- ChimeraX-users - RBVI Mailing Lists

Aligning two ligands
by Karim Rafie 25 Jun '23

25 Jun '23

Hi all, I was wondering if there's a command that will allow me align two ligands to each other? Couldn't find anything online and when I try the match command I constantly run into an error, even when specifying certain atoms between two ligands. Any help would be greatly appreciated. All the best, Karim ############################################## Karim Rafie; PhD, MRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå, Sweden [cid:e5366e3a-666f-40ea-9f71-eb5b2b395016]

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Changing spin movie default save location?
by Daniel Gilliam 21 Jun '23

21 Jun '23

Hi, How can I change the default filepath that 'Spin movie' saves to? The default for me saves to location without save permissions, so I have been unable to save images or movies. Apologies if I missed an easy answer to this in the documentation. Thanks, Daniel Gilliam

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Invert selection
by Leonardo Talachia Rosa 20 Jun '23

20 Jun '23

Dear ChimeraX community Apologies for the very naive question. In old chimera, there was a "Select - Invert selected models" command which would invert the selection solely in the selected model, whereas in chimeraX I could not find an equivalent command or option in the menu. The select invert menu will invert the selection for all open models. Is there a way to invert selection only in one model? Thank you for your time Kind wishes, Leonardo -- ************************* Leonardo TALACHIA ROSA, PhD Associated professor Department of Biochemistry and Tissue Biology (DBBT) Biology Institute Universidade Estadual de Campinas - UNICAMP Rua Monteiro Lobato, 255 - Campinas - SP - Brasil - CEP 13083-862 **************************

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ChimeraX - Without NVIDIA
by Nguyen, Tuan /US 16 Jun '23

16 Jun '23

Hi, I'm trying to install the ChimeraX 1.6.1 on Ubuntu 22 without NVIDIA driver, I can launch the chimerax, but it gives me an error about the graphic driver, and I'm trying to open a pdb file, I don't see the image at all. Please see attached below. Would you please help? Thanks, Tuan [cid:image001.png@01D9A02C.7D05AF30]

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600 DPI Quality Images
by Dillon P Cao 15 Jun '23

15 Jun '23

Hello, How would I save an image on ChimeraX as 600 dpi? Apologies if this has been answered before. Sincerely, Dillon P. Cao

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Selecting segments overlapping atomic model
by kizziah4＠uab.edu 15 Jun '23

15 Jun '23

Is there some degree to which a segment must overlap an atomic model to be selected with "Over Sel. Atoms"? Can it be changed? I frequently use Segment Map to create custom masks for focused refinement and classification and for signal subtraction. I tend to use reference atomic models to expedite this process, but I am having problems selecting segments overlapping atomic models (compared to older versions of Chimera). I am on Windows 10 with ChimeraX version 1.5 (2022-11-24). I have experienced the same on Ubuntu-20.04 with ChimeraX v1.6.1. For example, I have an unsharpened map estimated at 4.8A resolution from RELION and an atomic model of the same structure downloadeded (via ChimeraX) from the PDB. After deleting some unneeded chains and duplicating others, fitting the model into the map using simulated density (4.8A resolution, 0.77 correlation), segmenting the map at a low threshold that covers all (but a couple of loops) of the atomic model, ungrouping the segments once for granularity, selecting the entire atomic model, and clicking "Over Sel. Atoms", no segments are selected. If I try repeating the process with the backbone only (0.80 correlation), no segments are selected. I have succeeded in some cases by ungrouping all segments ~4 times, but in this particular case it only selects a few segments corresponding to parts of some alpha helices.

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Question about MatchMaker with nucleic acids
by Leonardo BETANCURT ANZOLA 14 Jun '23

14 Jun '23

Hello, I’m currently using ChimeraX to compare different DNA binding proteins and would like to align them using match maker and the DNA helix. The problem is that the structures do not have the same DNA sequence and that is the parameter the MM uses to align. Would it be possible to align DNA using only the phosphate-sugar backbone of the molecule? In that case I’d like to tell chimera which phosphates should one aligned to which. Thank you, Leo B.

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Isolde installation in chimeraX
by Chiara Rapisarda 13 Jun '23

13 Jun '23

Hi, I am trying to install Isolde in chimera, I can successfully download the bundle, but nothing happens afterwards. Can you help me find out what is wrong? Thanks, Chiara

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Missing or invalid "sequence" argument: Sequences argument
by Adetoun Adeniji-Adele 13 Jun '23

13 Jun '23

Hello, I was trying to use the AlphaFold predict function earlier and received the following error. Missing or invalid "sequence" argument: Sequences argument "MNGIDIAVVTDDPAILKSVHERYPDGSKHSIELEHGHNVHIFVRTATLVLSSYIRDNEAIAVLGYSNVHESSMRAILESSPGVAHMNSALGQLIGAQWVVAIRKGAVRIQGTVSGLSRVYWSKRGSRFVASNRSRELARLLGSELDPTQVAFRTIHPMQHPFTSSSCWKDLEGVLPGEYLEVTGRSSPRTERWWTPATSYRSLEDGANETAAALFSVVRNQLSDHSAASCDISGGLDSSSIAAIAANAAKSGETHTVLHGTTSVSRDEFNSDADWAIELSKSLKLDSHSFLSWNDMPKEYDDLDALASYDLDEPSIASISHSRFTHLINVARSKGSQVHLTGFGGDELFIGSPTFCVDLFKTQPLLSARLLLTYRAMYRWTFRSLVRPLTTPMSYQQWMRTKSLSTDRSTLRIPPLSWGFHGVIPPWITRDARHSMYDHVRSASSATFPLAPTPGRHFELENLYQCARLFRTMSDIVSQTSGVLLVAPMLEQAVVEAAISVRTPERLTPHKYKPVLTHATRGLLPAVVAERQTKGGEDTDAAIGFSENISAIRELWDESRLASLGIVDGDYLSNALRRPDSAEFDDCAIAKTLATELWLRSLEK,MPVVGAMAIPSKTRISATERLRLASALSLGKALSHLPPGLLRRSMTAFAAKARPASYREAEAAVVSITQYSKASAGPGSCLQRSISVCILMRLDGRWPTWCVGVPSKPPFRAHAWIEAGGQIVAELGDMNSYSRLMTISTHAERTE" is not a chain specifier, alignment id, UniProt id, or sequence characters I am not sure what the message means and can't seem to find others who have had similar error messages. Any help would be appreciated. Best, Adetoun

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No chains in AtomicStructure
by Dominik Sordyl 13 Jun '23

13 Jun '23

Hi, I have created a python plugin that uses AtomicStructure() class to create a model based on the pdb file and custom trajectory file. The problem is that after creating the structure (adding residues and atoms) it has no chains. Due to this issue, I cannot use some of the ChimeraX features (e.g. rainbow coloring) - at least I think this is the reason. While adding new residues one has to specify the chain_id, but even if I do it those chains are not created automatically. Do I have to create chains separately or there is something that I am missing here. Would be grateful for your help. Best, Dominik

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How to play volume series in chimeraX?
by Rayees Mattoo 12 Jun '23

12 Jun '23

Hi, I want to play a volume series in chimeraX. There is an option "volume series" in chimera but could not find the equivalent option in chimeraX. Also, is it possible to 'movie record' the volume series while it is playing? Any suggestion would be helpful. Best

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Triangle attention for alphaFold2
by Cheng Fei Phung 10 Jun '23

10 Jun '23

Hi, This might not be directly related to use of ChimeraX gui software that this mailing list is targeted for. Might I ask if anyone have any suggestions for the use of triangle attention module in https://twitter.com/salmon_shitake/status/1663176260632346624 ? Regards, Phung Cheng Fei feiphung(a)hotmail.com

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sym command
by postmaster＠cgl.ucsf.edu 09 Jun '23

09 Jun '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: sym command Date: June 9, 2023 at 11:55:38 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to generate symmetric copies of the atomic structure in a filament map and I get the following error sym #1 group c6*h,39.1,19.3,7,-1 coord #2 (atomic structure is #1 and the map is #2) error - Expected a keyword What is incorrect in the command. Stay safe & Regards Anindito Sen. Ph.D <> Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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ChimeraX not able to install for ubuntu22
by himanshi singh 07 Jun '23

07 Jun '23

Greetings! Kindly find the attached screenshot for installing in ubuntu22, it says dependencies unmet. Kindly guide me. Thankyou Regards Himanshi PhD candidate IIT Kanpur India

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ChimeraX .cxs session file
by Moustafa, Ibrahim M. 06 Jun '23

06 Jun '23

Dear ChimeraX, I have a ChimeraX session .cxs file that was created a while ago. I wonder if there is a way to open the file to see the actual commands, parameters used in that session. Is there is tool/way to read .cxs file? Thank you for your help. Ibrahim Ibrahim M.Moustafa, Ph.D. Pennsylvania State University Biochemistry & Molecular Biology Dept. Millennium Science Complex University Park State College, PA16802 Phone: (814) 863 5940 Fax: (814) 865 7927

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clashes & contacts
by Dmitry Semchonok 06 Jun '23

06 Jun '23

Dear colleagues, Probably very simple question, non the less - how to calculate&show the contacts/clashes in the model? We have heptamer and we would like to find out what are the contacts & clashes with 6 surrounding units. I know that chimera can do that. Also, I heard that there is also software called DIMPLOT. Does ChimeraX do the same? Thank you in advance. Sincerely, Dmitry

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Daily builds
by BARRY E DEZONIA 05 Jun '23

05 Jun '23

Hello, I am looking for the daily build for Ubuntu. I go to this page: https://www.rbvi.ucsf.edu/chimerax/download.html No daily build releases are shown for Ubuntu. Are you having trouble with the website?

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The AlphaFold predicted model is always saved as best_model.pdb. It would be nice if you could specify a different name when you start the prediction run but that is not available. I made a ChimeraX feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9128 You can request new features directly with ChimeraX menu entry Help / Report a Bug.... This can be used for both bugs and new feature suggestions. Tom > On Jun 5, 2023, at 11:51 AM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thank you. I am slowly learning how to use ChimeraX. > One other question that I haven't solved yet: when I paste a sequence into the box for structure prediction, is there a way to name it right at the beginning? > All my previous jobs are given the same name "best_model".I know I can rename them later, but it would be easier if I could name them at the start. > Jim > > > On Mon, Jun 5, 2023 at 11:30 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. >> >> Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command >> >> ui dockable false "AlphaFold Run" >> >> Tom >> >> >>> On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu <mailto:james.raymond@unlv.edu>> wrote: >>> >>> Thanks, Tom, >>> I sent another email to say that I think I solved the problem but you didn't see that one. >>> >> >>> >>> >>> Here's a cool protein structure I made today with ChimeraX. >>> I used Yasara to view it. >>> This is so great! >>> Jim >>> >>> >>> >>> On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Jim, >>>> >>>> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >>>> >>>> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >>>> >>>> Tom >>>> >>>> >>>> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> > >>>> > Dear ChimeraX, >>>> > I keep losing this window, whenever I click on it or move it. >>>> > How do I get it back again? >>>> > thank you >>>> > Jim >>>> > >>>> > >>>> > <image.png> >>>> > _______________________________________________ >>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>> > Manage subscription: >>>> >> >>

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ChimeraX - windows 10 installation/running issue
by Dmitry A. Semchonok 05 Jun '23

05 Jun '23

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command ui dockable false "AlphaFold Run" Tom > On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thanks, Tom, > I sent another email to say that I think I solved the problem but you didn't see that one. > > > Here's a cool protein structure I made today with ChimeraX. > I used Yasara to view it. > This is so great! > Jim > > > > On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >> >> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >> >> Tom >> >> >> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear ChimeraX, >> > I keep losing this window, whenever I click on it or move it. >> > How do I get it back again? >> > thank you >> > Jim >> > >> > >> > <image.png> >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> > Manage subscription: >>

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AlphaFold2 coloring is not according to the database
by Julia Varga 05 Jun '23

05 Jun '23

Hi, I was preparing a figure and we opened the same AF2 structure both in chimerax and pymol, and colored according to pLDDT. We expected something quite similar, but some of the residues were not colored the same (left chimerax, middle official AF2 coloring, right pymol) [image: image.png][image: image.png][image: image.png] These are the corresponding CA atoms from the file, there are several that are above 70. ATOM 2 CA MET B 1 26.541 -48.983 -34.346 1.00 49.18 C ATOM 10 CA ALA B 2 23.562 -47.870 -36.454 1.00 60.35 C ATOM 15 CA ASP B 3 25.250 -49.497 -39.528 1.00 68.46 C ATOM 23 CA ALA B 4 25.752 -52.804 -37.641 1.00 69.86 C ATOM 28 CA TRP B 5 22.024 -53.025 -36.747 1.00 68.46 C ATOM 42 CA GLU B 6 21.036 -52.590 -40.351 1.00 71.02 C ATOM 51 CA GLU B 7 23.249 -55.575 -41.294 1.00 76.21 C ATOM 60 CA ILE B 8 21.578 -57.739 -38.645 1.00 74.81 C ATOM 68 CA ARG B 9 18.177 -56.653 -39.803 1.00 70.07 C ATOM 79 CA ARG B 10 19.226 -57.507 -43.334 1.00 74.00 C ATOM 90 CA LEU B 11 20.598 -60.932 -42.264 1.00 74.36 C ATOM 98 CA ALA B 12 17.459 -61.553 -40.194 1.00 69.47 C ATOM 103 CA ALA B 13 15.384 -60.625 -43.205 1.00 69.30 C ATOM 108 CA ASP B 14 17.563 -62.981 -45.430 1.00 70.53 C ATOM 116 CA PHE B 15 17.273 -65.769 -42.888 1.00 71.78 C ATOM 127 CA GLN B 16 13.568 -65.190 -42.812 1.00 64.74 C ATOM 136 CA ARG B 17 13.352 -65.300 -46.586 1.00 65.36 C ATOM 147 CA ALA B 18 15.491 -68.455 -46.645 1.00 64.05 C ATOM 152 CA GLN B 19 13.261 -70.000 -44.028 1.00 60.46 C ATOM 161 CA PHE B 20 10.117 -69.389 -46.168 1.00 62.26 C ATOM 172 CA ALA B 21 11.642 -70.083 -49.654 1.00 56.65 C ATOM 177 CA GLU B 22 11.244 -73.693 -49.767 1.00 53.68 C ATOM 186 CA ALA B 23 7.622 -74.493 -50.250 1.00 56.47 C After looking at again the docs, I understood that chimerax has a different coloring [image: image.png] AFDB [image: image.png] Can you maybe change this? Most people are probably used to the database's coloring, and could interpret it wrong (like me... It drove me crazy when showing somebody else, why the plddt-s do not match to what I have shown before, just in a figure by chimerax). I understand that in the documentation the colorbar is according to the coloring that chimerax does, but it would be better if it was according to the standard. Thank you so much! Kind regards, Julia Varga

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smooth object surface
by Jesse Hansen 05 Jun '23

05 Jun '23

dear all, I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks Jesse

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makind disulfide bonds in Chimera x
by Vladimir Saudek 03 Jun '23

03 Jun '23

Hello, Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file? Thank you Vladimir

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how to view Alphafold Run window
by James Raymond 02 Jun '23

02 Jun '23

Dear ChimeraX, I keep losing this window, whenever I click on it or move it. How do I get it back again? thank you Jim [image: image.png]

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Blast protein results
by postmaster＠cgl.ucsf.edu 02 Jun '23

02 Jun '23

From: Lynne Howell <howell(a)sickkids.ca <mailto:howell@sickkids.ca>> Subject: Blast protein results Date: June 2, 2023 at 2:18:42 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> HI I’m a novice ChimeraX user and wondered whether there is a way of saving to an excel file the blastprotein results against the Alphafold database that appear in the session window? Was looking to capture all the information for cross reference to another file. Thanks in advance Lynne This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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MolecularDynamicsViewer
by Michael Patzschke 01 Jun '23

01 Jun '23

Dear colleagues, I would like to use the MolecularDynamicsViewr more often. My problem is, that I work with small metal organic systems and we never generate pdf files. What I do get a loot are multiple .xyz files. In these files the different images are just put one after the other without any extra new line or anything. Here are the first few lines from the optimisation “trajectory” for water as created by orca: 3 Coordinates from ORCA-job h2o E -76.051642020209 H 1.200000 0.000000 1.000000 H -1.200000 0.000000 1.000000 O 0.000000 0.000000 0.000000 3 Coordinates from ORCA-job h2o E -76.099647985008 H 1.102275 0.000000 0.980787 H -1.102275 0.000000 0.980787 O -0.000000 0.000000 0.038425 3 Coordinates from ORCA-job h2o E -76.150106142663 H 1.008335 0.000000 0.959926 H -1.008335 0.000000 0.959926 O 0.000000 0.000000 0.080147 Would it be possible to enhance the MolecularDynamicsViewr to accept such files? Thank you very much for your time and effort. Kind regards, Michael

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displaying different segmentations together
by Jesse Hansen 01 Jun '23

01 Jun '23

dear all, I have segmented different parts of my tomogram using different software packages. One outputs an MRC file which I Can display as either volume or surface. The other is exported from Dragonfly and I am unable to figure out how to export MRC so I have tried STL and OBJ. STL/OBJ will display in ChimeraX, but then if I try to load in the other segmentation MRC then the STL/OBJ will disappear. I cannot view both simultaneously. If I hide the mrc and "view all" then I can view the object. Conversely, if I hide the object and "view all" I can see the MRC. Any help would be appreciated. Is there any way to convert obj/stl to an mrc? thanks! Jesse

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Virus detected on Chimera X download
by Amy E. Kennedy 30 May '23

30 May '23

To whom it may concern: I downloaded the Windows executable from https://www.rbvi.ucsf.edu/chimerax/download.html this afternoon, and my antivirus software intercepted and neutralized a suspicious item when I opened the file. You may want to do a thorough check of your systems. Best, Amy Amy E. Kennedy (she/her) Doctoral Candidate, Mierke-Pellegrini Lab Biochemistry & Cell Biology, MCB, Guarini School of Graduate Studies PhD Innovation Fellow | E. E. Just Fellow

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Can I use autodock vina
by NAGANO Kyogo 30 May '23

30 May '23

Hello. I started using the ChimeraX from today. And, I want to use the autodock vina with ChimeraX. In the case of Chimera, Tools→Surface/Bindind/Analysis→Autodock vina. But,in the case of ChimeraX, I couldn't find it. So, I want to know how to use Autodock in ChimeraX. Thank you.

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Run Session Command Not Working
by Aashna Soni 30 May '23

30 May '23

Hi, I hope this email finds you well. I am trying to use the ChimeraX Python shell to run commands programmatically. When I try to run this command: run(session, "open <insert filepath>"), I am getting this error: "AttributeError: module 'chimerax.core.session' has no attribute 'models'." I have not written any import statements at the top (this is the first line in the Python shell). I am getting similar errors when I run any run(session, ...) command. Could you please help me resolve this issue? Thanks in advance. Warm regards, Aashna

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ChimeraX server problems
by Tom Goddard 25 May '23

25 May '23

ChimeraX web services (BLAST protein, Modeller, sequence alignment) are currently down. Also ChimeraX bug reporting is down. We updated our servers last week (CentOS 7 to Rocky 8) and are working on restoring these services. Thanks for your patience. Tom

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chimerax-users mailing list should be working
by Greg Couch 24 May '23

24 May '23

But the web interface to look at old messages will take some time to get to work. -- Greg

1 0

chimerax-users mailing list will be down temporarily
by Greg Couch 23 May '23

23 May '23

We're upgrading the mailing list software. Should be back "soon".

1 0

ChimeraX 1.5 Issue - Observations
by Ethan Crofut 22 May '23

22 May '23

Hello, I am Ethan Crofut, an undergraduate at UCLA and member of Professor Hong Zhou's lab. I wanted to comment on an issue brought up at the Stanford-SLAC Image Processing Workshop. I am using ChimeraX 1.5, but I have also experienced the issue where scrolling, panning, and zooming stop working in the middle of my session. In my experience, this issue is specific to Apple Macbook trackpads (as someone else commented, I haven't seen the same issue on Linux desktops). Here are my observations on the issue: - The problem can always be resolved by clicking on the ChimeraX window in which the 3D structures are being viewed. - A scroll, pan, and zoom functions are lost if I click on a separate ChimeraX window, such as the Log, an ISOLDE window, etc., but as stated above, I can rescue this by clicking on the main window again. This also occurs for windows that are embedded into the main window, as the Log usually is. - The scroll, pan, and zoom features are more likely to break right after I use a multi-fingered gesture on the trackpad, especially three fingered gestures. I think this may have to do with the Mac's three-fingered swipe shortcut. - Sometimes, some functions are lost but others are retained. I almost always retain the ability to rotate the model using the regular left click, but multi-fingered gestures, such as the zoom and panning options, break more frequently. I am not very technologically savvy, but my guess is that it is very easy for Macs to lose track of the main ChimeraX window being the currently active window, which causes the controls to stop working. For me, this is usually caused by using multi-fingered gestures or toggling between multiple different ChimeraX windows. Best, Ethan

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symmetry axis
by Tianyang Liu (Staff) 22 May '23

22 May '23

Dear ChimeraX team, I have attached my cryo-EM map with C2 symmetry. The symmetry axis is shown with a yellow rod, not along the z-axis. How can I save a new map in ChimeraX with the symmetry axis along z? Many thanks, T

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interfnal error toolshed
by steffen＠sthomas.de 19 May '23

19 May '23

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Support pages are not reachable
by Lars Hangartner 18 May '23

18 May '23

To whom it may concern: There seems to be issues with your web servers, as several pages cannot be reached, e.g. <https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> cgl.ucsf.edu<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> [X]<https://www.cgl.ucsf.edu/Outreach/Workshops/UCSF-Fall-2005/09-ScriptDemo/Sc…> Best, Lars –––––––––––––––––––––––––––––––––– Lars Hangartner, PhD Associate Professor The Scripps Research Institute Department of Immunology & Microbiology - IMM2 10550 North Torrey Pines Road La Jolla CA, 92037 U.S.A. Phone: +1 (858) 784 9876 Cell: +1 (858) 952 2282

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UCSF website
by Raneem Akel 18 May '23

18 May '23

Hello, I was trying to download ChimeraX but I’m getting an error saying that the website cannot be reached. Could you please advise. Thanks, Raneem

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Re: [chimerax-users] [Chimera-users] 3D_printing
by Elaine Meng 18 May '23

18 May '23

Dear François-Hugues Porée, In ChimeraX, there is no GUI tool but you can use the "cartoon style" command to increase ribbon (cartoon) width and thickness to specific angstrom values. For details see the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> However, ChimeraX also has a "struts" command that will automatically increase ribbon thickness in addition to adding some stick pseudobonds specifically to make a 3D model stronger. So you may want to use "struts" instead : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/struts.html> Another thing to consider for 3D printing is the number of triangles of the object, which you can adjust with "graphics quality": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> For ChimeraX questions in the future, you may want to use the other address chimerax-users(a)cgl.ucsf.edu (CC'd here) -- since the answers are different for the two programs, we try to not confuse people between them. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. you may also be interested in the NIH 3D website: <https://3d.nih.gov/> > On May 15, 2023, at 6:58 AM, Francois-Hugues Poree via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team, > first of all, I would like to thank you for providing a sotfware solution to molecular visualization and by the way 3D-printing. > > I send you this message concerning the UCSF Chimera X version. We usually are preparing our 3D-printing files from data collected from the pdb and to ensure the rigidity of the system, we thick the ribbon size and also add some H-bonds (mainly for helices). However, we are not able to find the way to do it in this version. > In the previous version (1.17), the command line was : Tools-depiction-ribbon style editor > > Could you explain us the new procedure to make this ? > > > We also noticed that the opportunity to save the file in a stl extension was not allowed in the 1.17 version. This option is running in the X version. > > Thank you very much for your reply > > Best regards. > > > fhporee > > François-Hugues Porée > Professeur de Chimie Thérapeutique > Institut des Sciences Chimiques de Rennes UMR CNRS 6226 > Faculté de Pharmacie - Université de Rennes > 2 Avenue du Pr Léon Bernard > F-35043 Rennes > France > Tel.02 23 23 41 87

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'Tunnel' hydrophobic colouring
by Kelly May Frain 16 May '23

16 May '23

Hello, Previously you were super quick and helping when answering my ‘tunnel’ question, so I thought I could try another question for chimeraX. I have a protein which via Caver I have found a tunnel which runs through. This tunnel has been exported as a pdb and using your help and python, the tunnel now changes diameter perfectly as it weaves through the structure. I had this idea to colour the tunnel according its surrounding residues and their hydrophobicity. So in chimeraX I can colour my model ‘hydrophobically’ from cyan to gold. Then I wanted to 'zone’ these colours into my tunnel pdb. But when I use color zone #2 near #1 distance 20 for example, the tunnel is coloured in red and blue patches? Even though the model is cyan and gold. Is there a way to achieve my goal please? Best wishes, Kelly

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Duplicate the model
by tim smith 15 May '23

15 May '23

Hello everybody, I would like to create copy of the model in the same session but with a different model number. Please, could you suggest how to do that. Thank you. Best Tim

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rendering of bond making/breaking along a trajectory
by Hassan, Sergio (NIH/NIAID) [E] 15 May '23

15 May '23

Hi, I am not sure whether this is a bug or something not yet implemented or else. I performed QM/MM simulations of a proton translocating along a water chain. This involves the breaking of a bond and the making of a new bond. The visualization of the trajectory does not show this process; instead, the original definition of bond is retained, without being updated at each timeframe. Is there a way to tell ChimeraX to automatically check covalent bonds at each snapshot and update the bond accordingly? A simple distance criterion will do. This is only for rendering purpose. In case further clarifications are needed: D—H.......A (with -- indicating the covalent bond between proton and domor and .... indicating the proximal acceptor) must be transformed to D.......H—A. Instead, it is rendered as D-------H..A (with an artificially elongated DH bond and no new HA bond) thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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REMINDER: ChimeraX website downtime
by Elaine Meng 15 May '23

15 May '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. Please pardon any inconvenience, 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] Measuring distance between two atoms in a single protein
by Cheng, Jiaxuan (NIH/VRC) [F] 14 May '23

14 May '23

Hi Elaine, I met a problem when measuring the distance between two atoms. I entered “distance #1.16/B:94 at CA #1.35/B:94 at CA” , but the ChimeraX reports “expected a keyword”. Could you let me know how to solve it? Thanks! Jiaxuan [cid:image001.png@01D98530.82126BB0]

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Scrolling wheel feature request
by vincent Chaptal 12 May '23

12 May '23

Dear ChimeraX team, a very useful feature in Pymol is the use of the scrolling wheel on the mouse to clip the view plane and add depthcue. After centering on one element, it is very convenient to focus on some areas and remove things from the view, for both viewing and article figures. I haven't find a similar feature in ChimeraX, would it be possible to implement it? I've tried to play with the depthcue command, but it I find it much harder to get to what I would like. lighting depthcue true depthCueStart 0.3 depthCueEnd 0.5 If the view with the clipping can be saved with the "view matrix" command, it would be extremely useful. Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Re: [chimerax-users] unifold
by Tom Goddard 11 May '23

11 May '23

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coloring a clipped surface cap by property
by Elaine Meng 10 May '23

10 May '23

Hi Noam, Glad you like ChimeraX! (A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#c…> (B) The way to color a clipped surface cap by an atomic or residue attribute is to: 1) color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool) 2) use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model. Example: color zone #1.1.1 near #1 distance 3 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> Since "N" heads are better than one, we generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 10, 2023, at 7:40 AM, Noam Prywes <noam.prywes(a)gmail.com> wrote: > > Dr. Meng, > > I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. > > Do I need to make a .defattr file that colors by atom instead? > > Thanks for your help and the amazing service that is chimeraX. > > Best wishes, > Noam

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Hiding distance labels during trajectory playback
by Lewandowski, Jozef 10 May '23

10 May '23

Hi, Is there an easy way to hide distance labels during the playback of an MD trajectory? Even if I delete or hide the labels in one frame they get generated when next frame is loaded. I tried to include hiding/deleting the labels command in perframe but they flash on before they are removed. Ultimately, I would like to record a movie where only the pseudobonds are shown but not the labels. Thank you, Józef

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ChimeraX 1.6.1 release
by Eric Pettersen 10 May '23

10 May '23

UCSF ChimeraX version 1.6.1 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html> Updates since version 1.5 (Nov 2022) include: - ESMFold protein structure prediction and residue-residue error plot - Add Charge GUI - Dock Prep GUI to repair side chains, add hydrogens, etc. - Render by Attribute GUI for coloring by atomic or residue values - swapna command to mutate nucleic acid residues - invert chiral center - read SwissDock docking results - Blast Protein query sequence can be pasted in or specified by UniProt ID - browse/fetch medical images from The Cancer Imaging Archive - read medical images in NIfTI (.nii) and NRRD (.nnrd) formats For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> For those of you who downloaded plain 1.6 while it was briefly available, please upgrade to 1.6.1. It has several bug fixes that 1.6 should have had but didn't. --Eric Eric Pettersen UCSF Computer Graphics Lab

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