- ChimeraX-users - RBVI Mailing Lists

Side view in command line
by HONG ZHAN 31 Jul '22

31 Jul '22

Hi all, I would like to setup a movie sequence using cxc file. It is very useful to setup in the UI window, however, any tricks could I use to set the clip plane in the command line to generate a view as in the attached picture? So that I can run my cxc file together with other actions? Many thanks! Hong [cid:12317B70-9FE5-4C25-933C-E56EF2888E9D]

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ChimeraX on Mac
by Lisa Käshammer 30 Jul '22

30 Jul '22

Dear developers, I have problems to get chimeraX to work on my computer. It had a previous version installed (1.1) which did not work anymore. So I removed that version and installed the newest version, however, it does not open. There is no error message so I am a bit lost at what I can do to resolve this issue. The macOS is 10.15.7. Thank you very much in advance. Best, Lisa

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command inquary
by Kwangjun Lee 29 Jul '22

29 Jul '22

Hello, Do you have any command that displays a selected region only? For example, I have a protein structure AA1 to AA300. I only want to display AA100 to AA200. Thanks!

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Re-scaling maps
by Nebojsa Bogdanovic 29 Jul '22

29 Jul '22

Hello, I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same. Is there any command in chimeraX or chimera to play with pix sizes to find the right one? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Application to enter the chimeraX user's group
by Xiaofeng CHU 28 Jul '22

28 Jul '22

Dear chimeraX team Sorry for the interruption. My name's Xiaofeng Chu, the phd candidate in Misha Kudryashev's group working on cryoET and structural biology. Could you please help me to enter the group of chimeraX users? So I can raise some questions about how to use it. Thank you very much in advance! And have a nice day. Best regards Xiaofeng -- Xiaofeng Chu (he/him) Ph.D. candidate in M. Kudryashev's research group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association 13125 Berlin, Germany

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Re: [chimerax-users] Assembling 2 proteins
by Elaine Meng 27 Jul '22

27 Jul '22

Hi Tata Santosh Rama Bhadra Rao, I already gave my suggestions in the previous message, so there is not really anything else I can do to teach you. Since you didn't give the details of all the steps that you tried and which step(s) gave results you didn't like, I can't tell you how to do it differently. My only idea is to go back to what I already suggested: you could use Matchmaker if you already had a pentamer, which you show in the bottom figures. So, following the instructions in my first reply, maybe you can take the chains shown in the top figures and match them onto the chains in the bottom figures to make the pentamer. However, that will only work if the proteins are very similar. If you did it already and it gave the bad result, maybe these proteins are not similar enough to use that approach. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 30, 2022, at 9:22 PM, SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> wrote: > > Hi Elaine, > > I tried doing and it came out like this. Final 2 figures are homomeric pentamers. First 2 are heteromers with 3A subunits (A, B, D chains) and 2D (C, E chains) subunits. Could you please help me or teach me assembling them properly. > > Thanking you, > > With best wishes, > Tata Santosh Rama Bhadra Rao, > PhD Scholar, > C/O Prof Helen Irving, > La Trobe university, > Bendigo, Vic-3550, > Australia. > Email: 19807877(a)students.latrobe.edu.au; > S.Tata(a)latrobe.edu.au > Phone: 0499263974 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Wednesday, 25 May 2022 2:08 AM > To: SANTOSH RAMA BHADRA RAO TATA <19807877(a)students.latrobe.edu.au> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Assembling 2 proteins > > Hello Tata Santosh Rama Bhadra Rao, > It all depends on what information you have already. If you don't know how the pentamer is supposed to look (how the proteins fit together), then there may not be enough information: ChimeraX is not going to predict the pentamer structure for you. > > You said "5 different proteins" which I interpret to mean they are not 5 copies of the same thing, that it is a heteropentamer and not a homopentamer. If they were 5 copies of the same thing (homopentamer), then you might be able to use the "sym" command to build it from one copy, if the input file contains symmetry matrices in the header, or you know the symmetry and can specify it separately: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> > > Otherwise: > You would only use Matchmaker if you also have an already-known structure of a similar pentamer. Then you would open the structure of that pentamer, open the structures of your five proteins (if the same one is multiple copies in the pentamer, you would open it multiple times), and then match each one of them to the similar subunit of the known pentamer. In other words, you would open 6 different PDB files and then use Matchmaker 5 times, once to match each of your proteins to the corresponding subunit of the pentamer. > > Just start Matchmaker (menu: Tools... Structure Comparison... Matchmaker) and in that dialog's Chain Pairing, choose "Specific chain(s) in reference structure with specific chain(s) in match structure". Choose one of your protein chains as the match structure and choose the corresponding chain in the known pentamer as the reference. Apply. Repeat with your second protein chain, etc. > > Here is the Matchmaker help with detailed explanations of all the options: > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#top> > > 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 23, 2022, at 9:49 PM, SANTOSH RAMA BHADRA RAO TATA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi, > > > > I would like to create a pentamer, how can I assemble 5 different proteins subunits into a pentamer. I was trying to use matchmaker but I couldn't. can you please help me with some video how to get in use it or if there is any other way to use the software and create pentamer please let me know. > > > > Thanking you, > > > > With best wishes, > > Tata Santosh Rama Bhadra Rao, > > PhD Scholar, > > C/O Prof Helen Irving, > > La Trobe university, > > Bendigo, Vic-3550, > > Australia. > > Email: 19807877(a)students.latrobe.edu.au; > > S.Tata(a)latrobe.edu.au > > Phone: 0499263974

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FitMap/FitList scripting
by Christian Tüting 27 Jul '22

27 Jul '22

Dear ChimeraX DevTeam, I am currently working on a project which requires fitting a single model multiple times in a map. This is easy doable with the global search parameter, and if n is big enough, all correct locations are found. My collegue Ioannis wrote you a couple of weeks ago to implement a copy function to the fitlist, but this includes only the statistics, but not the translation information of each model. This is only possible by clicking the button "Place Copy", which creates a copy of the model and applies the translation to this model. In the log, there is only the best model with the translation matrix, but if my map does have multiple correct locations, I'm missing this information. I extended the fitmap function in fitcmd.py, so it writes this to a file to the current location called fitmap.txt. This file contains all the statistics and the rotation/translation information. This might be handy for some users. Here is the code: f = open("fitmap.txt", "w") if len(flist) == 0: f.write("No fit found") else: for i, f0 in enumerate(flist): msg = f0.fit_message() f.write(f"Fit #{i+1}\n" + msg + "\n") f.close() Maybe you can include an option "to_text" (which is false by default), to actually add this functionality. Best Christian

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renumber command is unknown
by Kwangjun Lee 27 Jul '22

27 Jul '22

Hello, I am a new user of ChimeraX. I have tried to renumber AA but renumber is an unknown command. Is there any way that I renumber? For example, my current model starts C 1, I want to renumber it to C 20. Thanks for developing a great software.

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Fw: Cofactor Morph
by Colin Levy 27 Jul '22

27 Jul '22

Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:7fc572c6-1ad9-414b-9ab5-b520385d1c2d] ________________________________ From: Colin Levy Sent: 27 July 2022 12:58 To: chimerax-users(a)cgl.ucsf.edu Subject: Cofactor Morph Hello, I am new to Chimera X but looking to generate a morph between 4 states of my protein. The protein morph was very simple to achieve but I have been unable to figure out how to include the cofactor in my morph. The cofactor undergoes important rearrangements during the catalysis which I would like to capture in the movie. Thanks in advance, Colin Dr. Colin Levy c.levy(a)manchester.ac.uk Senior Technical Specialist (XRD) Manchester Institute of Biotechnology, Faculty of Science & Engineering Tel: +44 (0) 161 306 5168 The University of Manchester [cid:736ce72a-e048-40a9-88c8-978c7e7ced3b]

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movie recording while changing threshold level
by Elaine Meng 26 Jul '22

26 Jul '22

Hi Dmitry, You could do it using "perframe" with an embedded "volume level" command in your movie script. For example, the following gradually changes map #2 contour level from 2.5 to 0.5 over 50 image update frames: perframe "volume #2 level $1" range 2.5,0.5 frames 50 See the "perframe" help for details: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > > From: Dmitry Semchonok <semchonok(a)gmail.com> > Date: July 26, 2022 at 8:17:36 AM PDT > > Thank you very much for your tips. > Works as a charm. > How 1 more question if you please - > Is it possible to record a movie while your 3D map constantly changing its threshold volume level (from low to high - which is possible to set) ? > If yes, how? > Thank you in advance. > Sincerely, > Dmitry > >> >> Although it would still be nice to have a separate option, currently >> ndependent rotation can be scripted by using separate turn (or roll) >> commands as in this example from Tom Goddard: >> >> You can use the "model" and "center" options of the turn command to rotate >> each model about their own center. For example, rotating 2 models in 1 >> degree steps around the y axis for a total of 360 degrees >> >> movie record >> turn y 1 360 model #1 center #1 >> turn y 1 360 model #2 center #2 >> wait 360 >> movie encode side-by-side-spin.mp4 >> >> In this example the two models rotate at the same time. The turn command >> like other commands that create a motion returns immediately before any >> motion is done to allow you to start simultaneous motions. Then you use >> the "wait 360" command to wait until 360 frames have been rendered, then >> the .mp4 movie file is made. >>

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Adding H atoms
by Daniel VillanuevaAvalos 25 Jul '22

25 Jul '22

Hello, I am adding hydrogen atoms by entering addh#1 to the command line, and it works but when I export the pdb and import it into houdini, things are messed up. Sometimes it just doesn't show up and other times, just part of the structure shows up. Am I missing something? Thank you, Daniel.

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Re: [chimerax-users] Colab Modelled, but no PDB
by Tom Goddard 25 Jul '22

25 Jul '22

Hi Anthony, Predicting a dimer where the monomer is 1182 residues, so a total of 2364 residues is guaranteed to run out of memory on Colab or Colab Pro -- the GPUs they offer don't have enough memory (at most 16 GB). The web page on AlphaFold performance test cases shows that only an Nvidia A40 with 48 Gbytes of memory handles over 2100 residues. That web page gives results for running AlphaFold via ChimeraX on Colab, but also running AlphaFold installed on our machines at UCSF with either an A40 GPU or an RTX 3090 GPU (24 GB memory). The "no templates" means structure templates were not used when running on our UCSF machines. Tom > On Jul 24, 2022, at 1:35 AM, Anthony Morgan <anthony.morgan(a)pharm.ox.ac.uk> wrote: > > Dear Tom, > > Thanks so very much, this is low-hanging fruit for you, but invaluable for me as I am a newbie. Really appreciate it. The Test link is really illuminating too thank you. > > I had wanted to try a dimer of 1182 residues each, but I am doubting that this is going to work, even with the paid service. Agreed? > On the test page, one of the runs is annotated as “no templates”. I cannot see how you can add templates to the Alphafold panel. I only see Energy Minimization under Options. Am I missing something? > > I’ve now got the pdb of the one model, thank you. It’s obvious once it’s pointed out, but I couldn’t see the wood for the trees. > > Really appreciate your time. > > Kind regards, > > Anthony > > >> On 24 Jul 2022, at 00:37, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Anthony, >> >> AlphaFold predictions on Google Colab of 1200 amino acids often fail as you can see from test cases on this web page >> >> https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> >> >> With free Google Colab you often get a very old Nvidia K80 GPU with 12 Gbytes of memory. With Colab Pro ($10/month) I usually get an Nvidia P100 GPU with 16 Gbytes of memory which can handle slightly bigger proteins. You can check what GPU you got by pressing the "+ Code" button on the Google Colab window, then entering the command "!nvidia-smi" and pressing the play button, which gives output like this >> >> Sat Jul >> 23 23:28:55 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 460.32.03 Driver Version: 460.32.03 CUDA Version: 11.2 | |-------------------------------+----------------------+----------------------+ | GPU Name >> Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 Tesla P100-PCIE... Off | 00000000:00:04.0 >> Off | 0 | | N/A 38C P0 34W / 250W | 16259MiB / 16280MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ >> >> >> To download a completed model after an AlphaFold error (typically out of memory), click on Files in the Google Colab window, then click on the predicted structure, "af1182_unrelaxed_model_1.pdb" in your image, and click the "..." to the right of the file and choose Download from the menu that appears. The file will then appear on your local computer in >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_1 >> >> I'll see if I can add to the ChimeraX ColabFold output the GPU and also make it automatically download partial results in case an error occurs. >> >> Tom >> >> >>> On Jul 23, 2022, at 4:41 AM, Anthony Morgan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear All, >>> >>> I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. >>> >>> I’m running Chimera X 1.4 on a Macbook Air. >>> I want the predicted structure of a fairly large protein (1182 residues). >>> When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). >>> I re-ran the same sequence *without * Energy Minimization. >>> After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. >>> >>> Two questions: >>> >>> There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? >>> If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? >>> >>> Thanks for advice. >>> >>> Kind regards, >>> >>> Anthony >>> >>> <Screen Shot 2022-07-23 at 12.17.14.png> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >

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Movie recording
by Dmitry Semchonok 25 Jul '22

25 Jul '22

Dear colleagues, I have several maps and models that I would like to spin around independently at once and record as a movie. How to do that? Thank you in advance. Kind regards, Dmitry

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Question about commands similar to openModel in Chimera
by Thu Nguyen 25 Jul '22

25 Jul '22

Good morning, I am editing a python script that previously used the command chimera.openModels.list(modelTypes=[chimera.Molecule])to return a list of open molecules. Do we have a similar command in ChimeraX or is there any other way to get a list of protein chains in ChimeraX? Thank you very much. Best regards, Thu

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Colab Modelled, but no PDB
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X and to Colab Alphafold (AF), hope you can help please. * I’m running Chimera X 1.4 on a Macbook Air. * I want the predicted structure of a fairly large protein (1182 residues). * When I first ran Colabfold_predict, it terminated after 90 min (RAM issue). * I re-ran the same sequence *without * Energy Minimization. * After 20 mins, it successfully returned the first model (see attached), but ran into RAM issues again. Two questions: * There is no ‘Prediction’ folder in my Downloads, so how can I download the *.pdb file of model #1 that it clearly has generated? * If I cannot do this, will an upgrade to Colab Pro solve this issue for this size of protein? Thanks for advice. Kind regards, Anthony [cid:8B6C8DAE-A4C3-4F95-8B26-037B6B318679]

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Chimera X Runs But does Not Install
by Anthony Morgan 23 Jul '22

23 Jul '22

Dear All, I’m new to Chimera X, so I am probably doing something wrong. Hope you can help please. I have ‘installed' either v1.3 and, more recently, 1.4 on my Macbook Air (under OSX 10.15.5; 1.1GHz processor, Intel Iris Plus Graphics 1536 MB). * Whilst I can run Chimera X fine (the first time after ‘installing'), it doesn’t appear to be installed locally on my laptop (that I can find). * If I close the App and try and reopen in, it’s not local, and I have to run the Install .dmg every time I want to ‘run’ it, which takes an age. * Under Security > Privacy, Chimera has Full Disk Access. Is this normal behaviour? Thanks for any advice. Regards, Anthony

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Model panel for multi-state objects of dimeric protein
by Enrico Martinez 22 Jul '22

22 Jul '22

Dear ChimeraX users! I am working on the visualization of protein-ligand interactions obtained from docking. In the ChimeraX session I have a loaded session with 88 docking poses (consisting of each frame receptor and ligand) corresponded to the separate objects (1.1 .. to 1.88) >From this ensemble I need to keep only the X object from these multiple states. I have tried to use the following command: close #1 & ~ #1.x which works perfectly for the monomeric protein. But when I am dealing with the analysis of the dimer (with A and B chains) it does not work. Only close #1 still can be used to close ALL objects. Which command could be used to keep the selected state from the ensemble for both monomer and dimer in the same way? Many thanks in advance Cheers Enrico

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Match/Matchmaker multiple segments of two protein sequences
by Gong, Zhen 21 Jul '22

21 Jul '22

Dear Chimerax developers and users, I am wondering if chimerax is able to do match/matchmaker multiple segments of two protein sequences, something like: match #1:3-13, 23-70, 72-81, 86-101 to #2:7-17, 18-66, 67-76, 77-92 cutoffDistance 3 showAlignment true Maybe it can but I did not put the command in correct format. Please help. A related question would be that the default alignment algorithm in chimerax (Needleman-Wunsch or Smith-Waterman) did not do a good job when the two proteins share high structural similarities with low sequence identity. I would like to do the manual sequence alignment, save the alignment as .aln file and use that for matchmaker, iterate with cutoff and get final rmsd of aligned atoms. Is it possible to execute such procedures in chimerax? Many thanks in advance for any helpful suggestion and discussion! Best regards, Zhen

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Difficulties running ChimeraX
by Douglas Marr 21 Jul '22

21 Jul '22

Hey everyone, I've recently updated my laboratory's computer to run linux and ubuntu 22.04. Afterwards, I installed chimeraX for that distribution of ubuntu, but whenever I try to run it, the chimeraX will open, but will be completely frozen. Nothing can be clicked on, nor can the protein structure be rotated. After a few seconds, the computer reports that ChimeraX has stopped and gives me the choice to either wait or force quit. I've tried waiting a very long time, but it always remains frozen, so I think there must be something wrong with my install. Do you guys have any advice on how to fix it? Best, Douglas Marr

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Combining 2 cryo-em maps in one
by Dmitry Semchonok 20 Jul '22

20 Jul '22

Dear colleagues, What are the ways to combine 2(or more) 3D Cryo-em maps in one? Thank you Sincerely, Dmitry

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measure volume using radii
by Noriega, Heather 19 Jul '22

19 Jul '22

Hello Elaine, I hope this email finds you well. I have a couple of questions for you. I have been working on the measurement of enclosed volumes, these are the commands I have been using: molmap #1 12 volume level 0.07 "blob" surface splitbycolor #2.1 view position #3 sameAs #2 measure volume #3.2 I am curious if there is a command to change the map radius to: outer radium: 145 ave radium: 141 inner radium:84 Or if you are aware of a map that already has these coordinates? Lastly, for the volume level is there a default level that maybe is recommended once these radii are in place? The 0.07 level seems to render lower inner volumes (i.e. 2.348 x 10^6) compared to the one below for example. I am going to attach one of my PDB files if you need it. The inner volume calculation through the review is 2.48 x 10^6 cubic angstroms, just as a reference for this file. Thanks so much, and hope to hear soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 AAV_3B_VP3_only.pdb <https://drive.google.com/file/d/12YVgV54awWkEqZe3UWIgUFMhCuWoYl4N/view?usp=…>

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Align command; designating the positions to align
by McClean, Phillip 18 Jul '22

18 Jul '22

Hi, I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details: Model 1 is to be aligned to Model 2; each model only has one chain Model 1 positions (residues=amino acids) 11-323 Model 2 positions ( residues=amino acids) 24-336 When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms. Here is what I thought would work: align #1:11-323 to_atoms #2:24-336 Here is the error message: Unequal number of atoms to pair, 2483 to 2371 I am still trying to understand the nomenclature for understanding residues and atoms. Thanks for any help you can provide. Phil McClean

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showing detergent around the protein
by Dmitry A. Semchonok 18 Jul '22

18 Jul '22

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ChimeraX 1.4 frozen on RHEL 8.6 and 9.0
by Steven Chou 17 Jul '22

17 Jul '22

Dear ChimeraX developers, I installed ChimeraX 1.4 (both stable release and daily built) on RHEL 8.6 and 9.0. I installed all the ChimeraX 1.4 dependencies using "yum install" from RHEL installation USB. After the installation, I was able to start the GUI, but unable to click any button on the GUI, therefore, I was unable to report the bug from the GUI either. I also tried ChimeraX 1.3 stable release on RHEL 8.6, and everything was normal. Steven -- Steven Chou

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ChimeraX/1.3 could not start in CentOS 7
by Long Gui 15 Jul '22

15 Jul '22

Dear ChimeraX developers, I am installing the ChimeraX/1.3 in one of our GPU workstation (CentOS Linux 7). The installation processed well but after I tried to start the chimerax program, it showed: QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms" ... QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqeglfs.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "eglfs" ] }, "archreq": 0, "className": "QEglFSIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("eglfs") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqlinuxfb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "linuxfb" ] }, "archreq": 0, "className": "QLinuxFbIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("linuxfb") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimal.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimal" ] }, "archreq": 0, "className": "QMinimalIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("minimal") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqminimalegl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "minimalegl" ] }, "archreq": 0, "className": "QMinimalEglIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("minimalegl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqoffscreen.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "offscreen" ] }, "archreq": 0, "className": "QOffscreenIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("offscreen") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqvnc.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "vnc" ] }, "archreq": 0, "className": "QVncIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("vnc") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-egl" ] }, "archreq": 0, "className": "QWaylandEglPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-egl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-generic.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland" ] }, "archreq": 0, "className": "QWaylandIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-egl.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-egl" ] }, "archreq": 0, "className": "QWaylandXCompositeEglPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-xcomposite-egl") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqwayland-xcomposite-glx.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "wayland-xcomposite-glx" ] }, "archreq": 0, "className": "QWaylandXCompositeGlxPlatformIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("wayland-xcomposite-glx") QFactoryLoader::QFactoryLoader() looking at "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so" Found metadata in lib /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so, metadata= { "IID": "org.qt-project.Qt.QPA.QPlatformIntegrationFactoryInterface.5.3", "MetaData": { "Keys": [ "xcb" ] }, "archreq": 0, "className": "QXcbIntegrationPlugin", "debug": false, "version": 331520 } Got keys from plugin meta data ("xcb") QFactoryLoader::QFactoryLoader() checking directory path "/usr/libexec/UCSF-ChimeraX/bin/platforms" ... Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory) QLibraryPrivate::loadPlugin failed on "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so" : "Cannot load library /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so: (libxcb-icccm.so.4: cannot open shared object file: No such file or directory)" 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 0x00007f107e0f8740 (most recent call first): File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 159 in __init__ File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 577 in init File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in <module> File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main Aborted (core dumped) I have also typed: ldd /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/libqxcb.so linux-vdso.so.1 => (0x00007ffc9f19e000) libQt5XcbQpa.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5XcbQpa.so.5 (0x00007f760e4a4000) libfontconfig.so.1 => /lib64/libfontconfig.so.1 (0x00007f760e245000) libfreetype.so.6 => /lib64/libfreetype.so.6 (0x00007f760df86000) libz.so.1 => /lib64/libz.so.1 (0x00007f760dd70000) libQt5Gui.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Gui.so.5 (0x00007f760d43e000) libQt5DBus.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5DBus.so.5 (0x00007f760d1b2000) libQt5Core.so.5 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libQt5Core.so.5 (0x00007f760c9bc000) libGL.so.1 => /lib64/libGL.so.1 (0x00007f760c712000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f760c4f6000) libX11-xcb.so.1 => /lib64/libX11-xcb.so.1 (0x00007f760c2f4000) libxcb-icccm.so.4 => not found libxcb-image.so.0 => not found libxcb-shm.so.0 => /lib64/libxcb-shm.so.0 (0x00007f760c0ef000) libxcb-util.so.1 => /lib64/libxcb-util.so.1 (0x00007f760bee8000) libxcb-keysyms.so.1 => /lib64/libxcb-keysyms.so.1 (0x00007f760bce5000) libxcb-randr.so.0 => /lib64/libxcb-randr.so.0 (0x00007f760bad5000) libxcb-render-util.so.0 => not found libxcb-render.so.0 => /lib64/libxcb-render.so.0 (0x00007f760b8c6000) libxcb-shape.so.0 => /lib64/libxcb-shape.so.0 (0x00007f760b6c2000) libxcb-sync.so.1 => /lib64/libxcb-sync.so.1 (0x00007f760b4ba000) libxcb-xfixes.so.0 => /lib64/libxcb-xfixes.so.0 (0x00007f760b2b2000) libxcb-xinerama.so.0 => /lib64/libxcb-xinerama.so.0 (0x00007f760b0af000) libxcb-xkb.so.1 => /lib64/libxcb-xkb.so.1 (0x00007f760ae92000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f760ac6a000) libXext.so.6 => /lib64/libXext.so.6 (0x00007f760aa58000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f760a719000) libxkbcommon-x11.so.0 => /lib64/libxkbcommon-x11.so.0 (0x00007f760a511000) libxkbcommon.so.0 => /lib64/libxkbcommon.so.0 (0x00007f760a2d1000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f760a0cc000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f7609dc4000) libm.so.6 => /lib64/libm.so.6 (0x00007f7609ac2000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f76098ab000) libc.so.6 => /lib64/libc.so.6 (0x00007f76094dd000) libxcb-icccm.so.4 => not found libxcb-image.so.0 => not found libxcb-render-util.so.0 => not found libgthread-2.0.so.0 => /lib64/libgthread-2.0.so.0 (0x00007f76092da000) libglib-2.0.so.0 => /lib64/libglib-2.0.so.0 (0x00007f7608fc3000) libexpat.so.1 => /lib64/libexpat.so.1 (0x00007f7608d99000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00007f7608b93000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f7608983000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00007f7608758000) libdbus-1.so.3 => /lib64/libdbus-1.so.3 (0x00007f7608507000) libicui18n.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicui18n.so.56 (0x00007f760806e000) libicuuc.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicuuc.so.56 (0x00007f7607cb5000) libicudata.so.56 => /usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PyQt5/Qt/plugins/platforms/../../lib/libicudata.so.56 (0x00007f76062d2000) /lib64/ld-linux-x86-64.so.2 (0x00007f760ea02000) libGLX.so.0 => /lib64/libGLX.so.0 (0x00007f76060a2000) libGLdispatch.so.0 => /lib64/libGLdispatch.so.0 (0x00007f7605dce000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f7605bca000) libpcre.so.1 => /lib64/libpcre.so.1 (0x00007f7605967000) libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f7605736000) libcap.so.2 => /lib64/libcap.so.2 (0x00007f7605530000) librt.so.1 => /lib64/librt.so.1 (0x00007f7605328000) libselinux.so.1 => /lib64/libselinux.so.1 (0x00007f7605101000) liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f7604eda000) liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f7604ccb000) libgcrypt.so.11 => /lib64/libgcrypt.so.11 (0x00007f7604a4a000) libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f7604844000) libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f760462a000) libdw.so.1 => /lib64/libdw.so.1 (0x00007f76043d9000) libattr.so.1 => /lib64/libattr.so.1 (0x00007f76041d3000) libelf.so.1 => /lib64/libelf.so.1 (0x00007f7603fbb000) I have searched the ChimeraX mail list and found several previous email talking about this issue but I have tried all of them For instance, I have re-install the libxcb library: sudo yum reinstall libxcb but none of it could work. Would you like to check this and let me know how to solve this problem? Thanks a lot! Long Gui, Ph.D. Postdoc Researcher, Nicastro Lab University of Texas Southwestern Medical Center Long.Gui(a)utsouthwestern.edu Tel: (214)-645-1561 ________________________________ UT Southwestern Medical Center The future of medicine, today.

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