- ChimeraX-users - RBVI Mailing Lists

Feature Request From Chimera
by Anderson, Jacob 05 Apr '22

05 Apr '22

Love ChimeraX - the UI is really enjoyable! I was curious if I could put in a plug for biomtSet true option to be ported to ChimeraX's sym command! I expect a lower priority, but would love to use this tool in ChimeraX in some future version.

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Re: [chimerax-users] [Chimera-users] Question regarding chimerax module
by Tom Goddard 04 Apr '22

04 Apr '22

Hi Prathvi, There is no ChimeraX Python library yet, it is only distributed as a standalone application including its own Python. But we have funding to make a library for PyPi and/or Anaconda so that should happen in the next year. You can use the ChimeraX Python Jupyter shell to try out Python code, menu entry Tools / General / Shell. Tom > On Apr 2, 2022, at 10:30 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello again Elaine, > > Is it possible to install the chimerax module in anaconda for usage in jupyter notebook? > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] ChimeraX-users Digest, Vol 64, Issue 4
by Martti Tolvanen 04 Apr '22

04 Apr '22

As a pragmatic solution to the task of seeing both chains even when one is sometimes behind the other (as is inevitable with any superimposed models), you could make one ribbon semi-transparent. -Martti -----Original Message----- From: chimerax-users-request(a)cgl.ucsf.edu [mailto:chimerax-users-request@cgl.ucsf.edu] Sent: 2. huhtikuutata 2022 22:00 To: chimerax-users(a)cgl.ucsf.edu Subject: ChimeraX-users Digest, Vol 64, Issue 4 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via the World Wide Web, visit https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users or, via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..."

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Saving ChimeraX log, saving protein sequence to file
by Elaine Meng 03 Apr '22

03 Apr '22

Hi Prathvi, These answers are both for ChimeraX so I CC'd the chimerax-users list. (1) ChimeraX command "log save" saves it as HTML <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> (2) in ChimeraX, open the structure, show the sequence of the chain of interest (menu: Tools... Sequence... Show Sequence Viewer, choose chain if there is more than one chain preset). Showing the sequence can also be done with the ChimeraX "sequence chain" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#chain> Then in the sequence viewer window, the context menu has a choice to save the contents (File... Save As...). <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#context> You show a context menu in ChimeraX with Ctrl-click or right-click (depending on your system) in the tool window. <https://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> In Chimera, #2 is similar, use main tools menu to show sequence, use sequence-viewer tool's menu to save it to file. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/…> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 2, 2022, at 9:51 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot Elaine. It helped enormously. I just have 2 more questions: > > 1. After running the dssp command in chimeraX, is there a command to save the reply log to file using a command? I searched for it & landed up at: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003739.html but chimeraX throws the "Unknown command" error. > > 2. Is there a way to extract polypeptide sequence from a PDB file & save as a FASTA file or even a simple text file which simply contains a string representing the amino acids as single letters alphabets? >

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How to draw the surface of cavity
by 令怡 01 Apr '22

01 Apr '22

Dear ChimeraX Staff, Hello! I would like to know if there's a way to display the cavity like this? I've been studying for a long time without a clue. Thank you for your attention! Best Regards, Lingyi | | Xu, Lingyi Ph.D. | | Zhejiang University School of Medicine | 签名由网易邮箱大师定制

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Analysis of Hydrogen bonds in multi-model pdb
by Enrico Martinez 01 Apr '22

01 Apr '22

Dear ChimeraX users! Another question related to the analysis of the multi-model pdb obtained from protein-ligand docking calculations. I am using ChimeraX to visualise protein-ligand interactions between each pose predicted by docking and protein in my script: # calculate H-bond in first 10 frames of the multi-model pdb hbonds #1.1-10&protein restrict #1.1-${hb_poses}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile output.log Is it possible to print (or save somewhere?) the number of the state that has 1) the maximal number of the hydrogen bonds? 2) has a particular hydrogen bond of my interest? Cheers, Enrico

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A question about model position matrix
by Zheng Ruan 31 Mar '22

31 Mar '22

Dear ChimeraX users, I'm trying to understand the model position matrix. According to the documentation, "Each matrix is reported as 12 comma-separated numbers, corresponding to a 3x3 rotation matrix and a translation vector in the fourth column. Ordering is row-by-row, such that the translation vector is given as the fourth, eighth, and twelfth numbers." When I load a model into ChimeraX and use "view matrix" command to check the model position, I got "#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The rotation matrix for #1 is an identity matrix with translation vector to be 0 for all directions. However, if I rotate the model using the command "turn z 90 models #1" and then check the model position using "view matrix", I got something like "#1,1.1102e-16,-1,0,689.33,1,1.1102e-16,0,-1.9358,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0". The translation vector for #1 becomes (689.33, -1.9358, 0). Since I only applied a simple rotation of the model along z-axis, why the translation vector becomes non-zero in this case? I hope to have a better understanding of how ChimeraX handles the model position matrix to describe model positions. Thank you so much! Best, Zheng

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Bundle Module Import
by Zeng, Katie 31 Mar '22

31 Mar '22

Hi all, I am currently working on a membrane builder bundle called AmberLipidBundle. I have folder './src/ui' (containing several .py files, e.g. lipid_form.py) and I import it inside .py files with the line 'from AmberLipidBundle.ui.lipid_form import xxx'. I have been testing the bundle using the command 'devel build [path]' and everything works fine. But when I switch to the command 'devel install [path]', I get an error: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Membrane Builder in bundle AmberLipidBundle: No module named 'AmberLipidBundle.ui' Do you have any idea how to fix this? Thank you so much for your help! Best Regards, Katie

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get current clipping plane positions
by Pranav Shah 31 Mar '22

31 Mar '22

Hi Elaine and Co., Is there a way to read the current clipping plane positions in chimerax? 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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get current clipping positions
by Pranav Shah 30 Mar '22

30 Mar '22

Hi Elaine and Co., Is there a way to read the current clipping plane positions in chimerax? 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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Selection of the organic ligand
by Enrico Martinez 30 Mar '22

30 Mar '22

Dear ChimeraX users! Normally I use the selection name "ligand" to select all atoms of the organic ligand. For example: define centroid ligand name lig_com sometimes depending on the pdb file, this command also selects one residue (located in the pdb file just near the ligand), considering it also as a part of the ligand.. May I use another selection to explicitly exclude all 20 natural amino-acids from the ligand selection? Many thanks in advance! Enrico

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Re: [chimerax-users] [Chimera-users] using old cmd files in chimerax
by Elaine Meng 29 Mar '22

29 Mar '22

Hi Bryan, If I understand correctly, by "old" you mean works in Chimera... and would like to know how to get to the same end results except in ChimeraX, so I also CC'd chimerax-users(a)cgl.ucsf.edu. Since ChimeraX and Chimera commands do have differences, you cannot simply open Chimera command files in ChimeraX. Possible routes to getting what you want: (1) text-edit the cmd file to change Chimera commands to ChimeraX commands, change the filename suffix of that plain-text file to .cxc and then open it in ChimeraX. ChimeraX does have the capability to read ResMap maps and then use the values to color a surface, so this is a viable route. The downside is that it requires knowing or looking up the differences in the commands. Many commands are highly similar so it wouldn't necessarily be as bad as it sounds, however. You can open both the original map and the ResMap map files with ChimeraX command "open", control which is shown as a surface with the ChimeraX Volume Viewer tool or "volume" command, and color the surface by the values of the other map using "color sample". See ChimeraX User Guide: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/volumeviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map> (2) or simply dispense with trying to use a command script and instead use ChimeraX tools and/or commands interactively. You can use ChimeraX menu: File... Open to open the maps (aka volume data), and there is a Surface Color tool (same function as "color sample" command): <https://rbvi.ucsf.edu/chimerax/docs/user/tools/surfacecolor.html> (3) in the more general case of Chimera command scripts involving atomic data, you can open/run the script in Chimera, export a session from Chimera as a ChimeraX python file (Chimera menu: File... Export Scene or Chimera command "export") and then open that file in ChimeraX to regenerate the session contents. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/export.html> However, this Chimera->ChimeraX export feature does not (yet) cover maps, map isosurfaces, and a few other things. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 28, 2022, at 12:01 PM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > How do I used/open old cmd scripts I have or outputs from things like resmap in chimerax? >

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addh
by Voss Jonathan Mark 28 Mar '22

28 Mar '22

Hello, I would like to protonate ASP, GLU, and HIS side chains throughout a model. I'm a little confused about the syntax of the useAspName, useGluName, etc. option. I've looked around but haven't found any examples. Could you provide one? Furthermore, once a side chain is protonated, will ISOLDE recognize that site as being charged? Or does this need to be specified somehow? Best -Jon

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Question about using ChimeraX
by 令怡 25 Mar '22

25 Mar '22

Dear developers, Hello! I recently encountered some problems when using ChimeraX. When displaying the structure with cartoon, some helix is displayed as loop (Fig A). How to force it to be displayed as helix? I checked the User Guide and used the command "setattr sel residues is_helix true" for the selected amino acids, but only some amino acids can be displayed as helix (Fig B). Is that need to change ss_ id? I have tried, but it didn't work. I will appreciate it if you could answer my question. Looking forward to your reply! Best Regards Lingyi

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Analysis of the protein-ligand docking results with the X-ray data
by Enrico Martinez 25 Mar '22

25 Mar '22

Dear ChimeraX users! First, I very much appreciate the support of the Chimera team related to my questions! I have another question regarding analysis of the protein ligand interactions in the docking poses saved in multi-model format. I need to find a possibility (e.g. via some script that could be executed in the chimeraX) to compare each docking pose with the X-ray structure (loaded as the separate model) in order to select automatically the model (= docking solution) which may fit better to the X-ray structure. The problem is that the ligand used in the docking is not the same as in the X-ray structure (although they are quite similar in the functional groups). Assuming that the both pdbs ((docking poses, and X-ray structure)) have been superimposed (based on the protein atoms) how could I automatically switch to the model (in the docking ensemble) that has the closest position of the ligand as in the X-ray structure? Here is the example of the workflow: open docking_ensemble.pdb open xray.pdb # fit X-ray structure to the first docking solution based on the protein atoms match #2 to #1.1 # compare each docking pose (ligand with X-ray and determine which model has the most similarity to it # determine the model #1.X which would have closest similarity to the X-ray structure # close all the models, with the exemption of the model #1.X close ~ #1.X I would be grateful for any suggestions for possible algorithms! With kind regards, Enrico

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Problem with ChimeraX
by Gawargi, Flobater I 23 Mar '22

23 Mar '22

Hi, I am a new Chimerax user and I have encountered a problem that I hope you can help me fix. I installed 1.4 version and it shows "Startup Messages notes available bundle cache has not been initialized yet Updating list of available bundles failed: Internal Server Error” all I am trying to do is use alpha fold to predict structure of 2 proteins separated by comma. And it shows this error "Missing or invalid "sequences" argument: Sequences argument "cvfpfvflgkqyssctsdgrrdgrlwcattsnfdtdkkwgfcpdqgyslflvaahefghalgldhssvpealmyplysylegfplnkddidgiqylygrgskpdprppattttepqptapptmcptipptayptvgptvgptgapspgptsspspgptgapspgptapptagsseasteslspadnpcnvdvfdaiaeiqgalhffkdgwywkflnhrgsplqgpfltartw" is not a chain specifier, alignment id, UniProt id, or sequence characters” I am using an M1 MacBook, but I have also tried it on windows running windows 10 and got the same issue. I would appreciate your input to fix this issue. Thank you, Flobater Gawargi The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Re: [chimerax-users] [Chimera-users] tile function
by Elaine Meng 23 Mar '22

23 Mar '22

Hi Bryan, I'm happy to report that current versions of ChimeraX work the way that you describe. I.e. you need to get the daily build <https://www.rbvi.ucsf.edu/chimerax/download.html#daily> ...since according to the ChimeraX change log, this feature was added in January, after the 1.3 release. <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> By the way, there is a chimerax-users(a)cgl.ucsf.edu address for asking about ChimeraX, which I've CC'd on this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2022, at 11:39 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Is there an option with the tile command in ChimeraX to get the volumes to rotate in place like it did with Chimera or maybe a different command now that I haven’t found yet? Right now when I use Tile the maps rotate together round a single axis, but I liked it a lot in chimera with the tile were the maps rotated on their own axis. Thanks I’m sure it’s most likely a command option that I missed in the documentation or a new command I haven’t found yet. > > Bryan Hansen > Computational Biologist / Electron Microscopist > NIH/NIAID/RTB/RML/EMU > Rocky Mountain Laboratories > 903 S. 4th St > Hamilton, MT 59840 > 406.363.9202 > > *********************************************************** > The information in this e-mail and any of its attachments is confidential and may contain sensitive information.It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error, please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. > *********************************************************** > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Query regarding plugin development
by KUSHAGRA RUSTAGI 23 Mar '22

23 Mar '22

Greetings, I am Kushagra Rustagi an undergraduate student at IIT Roorkee who is working on developing a ChimeraX plugin. I had some doubts: 1. Can we open a session in ipython? Basically while developing codes for chimerax is there a way to open chimera command line in ipython? 2. For example if we want to run an inbuilt function of any particular class in ChimeraX and we want to find all methods associated with that class. How do we go about doing it? 3. How to go about exploring surface generation functions in ChimeraX? Regards, Kushagra Rustagi

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chimerax fails to start
by ZOUHIR Samira 23 Mar '22

23 Mar '22

Hello, I have an issue starting ChimeraX_1.3 for ubuntu20.04. "chimerax" command gives the following: NOTE: available bundle cache has not been initialized yet NOTE: Updating list of available bundles failed: Internal Server Error WARNING: WebEngineContext used before QtWebEngine::initialize() or OpenGL context creation failed. WARNING: QGLXContext: Failed to create dummy context ERROR: Could not create OpenGL context BUG: Failed to create OpenGL context for format QSurfaceFormat(version 2.0, options QFlags<QSurfaceFormat::FormatOption>(), depthBufferSize 24, redBufferSize -1, greenBufferSize -1, blueBufferSize -1, alphaBufferSize -1, stencilBufferSize 8, samples 0, swapBehavior QSurfaceFormat::DefaultSwapBehavior, swapInterval 1, colorSpace QSurfaceFormat::DefaultColorSpace, profile QSurfaceFormat::NoProfile) Aborted (core dumped) Any advice please? Best, Sam

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how to vizualise hydrogen bonds between ligand and back-bone of protein?
by Enrico Martinez 23 Mar '22

23 Mar '22

Dear ChimeraX users! I am using the following command to calculate and save in the log information regarding hydrogen bonds based on the consideration of multi-frame pdb of the complex # calculate hydrogen bonds for the first 14 frames of pdb hbonds #1.1-14}&protein restrict #1.1-14}&ligand coordsets false interModel false makePseudobonds false log true intraRes false saveFile log.txt which gives me something like this: structure_name: 18 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): #1.1/? ASN 142 ND2 #1.1/A UNL 1 N #1.1/? ASN 142 2HD2 3.313 2.522 #1.1/? SER 144 N #1.1/A UNL 1 O #1.1/? SER 144 H 2.953 2.224 #1.1/A UNL 1 O #1.1/? LEU 141 O #1.1/A UNL 1 H 2.753 1.877 #1.2/? ASN 142 ND2 #1.2/A UNL 1 N #1.2/? ASN 142 2HD2 3.240 2.429 #1.2/A UNL 1 O #1.2/? HIS 163 NE2 #1.2/A UNL 1 H 3.317 2.389 #1.3/? SER 144 N #1.3/A UNL 1 O #1.3/? SER 144 H 3.005 2.272 #1.3/A UNL 1 O #1.3/? LEU 141 O #1.3/A UNL 1 H 2.738 2.098 #1.3/A UNL 1 O #1.3/? SER 144 OG #1.3/A UNL 1 H 3.054 2.250 #1.6/A UNL 1 O #1.6/? HIS 163 NE2 #1.6/A UNL 1 H 3.172 2.528 #1.7/? CYS 145 SG #1.7/A UNL 1 O #1.7/? CYS 145 HG 3.828 2.949 #1.7/A UNL 1 O #1.7/? LEU 141 O #1.7/A UNL 1 H 3.201 2.393 #1.8/? GLY 143 N #1.8/A UNL 1 O #1.8/? GLY 143 H 3.060 2.238 #1.8/? HIS 163 NE2 #1.8/A UNL 1 O no hydrogen 3.084 N/A #1.9/? GLN 189 NE2 #1.9/A UNL 1 O #1.9/? GLN 189 1HE2 3.148 2.139 #1.10/? GLN 189 NE2 #1.10/A UNL 1 O #1.10/? GLN 189 1HE2 2.941 2.289 #1.10/A UNL 1 O #1.10/? GLN 189 OE1 #1.10/A UNL 1 H 2.985 2.213 #1.11/? GLN 189 NE2 #1.11/A UNL 1 O #1.11/? GLN 189 1HE2 2.803 1.910 #1.14/? ASN 142 ND2 #1.14/A UNL 1 O #1.14/? ASN 142 2HD2 3.199 2.369 ----------------------------------------------------------------------------- I noticed that in the log there is always information regarding interactions between the ligand and the side chains of the protein but nothing regarding hydrogen bonds involved backbone of the protein (Which is confirmed by X-ray data for my complex). for the test I used py@ol to visualise h-bonds and may see in the 12th frame the hydrogen bond involved backbone of the protein.. How could I modify my script to consider additional hydrogen bonds involving backbone atoms ? Thank you very much in advance! Cheers Enrico

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Drawing rotation axis in ChimeraX
by lvhailiyaohui 23 Mar '22

23 Mar '22

Dear Sir or Madam, This is Yaohui Li, a ChimeraX user educationally. We are trying to prepare a figure with rotation axis by chimeraX, but haven’g found a way to draw the rotation axis yet. Could you give us any suggestions on drawing the rotation axis in ChimeraX? Thanks a lot! Looking forward to hearing from you! Bests, Yaohui 网易VIP邮箱提醒：安全收发邮件，务必核实往来邮件地址、银行账号等机密信息，请通过电话或视频等多种方式确认信息真实性，提高警惕，请勿轻易透露个人重要信息。 Alert message of Netease Vipmail：Never provide your password, security questions, verification codes, or any other personal important information details to anyone else. You can identify mail message by telephone,video-chat or other ways.You should make sure that your email address, bank account and other confidential information as secure as possible. Thank you for keeping your email account secure.

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ChimeraX does not work on windows server running RDS
by Fabian Glaser 22 Mar '22

22 Mar '22

Dear Elaine, When we try to run ChimeraX 1.3 on server 2016 windows on a computer farm (for teaching purposes), nothing happens, despite that the installation worked perfectly well. Any suggestion what we could do? Thanks a lot in advance, Fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

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find clash/contacts for protein-ligand complexes
by Enrico Martinez 21 Mar '22

21 Mar '22

Dear ChimeraX users! I would like to use the "find clash/contacts" command to find if the position of the ligand (predicted by docking) is in the proximity to the two residues located in the binding pocket. I have already tried #check contacts in first 10 docking poses contacts #1.1-10&protein& :41,49 restrict #1.1-10&ligand interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep$.log This gives me the output about 84 detected contacts: #1.14/? MET 49 CE #1.14/A UNL 1 C 0.191 3.449 #1.4/? MET 49 CG #1.4/A UNL 1 C 0.147 3.613 #1.7/? HIS 41 NE2 #1.7/A UNL 1 C 0.131 3.389 #1.10/? MET 49 CE #1.10/A UNL 1 C 0.120 3.520 #1.3/? HIS 41 CD2 #1.3/A UNL 1 C 0.095 3.425 #1.3/? MET 49 CG #1.3/A UNL 1 C 0.089 3.551 #1.8/? MET 49 CG #1.8/A UNL 1 C 0.070 3.510 #1.5/? MET 49 CG #1.5/A UNL 1 C 0.023 3.617 #1.4/? MET 49 CE #1.4/A UNL 1 C 0.006 3.754 ... #1.10/? HIS 41 CG #1.10/A UNL 1 C -0.377 3.837 #1.1/? HIS 41 O #1.1/A UNL 1 C -0.378 3.618 #1.14/? HIS 41 CD2 #1.14/A UNL 1 S -0.382 3.924 may I further limit the number of the detected contacts (e.g. via modifying geometrical criteria) in order to be able to draw a conclusion about the proximity of the ligand to the selected residues, which may be done according to the values in the Overlap column? Many thanks in advance! Enrico

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Re: [chimerax-users] ChimeraX does not work on windows server running RDS
by Tom Goddard 21 Mar '22

21 Mar '22

Hi Fabian, If Chimera works and ChimeraX does not it may be that your system graphics driver does not support the more modern OpenGL graphics version (3.3) required by ChimeraX. Our UCSF servers are down -- below is a PDF of the ChimeraX troubleshooting page which talks about inadequate graphics drivers. Maybe starting in debug mode will indicate if that is a problem. Tom > On Mar 21, 2022, at 11:14 AM, Fabian Glaser <fabian.glaser(a)gmail.com> wrote: > > Dear Tom, > > Thanks a lot for your quick answer. > Yes, Chimera works, and ChimeraX does not show anything, the link you provided seems to be not available at this moment. > > Can we provide you with additional information? > > Thanks, > > Fabian > > -------------------------- > Fabian Glaser, PhD > > Structural and Computational Biology Unit > The Lorry I. Lokey Center for Life Sciences and Engineering > Technion - Israel Institute of Technology, Haifa, Israel > >> On 21 Mar 2022, at 20:08, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Fabian, >> >> Do you mean the ChimeraX window does not appear? The ChimeraX troubleshooting web page describes how to start in debug mode to get an error message which might indicate the problem >> >> https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#winstart <https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#winstart> >> >> Have other versions of ChimeraX or Chimera worked on these computers? >> >> Tom >> >> >> >>> On Mar 21, 2022, at 5:26 AM, Fabian Glaser via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Dear Elaine, >>> >>> When we try to run ChimeraX 1.3 on server 2016 windows on a computer farm (for teaching purposes), nothing happens, despite that the installation worked perfectly well. >>> >>> Any suggestion what we could do? >>> >>> Thanks a lot in advance, >>> >>> Fabian >>> >>> -------------------------- >>> Fabian Glaser, PhD >>> >>> Structural and Computational Biology Unit >>> The Lorry I. Lokey Center for Life Sciences and Engineering >>> Technion - Israel Institute of Technology, Haifa, Israel >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

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ChimeraX does not work on windows server running RDS
by Fabian Glaser 21 Mar '22

21 Mar '22

Dear all, When we try to run ChimeraX 1.3 on server 2016 windows, nothing happens, despite that the installation worked perfectly well. Thanks a lot, Fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

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