- ChimeraX-users - RBVI Mailing Lists

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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Superimposition with chimeraX
by 이현숙 20 Mar '22

20 Mar '22

Hello. I would like to superimpose chemical structure to protein structure. Protein structure was created by tool - structure predict - alphafold. Chemical structure was added to the protein structure( via tool - structure edit - add smile string - build structure) My question is : when chemical structure is added on the protein structure, chemical structure is located at the active site OR just located at the center of protein structure ? I want the 1st one (located at the active site) then how can I do through ChimeraX? Thank you. Hyunsook

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Aligning volumes without resampling - Saving a map relative to another
by Helge Paternoga 17 Mar '22

17 Mar '22

Hi, I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map. Many thanks in advance, Helge

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Uninstalling ChimeraX
by Shivam Gupta 17 Mar '22

17 Mar '22

Dear Support team, I am using a ChimeraX commercial license ( RHEL-8 ) but now I am trying to uninstall it using the command 'yum remove chimerax' with and without root privileges but hard luck. I also tried to use 'ChimeraX_main.py --uninstall' from its own directory but again no success. Could you please guide me over uninstalling chimerax. Thank you Looking forward to hearing from you soon. Have a nice day ahead. Thanks -- 株式会社ファーマフーズ Biomedical Department グプタシヴァム Gupta Shivam 〒615-8245 京都市西京区御陵大原1-49 TEL:075-748-9811 FAX:075-948-9818 E-mail: *shivam-gupta(a)pharmafoods.co.jp <a-higashiyama(a)pharmafoods.co.jp>* URL: http://www.pharmafoods.co.jp/

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map segmentation
by Dmitry Semchonok 17 Mar '22

17 Mar '22

Dear colleagues, Fast questions. 1. How to segment the selected segment? So I have a) segmented the map using the segment map tool b) selected 1 piece. b) I want to segment that selected piece on the smaller parts 2. how to increase the threshold of the segmented map? Thank you Kind regards, Dmitry

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Fwd: Chimerax ISOLDE install Error
by Eric Pettersen 17 Mar '22

17 Mar '22

> Begin forwarded message: > > From: HONG ZHAN <hzhan3(a)wisc.edu <mailto:hzhan3@wisc.edu>> > Subject: Chimerax ISOLDE install Error > Date: March 17, 2022 at 8:02:25 AM PDT > > > Hi all, > > I am installing ISOLDE on my daily build ChimeraX (v1.4.dev202203170703 (2022-03-17) and it showed this error: > > Downloading bundle ChimeraX_ISOLDE-1.3-cp39-cp39-win_amd64.whl > Looking in indexes: https://pypi.org/simple <https://pypi.org/simple>, https://cxtoolshed.rbvi.ucsf.edu/pypi/ <https://cxtoolshed.rbvi.ucsf.edu/pypi/> > Processing c:\users\unchwaniwala\downloads\chimerax_isolde-1.3-cp39-cp39-win_amd64.whl > Requirement already satisfied: ChimeraX-Arrays~=1.0 in c:\program files\chimerax 1.4.dev202203170703\bin\lib\site-packages (from ChimeraX-ISOLDE==1.3) (1.0) > ERROR: Could not find a version that satisfies the requirement ChimeraX-AtomicLibrary~=4.2 (from chimerax-isolde) (from versions: none) > ERROR: No matching distribution found for ChimeraX-AtomicLibrary~=4.2 > > I tried to look up online but not very useful information I found. Is a missing package I should install? Or how can I chnage the range for ChimeraX-AtomicLibrary? > > Thanks! > Hong

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Placing Centroid at center of selection
by German Barcenas 16 Mar '22

16 Mar '22

Hello, I am trying to place a centroid <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/define.html#centroid> marker at the center of a selection of atoms, for example in the middle of a benzene ring that is at some arbitrary position in my system. I want to do some distance measurements here. I can do something like this: shape sphere color orange radius 0.25 center sel where the center sel places the sphere where I want, but these spheres can't be used to make measurements. Instead I think I need a marker object, such as: define centroid radius 0.25 color orange But I don't know how to recreate that `center sel` position. I have tried define centroid radius 0.25 color orange position center define centroid radius 0.25 color orange position center sel define centroid radius 0.25 color orange position sel These do not work. I am under the impression that the centroid is a marker object and should have some position argument. Can anyone help me? Thanks, -- German Barcenas Ph.D Candidate | Materials Science and Engineering Materials Modeling and Theory Group Boise State University germanbarcenas(a)u.boisestate.edu | 940-577-5094

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Chimera and ChimeraX commercial license
by Jai Vekeria 15 Mar '22

15 Mar '22

Hello, My name is Jai, I am a data scientist at Tectonic Therapeutics in Watertown MA, I would like to purchase 5 commercial licenses for Chimera and ChimeraX, I am assuming based on the little technical information included on the product page, that any windows 10 64-bit machine would suffice, we have some machine with a 1 Gb of ram and a 1.2Ghz processor and no GPU that we plan to use. Thanks, Jai Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.

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Outputting ChimeraX RMSD values after using matchmaker in a .PY script?
by Steven Truong 14 Mar '22

14 Mar '22

Dear ChimeraX admins, I am using matchmaker (mmaker) since the RMSD calculations done using the function have been very useful. However, I’m currently having some trouble outputting these values. At first, I tried to use matchmaker in a .PY script and then output these values via “log save”. Unfortunately, I haven’t been able to get this to work because whenever I try to do “log save” in a script (in terminal/command line), I get “no log tool to save”. Is there a way to “log save” if running a .PY script in a command line? Or is there a simpler way to get the values I need from matchmaker? Thank you for your help, Steven Truong sdt45(a)cam.ac.uk<mailto:sdt45@cam.ac.uk>

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solvate
by Joe Greenstone 13 Mar '22

13 Mar '22

In Chimera, solvation can be done via Tools/Structure Editing/Solvate How is solvation done in ChimeraX ? Thanks in advance.

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Aligning small molecules, ligands
by Noriega, Heather 12 Mar '22

12 Mar '22

Hello, I hope you are well Elaine. I am wondering if there is a way to align my combined model UNL to my model 2. In hopes this could be a reference model of my docking done in Chimera for future builds. I did figure out the bonding, thank you. :) I attached the session, and have read the align command. I am just unsure how to manipulate it to superimpose the ligand. align matchatoms (the whole model 2) toAtoms (UNL on model 1). Thanks for your help. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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2D Residue Plot
by Avinoam Aryeh Singer 11 Mar '22

11 Mar '22

Hey there, I was wondering whether there was a way to control the angle of the 2D residue plot generated from the "Interfaces" tool, such that creating plots from two aligned proteins will give me comparable plots. As you can see in the image below, the two structures are slightly rotated relative to one another, despite being aligned. Thanks! Avi Singer ?[cid:05b972a6-633f-4ee1-a7ce-ee7cf1f78284] Avinoam Singer PhD Candidate | Keating Lab Massachusetts Institute of Technology

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Joining models together in ChimeraX
by Christopher Camitta 10 Mar '22

10 Mar '22

Hi all, I am trying to join together two protein structures (in my case, one protein without the N-terminal domain combined with the NTD of a related protein). I came across a tutorial on how to do this in Chimera ( https://2019.igem.org/wiki/images/f/f3/T--UNSW_Australia--Daniel_Winter_Chi…) but from what I can tell ChimeraX's Build Structure tool doesn't have the options required to do this. Is there a way to join together two models in ChimeraX? Thanks, Chris

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ChimeraX
by Alejandro Amor 10 Mar '22

10 Mar '22

Hi there: I am trying to download ChimeraX for academic use and can't find a link to do it. Can you please provide some guidance? Thanks, Alex ______________________________ Alejandro Amor-Coarasa, PhD Assistant Professor of Nuclear Medicine in Radiology Director of the Radiochemistry Laboratory Albert Einstein College of Medicine 1300 Morris Park, 703-GB Bronx, NY 10461 Work: 718-430-3776 cell: 786-543-1534 e-mail: alejandro.amor(a)einsteinmed.org

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Analysis of the protein-ligand interactions using ViewDock
by Enrico Martinez 09 Mar '22

09 Mar '22

Dear ChimeraX users! I would like to use ChimeraX to calculate protein-ligand contacts established in docking calculations for the ensemble of the docking solutions (88 conformations of the ligand saved in multi-model format). Basically using the GUI of the UCSF Chimera previously I could do the following routine for the analysis of docking results: 1. Open the protein PDB 2. Use the Surface/Binding Analysis > ViewDock tool to open the docking poses 3. Using the Model Panel, select all docking poses 4. Use the Surface/Binding Analysis > FindHBond tool to locate all H-bonds. Make sure to check "Only find H-bonds with at least 1 end selected". You can check "write information to file" to save the H-bonds. May I adapt this protocol with the ChimeraX to perform such computing in batch (no-gui mode)? What should be the differences in the commands between Chimera and ChimeraX ( I've already seen that ViewDock is available in the ChimeraX as well...) Many thanks in advance! Cheers Enrico

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Unable to vary atomRadius by relative amounts
by Christopher Handelmann 04 Mar '22

04 Mar '22

Hi, I am trying to adjust the size of multiple individual residues in a molecule. I am attempting this with the "size [Target] atomRadius +[value]" command. When I run this, it doesn't perform a relative shift of each atom size in the residue but appears to set all atoms in the residue to an absolute size of the value. The documentation states that including the plus sign should make it a relative change. I am using ChimeraX 1.2.5. I appreciate your help figuring this out, Christopher Handelmann

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How to view consurf result in chimerax
by Shin, Yeonoh 03 Mar '22

03 Mar '22

Hello, I ran MSA in Consurf website, however I can not open the color-coded pdb result in Chimera or ChimeraX. When I click the link, attached error shows up. When I tried to open the link in chimeraX command line, another error shows up (attached). Could you tell me what I need to do to see the color-coded result in Chimera or X? Thank you. Yeonoh

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Commands - bond angle and minimize
by chung kelvin 02 Mar '22

02 Mar '22

Hello all and Elaine, I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity. Long story short, I have 3 problems in creating an enzyme-substrate model 1. I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera? 2. 3. If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case? 4. 5. In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX? 6. Again, thank you very much for your help. Cheers Kelvin Chung ABCT Department The Hong Kong Polytechnic University

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Permission denied writing file...
by 翼翱张 01 Mar '22

01 Mar '22

Hi Sir/Madam, When I press the button ‘save snap shot to desk’, it shows ‘Permission denied writing file C:\Users\zhang\Desktop\image1.png’. how should I open the permission? Please help me. Looking forward to your reply. Sincerely, Wing 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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Surface rendered trajectory
by Venkatareddy Dadireddy 01 Mar '22

01 Mar '22

Hi, I am visualizing MD trajectory in ChimeraX and making movie of a trajectory. I want to incorporate "time stamp" of a trajectory into my movie. How can I do it in ChimeraX? Thank you, Venkat

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Re: [chimerax-users] How to view SwissDock output in ViewDockX
by Eden Fussner - Dupas 27 Feb '22

27 Feb '22

Hi Elaine, I’m not sure if you’ve answered this elsewhere - but I am having the same issue another user was having. The output of Swissdock isn’t being recognized by the ViewDockX tool. I am trying to pick the best model stearic acid in this PLAT protein (an AlphaFold model). Any help would be most appreciated. Warmly, Eden

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Stack thickness question and cine playing?
by Rubenstein, Jason 25 Feb '22

25 Feb '22

Hi! Two questions: 1. This 3D dataset is only about 30 mm thick in the Z direction. When ChimeraX is displaying it, it shows the thickness about 50x too thick. Any way to adjust this? [cid:007921ae-20a5-4928-963c-23013d90a69e] 1. this is a "4D" dataset, with 20 phases of 3D stacks. Any way to "play" the cine? Thanks! Jason Rubenstein, M.D. Codirector, Cardiac MRI Associate Professor, Medical College of Wisconsin

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Surface zone and movie recording
by Lewandowski, Jozef 25 Feb '22

25 Feb '22

Hi, I would like to use "surface zone" command to visualise a substrate channel in an animation of an MD trajectory. For that I would like to regenerate the surface every frame with "perframe". However, if I do that when I record the movie the entire surface (instead of just the selected zone) will flash before the zone is displayed. Is there any way so that only the surface zone will be displayed from frame to frame without the entire surface flashing? I essentially just would like to follow the changes to the substrate channel without any distractions. Thank you, Józef ------------------------------------------------------------------------------------------------------ Józef R. Lewandowski Professor | Department of Chemistry | University of Warwick<http://www2.warwick.ac.uk/> j.r.lewandowski(a)warwick.ac.uk<mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map<http://www2.warwick.ac.uk/about/visiting/maps/interactive/> Lewandowski group website<https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website<http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Ask for help with chimeraX
by 培慧张 25 Feb '22

25 Feb '22

Dear UCSF ChimeraX： We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The SummerX? Hope to get help from your school and restore me, thank you.

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Re: [chimerax-users] correct format for attribute information file (.defattr)
by Rangarajan, Amith 24 Feb '22

24 Feb '22

Hello everyone, I am trying to add mutation counts as a attribute and use it to generate a map of hotspots on the protein . I followed the format provided on chimerax documentation and i am getting this error : SyntaxError: Line 12 in KIT-mutations-count.defattr is either not of the form 'name: value' or is missing initial tab File "C:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\std_commands\defattr.py", line 107, in defattr raise SyntaxError("Line %d in %s is either not of the form 'name: value'" i am on windows 11 using chimerax 1.3. thanks amith

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perspective or orthoscopic view - how to change
by Dmitry Semchonok 24 Feb '22

24 Feb '22

Dear colleagues, How to change the camera view for 3D map for from the perspective to orthoscopic or vice versa Thank you Sincerely, Dmitry

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Ask for help with chimeraX
by 泡沫 24 Feb '22

24 Feb '22

     We love the software you developed, ChimeraX. With high-performance rendering of large structures and data, the ability to quickly and microfiber slim readers and write millimeter ciliates, fast and robust solvent elimination surfaces, interactive ambient occlusion lighting, and curved cylindrical "tube" spirals with cartoon integration, our research team especially loves your software. Compared with UCSF Chimera1.16, we found that ChimeraX lacks the function of Organization, but we really need this function, how can we choose to use ChimeraX to solve the problem of missing this function? Can we use this feature as an external software plug into The ChimeraX?       Hope to get help from your school and restore me, thank you.

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Re: [chimerax-users] alphafold predict stops after MSA step (google colab pro)
by Rangarajan, Amith 23 Feb '22

23 Feb '22

Hi, I am new to using alphafold for prediction, i tried today with a reasonable size model ( 400 AA ) of a kinase domain. i opted to use 'high RAM " available on colab pro and after running for an few hours , the job stops without any error, the colab notebook had disconnected due to inactivity and it did not generate any models. please share with me your experience of using alphafold from within chimerax , helpful tips to get the job to finish . here is the output ( output on google colab): Sequence length 401 Have Colab GPU runtime Installing HMMER for computing sequence alignments Installing matplotlib to plot sequence alignment coverage Installing AlphaFold Installing OpenMM for structure energy minimization Finding fastest mirror for sequence databases using united states Searching sequence databases (147 Gbytes). Search will take 29 minutes or more. Searching uniref90 sequence database, 59 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 Searching smallbfd sequence database, 17 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 Searching mgnify sequence database, 71 Gbytes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 Computing multiple sequence alignment 327620 similar sequences found (311112 uniref90, 16008 smallbfd, 500 mgnify) [cid:4e178c51-cd4c-4958-b2e8-fa714cbfcd07] Computing structures using 5 AlphaFold parameter sets: model_1 thanks a lot again for all your support, best amith

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Drawing objects in ChimeraX?
by de Miranda Seabra, Gustavo 23 Feb '22

23 Feb '22

Hi, I was wondering if it is possible to draw objects in ChimeraX. More specifically, I'd like to show the gridbox used for docking calculations, so it would be nice if I could draw a cube, and even better if it can be drawn as a surface that could have color, transparency, etc. How to do this in ChimeraX? Thanks a lot! -- Gustavo Seabra Research Associate Professor Center for Natural Products, Drug Discovery, and Development (CNPD3) Department of Medicinal Chemistry College of Pharmacy University of Florida, Gainesville, FL, USA

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