- ChimeraX-users - RBVI Mailing Lists

All-numeric residue names
by Tristan Croll 16 Aug '21

16 Aug '21

Was just looking at 2rg6, which happens to have a ligand with an all-numeric 3-character ID (287)... clearly not much thinking went into allowing that. Anyway, does the residue selection syntax have a way to disambiguate residue *number* 287 from residue *name* 287?

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Coulombic color combined surface
by W. C. 13 Aug '21

13 Aug '21

ChimeraX has no way to color ONE continous surface formed by combining multiple chains with coulombic or hydrophobic. It always color each chain surface separatly . Even though I generated a surface of combined chains by "surface enclose" command, ChimeraX still colors each chian seperately. In Chimera (not ChimearX), I could use surfcat to combine chains, generate one surface for combind chains, and color the surface as one continous. However, that could color large set of molecules. So please make ChimeraX can do the same.

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(no subject)
by Haaris Ahsan Safdari 12 Aug '21

12 Aug '21

Rrg together with the university international realty of

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Morphing with ligands
by Volodymyr Dvornyk 10 Aug '21

10 Aug '21

Dear Colleagues, Tried to do morphing of the following structures: 6rdc, 6rep, and 6rd9. All three have the same ligands: ADP, ATP, Mg, and Zn. However, the resulting model lacks all of them. Any thoughts and/or suggestions? Thank you. Volodymyr ________________________________ DISCLAIMER: This electronic mail transmission contains confidential information intended only for the person(s) named. Any use, distribution, copying or disclosure by any other person is strictly prohibited. If you received this transmission in error, please notify the sender by reply e-mail and then destroy the message. Opinions, conclusions, and other information in this message that do not relate to the official business of Alfaisal University shall understand to be neither given nor endorsed by Alfaisal University. The contents of any attachment to this e-mail may contain software viruses, which could damage your own computer system. While "Alfaisal University" has taken every reasonable precaution to minimize this risk, we cannot accept liability for any damage which you sustain as a result of software viruses. You should carry out your own virus checks before opening the attachment.

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Trying to open .py files on Windows gives cPickle error
by Carnes, Jason 09 Aug '21

09 Aug '21

Hello, I am collaborating with someone using ChimeraX on a Mac. Their only option to save modified files results in a .py file extension. When I try to open .py files on my Windows install of ChimeraX I get an error: "ModuleNotFoundError: No module named 'cPickle'" Is there a way to manually install cPickle on my Windows computer that will allow me to open the .py files, or are Mac & PC not compatible? Thanks, Jason Jason Carnes, PhD Research Scientist IV | Center for Global Infectious Disease Research Seattle Children's Research Institute 206-884-3137 OFFICE CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Difficulties Visualizing Isosurfaces from Cube File - Nathan Wood
by Nathan Wood 09 Aug '21

09 Aug '21

Dear ChimeraX I was having difficulty attempting to visualize computationally generated electrostatic potential isosurfaces originating from a Gaussian *.cube file. I tried to open the cube file from the shell only for it to incompletely visualize. I can provide an image if necessary. I found the following correspondence concerning cube files and isosurfaces, but unfortunately I am unable to resolve the issues of the cube file visualizing. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-April/002126.html> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-May/001110.html> I was curious if anyone has had experience with cubefiles. Any assistance would be greatly appreciated, Very Respectfully, Nathan Wood

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Superimpose
by Wisoot Chanit 08 Aug '21

08 Aug '21

Dear ChimeraX team, I am having a quesition. I am going to superimpose 2 monomers of P domain of norovirus GII.3 into a template PDB 6if5, but the template showed that information of its chains are missing. What should I do to make a dimer into 6if5. This is different from PDB 3mfg, which was a templete I used for my previous paper. Thank you. Jay

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Re: [chimerax-users] Saving 300dpi high resolution images with ChimeraX
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Nada, ChimeraX questions should be sent to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time). ChimeraX does not set the dpi. You just figure out the number of pixels you need and then save in pixels. I.e. if you want 3 inches wide at 600 dpi then you know you need 1800 pixel width, e.g. save myfile.png width 1800 If you open the resulting image file in just about any general image application like Photoshop, Gimp, or Mac Preview (etc.) then you can set the "resolution" or "dpi", but it's really the number of pixels you save in the first place that matters. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 4, 2021, at 10:04 AM, Bejar, Nada <nbejar(a)houstonmethodist.org> wrote: > > Hello, > I am Nada, a postdoctoral fellow at Houston Methodist. > > I saw your name in this thread. https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000816.html > I tried your suggestion, but any number I put on width would still give me a 96dpi. > > I switched to the old Chimera and I can change the unit to print unit and that resolves the issues, but I have all my work done on ChimeraX. > > I do need to make figures today and help would be much much appreciated. > > Nada Bejar, Ph. D. > Postdoctoral Fellow > Kiss RNA Lab > Houston Methodist Research Institute > 6670 Bertner Avenue > Houston, TX 77030 USA

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Re: [chimerax-users] Error in ChimeraX application installation linux ubuntu
by Elaine Meng 04 Aug '21

04 Aug '21

Hi Vanessa, Please send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here, so no need to do anything this time). Since I don't know the answer, I kept waiting for somebody else to answer your question... and didn't notice until now that you had sent it to only me. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2021, at 1:51 AM, Vanessa Roy <vanessaroy(a)mail.tau.ac.il> wrote: > > Dear ChimeraX development team, > > We encountered issues while installing ChimeraX on our server and wanted to ask whether you could help us understand what the problem is? We haven't yet found a solution to our problem. > Here is the output after installation: > > # /home/apps/chimerax-1.2.5-rc-2021.05.24/bin/ChimeraX > X11 connection rejected because of wrong authentication. > qt.qpa.xcb: could not connect to display localhost:10.0 > qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found. > This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. > > Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb. > > Fatal Python error: Aborted > > Current thread 0x00007f479c05d740 (most recent call first): > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/chimerax/ui/gui.py", line 119 in __init__ > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 500 in init > File "/home/apps/chimerax-1.1/lib/python3.7/site-packages/ChimeraX_main.py", line 919 in <module> > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 85 in _run_code > File "/home/apps/chimerax-1.1/lib/python3.7/runpy.py", line 193 in _run_module_as_main > Aborted (core dumped) > > We would greatly appreciate your advice on how to solve this issue. > > Many thanks for your help! > > Best, > Vanessa > -- > Vanessa Roy > Gil Ast Lab > Department of Human Molecular Genetics and Biochemistry > Sackler Faculty of Medicine | Tel Aviv University

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Maps comparison
by Dmitry Semchonok 04 Aug '21

04 Aug '21

Dear colleagues, I have 2 cryo-em maps of different resolutions. What will be the correct strategy to compare them and what are the tools and steps? Thank you Sincerely, Dmitry

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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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