentioned a script in this answer, could you potentially send that to me? Thanks, Sam Marchant.

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Re: [chimerax-users] command line way for inverting selection
by Rangarajan, Amith 29 Jul '21

29 Jul '21

Hi, I am looking for a way to invert selection without reaching for the tool bar. I would like to know if there is a way to invert selection via the select command ( or some other command) thanks a lot, Amith

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ATOM has no alt loc B
by James Loy 28 Jul '21

28 Jul '21

Hi folks- I'm trying to add hydrogens to an mmCIF file (5byl) using the addh command. However, every time I try, I encounter the following error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 712, in init run(sess, cmd) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run results = command.run(text, log=log, return_json=return_json) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63, in cmd_addh add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214, in add_hydrogens _attach_hydrogens(atom, altloc_hpos_info, bonding_info) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema) File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862, in add_altloc_hyds h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema, File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 882, in new_hydrogen metal_pos = metal.get_alt_loc_coord(alt_loc) File "atomic_cpp/cymol.pyx", line 587, in chimerax.atomic.cymol.CyAtom.get_alt_loc_coord ValueError: Atom /A MG 702 MG has no alt loc B I'm using ucsf-chimerax_1.2.5-1_amd64.deb installed on Ubuntu 20.04. I've done some digging, and I cannot figure out what is going on. Any help would be appreciated. Thanks in advance! -James -- James Loy, Ph. D. 614.915.9792 LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>

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The PDB code for the demo picture on the website
by BAOCHENG LIU 28 Jul '21

28 Jul '21

Hi chimerax group, I am a postdoc in UCLA using chimerax. Thanks for providing all scientists this powerful software that makes life easier. I have a question here when I was learning the cartoon/ribbon style command line. So, I saw the 4 demo pictures on the website https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style and just realized the structure just looks similar to one of my structures. Could you please tell me the PDB code for that structure so I can compare it with mine in detail? Hope it is released. Thank you. Best regards, Baocheng

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resfit command for nuclei acid
by Wen-Jin Winston Wu 27 Jul '21

27 Jul '21

Hi Tom, I have just tried to use the "resfit" command ChimeraX Does the nice command of "resfit" in ChimeraX support inspection on nuclei acid? It seems that it only support protein residues as with the command " resfit #1/D:DT map #3", it returned with the message that "None of the 9 specified residues have backbone atoms N, CA and C". I have not checked out the daily build version yet, but thought that I can ask first. Thanks, Best wishes, Winston

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Custom colour for atoms with bfactor==0
by Lorena Zuzic 27 Jul '21

27 Jul '21

Hi, I wanted to know if there is a way of colouring my structure by bfactor, but with an additional condition where all bfactor==0 atoms are coloured in grey. Currently, I am using a white to red gradient for my B-factors: color bfactor range -2.2, 2.2 In this case, bfactor==0 values are coloured white. However, I would like them to be grey and outside the gradient (as they represent an unmapped portion of the protein). Thanks! Lorena

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create mask from "shapes"
by Roberto Marabini 27 Jul '21

27 Jul '21

Hi, It is possible to create a mask from a shape?. For example from the result of "*shape icosahedron".* If the command does not exist I guess I may create it as follows * the input would be the 3D map to be masked and the shape to be used as mask * request all the (varray, tarray) from the shape. * from varray,tarray build the triangles that define the surface of the shape * for each triangle create the normal vector * multiply each normal vector by the position of each voxel (dot product) * keep those voxels that have negative dot products for all the triangles. thanks for the help

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Automated Fitting of models into maps and saving fits with a correlation score > X
by Vorländer,Matthias Kopano 26 Jul '21

26 Jul '21

Dear all, I have a set of 100 “artificial” tomograms, each containing approx 100 copies of a simulated density map of my protein of interest. I would like to fit each tomogram with the PDB of my POI, and save copies for all fits with a correlation score > 90%. Using the fitmap command in Chimera and then manually selecting the fits that meet the criterium works, but takes quiet a long time for a larger amount of data. I wonder if this could be automated, and if somehow would be able me to put together a script (is it possible to execute such tasks in a non-gui way, by submitting it to a cluster so that it could be parallelized?). Thanks a lot in advance, Best, Matthias

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unexpected behavior of build start
by Alexis Rohou 26 Jul '21

26 Jul '21

Hi ChimeraX team, I'm running into unexpected behavior when using the build tool. Here's what I'm doing: - open map --> model #1 - open PDB --> model #2 - fit #2 in #1 (the PDB moves by ~20 Å at this step) - cofr centerOfView showPivot true - move the view around so that the pivot axes intersect where I want to place a new atom - build start atom #2 expected result: a new H atom is created exactly at the center of view (where the pivot axes intersect) actual result: the new H atom is created some distance away; I think the vector from where the new H atom is built to the cofr is the same vector as the PDB model was displaced by the fitting into the map (my second step, above), but I haven't checked that carefully. Is this what is expected? It confused me :) Is there a command I can use to move the atom to the correct location after it's been created? Interestingly, if I add a H atom into a new model, then it appears where I expect it, at the cofr: - build start atom "custom built" This is with 1.2.5 (2021-05-24) Cheers, Alexis

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question
by 王镐锋 26 Jul '21

26 Jul '21

Dear guys, Sorry to disturb you guys. When I use the UCSF ChimeraX, I try to define the second structure for part of model. I type the command like "dssp (#1 & sel) energy cutoff 0.5 minheliexlen 3", it works for the whole model instead of what I choose specially. Could you please help me? Thanks so much! Best, Haofeng Wang Ph.D student Tianjin University, China

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measure volume in ChimeraX
by Andrew Blyth 24 Jul '21

24 Jul '21

Hi, I am having trouble getting the ‘measure volume’ and ‘measure area’ command to work in chimera. I have been trying the command: measure volume #3/A:457 for the structure that I have been using, however, nothing happens when I execute this command. Could you please provide me with an example command that will work for measuring the volume or area of a residue? Thanks, Andrew Blyth PhD Candidate Medical Biochemistry - Flinders University Room 6E109 Flinders Medical Centre | South Australia 5001, Australia Phone: +61 8 8204 5098 | E: andrew.blyth(a)flinders.edu.au<mailto:andrew.blyth@flinders.edu.au>

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Model missing residues in Chimera X
by He, Amy 23 Jul '21

23 Jul '21

Dear Chimera X community, I’m a new user of Chimera X and I have a question about the built-in Modeller function in Chimera X Previously in Chimera 2, we use the “Model/Refine Loop” function to model missing residues in the experimental structure, before any further calculation or simulations. The “Model/Refine Loop” function uses Modeller and the function provides modeled, complete structures in which the non-missing residues do not move. In Chimera X, a similar function is “Modeller Comparative” but it works differently. The “Modeller Comparative” performs a modeling for the full structure with the given sequence. Is possible in Chimera X to model the missing residues, without moving the existent residues? Thank you for your kind advice in advance! Thanks, Amy -- Amy He Chemistry Graduate Teaching Assistant Hadad Research Group Ohio State University he.1768(a)osu.edu<mailto:he.1768@osu.edu>

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How to access ChimeraX remotely from macbook (OS mojave)?
by Rayees Mattoo 22 Jul '21

22 Jul '21

Hi, I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! Best Rayees

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Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)?
by Tom Goddard 22 Jul '21

22 Jul '21

Hi Rayees, Mac Air graphics is pretty slow for running ISOLDE. But Tristan Croll who develops ISOLDE added a nice option "Sim Fidelity" to the ISOLDE panel in the middle -- by default it is set to "High" and setting it to "Quick" will make the simulations run much faster. Here is what Tristan told me about what it does: "The latest ISOLDE release has new “sim fidelity” radio buttons on the “Sim settings” tab. The “quick” mode (no implicit solvent, nonbonded cutoff tightened to 9 Å) runs about 4x faster on my MacBook Air and still gives reasonable results in good density. Still not *fast*, but I think definitely usable." This is in ISOLDE 1.2.2. If you need to update ISOLDE use ChimeraX menu Tools / More Tools.... If this is still too slow, I'm afraid it is a limitation. You have to use faster hardware. The realtime dynamics simulations used by ISOLDE need fast graphics - the molecular dynamics is done with OpenMM using OpenCL or CUDA GPU accelerated computation. CUDA is fastest and needs Nvidia graphics and the CUDA driver installed -- Macs don't support Nvidia gpus. The macOS OpenCL implementation is very slow, almost as slow as just running on the CPU. Tristan has ISOLDE benchmarks on different hardware here https://isolde.cimr.cam.ac.uk/performance-benchmarks/ Tom > On Jul 22, 2021, at 6:03 PM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Tom, > Thanks for responding. Actually, I wanted to run ISOLDE from chimeraX and already tried it running on Mac with my 500KDa protein complex. It was very slow, wanted to try on linux machine and ran into the OpenGL problem. Do you have any suggestions how to run ISOLDE faster on mac? > > Best > Rayees > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, July 22, 2021 5:32 PM > To: Rayees Mattoo <rmattoo(a)stanford.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu>; chimerax-bugs(a)cgl.ucsf.edu <chimerax-bugs(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] How to access ChimeraX remotely from macbook (OS mojave)? > > Hi Rayees, > > I guess you have X Windows (XQuartz) running on your Mac and are hoping that X remote display from Linux to the Mac will work with ChimeraX. Unfortunately X Windows remote display of 3D OpenGL graphics has not worked reliably since the days Silicon Graphics computers in the 1990s. It is possible to get it to work between two Linux machines with identical OpenGL drivers. But it would be a near miracle if the XQuartz implementation of X Windows on Mac could handle the OpenGL from a Linux machine. > > The sensible approach is to run ChimeraX directly on your MacBook Pro. We don't recommend remote display even when it works because rendering speed is likely to be poor. > > Tom > > >> On Jul 22, 2021, at 1:31 PM, Rayees Mattoo via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi, >> I am trying to access ChimeraX remotley using my mac book pro. The ChimeraX is installed on linux machine. Upon launching, the chimeraX GUI appears and suddenly disappears with the following error message: "ChimeraX requires OpenGL graphics version 3.3. Your computer graphics driver provided version 1.4, Try updating your graphics driver". >> My mac currently has macOS mojave version 10.14.6 and it seems it does not have OpenGL graphics version 3.3 required to display chimeraX remotely. Is there any way out to fix the problem? Not sure if updating my macbook to Catalina or BigSur is going to help! >> >> Best >> Rayees >> >> >> _______________________________________________ >> 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://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>

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Re: [chimerax-users] python loop with ChimeraX
by Rangarajan, Amith 21 Jul '21

21 Jul '21

Hi, I am new to chimeraX , i want to loop through a set of biological assemblies measuring SASA of selecting residues and write them to a file. I need some help with starting on this .How to include this into the .cxc script? is there a example somewhere? please share your tips and suggestions, thanks everyone ! warm regards, Amith

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Hide dust tool & threshold of the map
by Dmitry Semchonok 20 Jul '21

20 Jul '21

Dear colleagues, I would like to ask you for the common practice in showing the threshold of the 3D map and usage of the "hide dust tool”. Am I allowed to use the “hide dust tool” when making the figures for the paper? And if yes, if/how shall I specify that in the description to the figure? Thank you Sincerely, Dmitry

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Moving labels
by Maciej Basczok 15 Jul '21

15 Jul '21

Dear ChimeraX staff, I have a problem with moving 3D labels. I would like to move them in the z-axis, but I cannot find how to do it. My version is 1.2.5. In some earlier release it could be done with the right mouse button + ctrl, but it seems to be changed. I have also tried to find a solution in archive messages, but the hint to click favourites and preferences also appears to be no longer an issue. Under favourites, there are no preferences or mouse settings. I would be extremely grateful for any suggestions. Kind regards, Maciej

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scale_bar
by Dmitry A. Semchonok 09 Jul '21

09 Jul '21

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Making movie with crop function
by SHIQING LIAO 07 Jul '21

07 Jul '21

Hi there! I am trying to make movies with different cropped views in order to see the inside of my 3D model. I tried view name command and it cannot store the cropped information. The command seems to only work with rotation and translation. Any help would be appreciated! Best, Shiqing

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fit map and bring other maps or models with it
by Alpay Burak Seven 07 Jul '21

07 Jul '21

Hi ChimeraX developers, I would like to fit one map to another and move some other maps with it using ChimeraX. This was possible with matrixcopy in Chimera. In ChimeraX, this type of translation/rotation is possible with matchmaker using "match #2 to #1 bring #3" I believe bring option is not available to "fitmap" command. Please let me know if there is a way. Would it be possible to implement the bring option to fitmap command or implement the matrixcopy command to ChimeraX? Kind regards, -- Alpay B. Seven Stanford University

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Question about libLLVM
by Zhe Wang 07 Jul '21

07 Jul '21

Hi, We were trying to install ChimerX 1.2 on our Centos 8 system. It seems like ChimeraX 1.2 asks for libLLVM with version 10 which is not a default package that built in the rpm. The default one for CentOS 8 is version 9. Centos 7 does not provide and not available in EPEL either. Could ChimeraX provide the corresponding library for centos 8 and 7? Another question that I have is if the following is correct for ChimeraX 1.1: ChimeraX 1.1 is using the default libLLVM3.9-mesa.so for centos 8. And for centos 7, you have ChimeraX 1,1 using the libOSMesa.so.8.0.0 which ChimeraX provided, as I see ChimeraX 1.1 works fine one both, but not 1.2. Best, Zhe

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