- ChimeraX-users - RBVI Mailing Lists

Error when opening session file cross-platform
by Alexander Lee 17 Sep '24

17 Sep '24

I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

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Change fetch download location
by Walker Orr 13 Sep '24

13 Sep '24

Hi, I was wondering how to change the fetch download location from downloads to a custom-assigned folder. I saw how to do this on chimera, but couldn't find guidance for ChimeraX in the documentation. Is there a way to do this? Thanks, Walker

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Molmap default to cubic box?
by Oliver Clarke 13 Sep '24

13 Sep '24

Hi, Currently, molmap defaults to creating the new map in a minimal bounding box - a minimal rectangular prism. Most cryoEM software doesn't like rectangular prisms, and rather prefers cubes (ideally with sides that are an even number of voxels). Would it be possible to either (a) alter molmap so it defaults to a minimal cubic box or (b) add an option to automatically resample to a cubic box of specified dimensions? Often this doesn't really matter as we have a map already loaded that we can resample on the grid of, but it would be convenient to be able to do this in a single command. Cheers Oli

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Save Session
by F.Xavier Gomis-Rüth 12 Sep '24

12 Sep '24

Dear Elaine, I am trying to save the session under ChimeraX v. 1.8 but the program refuses to do so with the message below. Any suggestion is welcomed. Best, Xavier --

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Chimerax's download link is no longer working
by 卢健之 11 Sep '24

11 Sep '24

Hello, I tried to dowonload the chimerax from the link https://www.rbvi.ucsf.edu/chimerax/download.html. But it seems the server is down. I wonder if you could provide me with a new download link. I would really appreciate it.

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no template at MD forcefield
by Dmitry Semchonok 11 Sep '24

11 Sep '24

Dear Tristan and colleagues, I hope you are doing well. I have a question about the cofactors and residues that ISOLDE cannot see immediately. [cid:17de3c4d-4ac6-471b-b5b9-ecaa4e534d18] What is the proper way to treat them? The program proposes that I do a search and then give the options. Shall I select the most probable one out of the list? And how do we deal with Chlorophylls (Chl a; Chl b) and carotenoids (car)? And sometimes, even with regular ones like ARG [cid:8ff9222b-feb1-47b3-9b5e-a52e714e2355] Thank you in advance. Kind regards, Dmitry

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Select all connected atoms to selection
by Alexander Lee 10 Sep '24

10 Sep '24

Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command select @{atom_name}; select zone select 2 It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks!

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atoms.scene_coords inconsistency before and after saving
by Roden Deng Luo 10 Sep '24

10 Sep '24

Hi, With version 1.7.1 (2024-01-23), if I open a structure (tested with 6MEO and 6ARA), select the whole molecule, change "Right Mouse" to "Rotate model", rotate the model by dragging with the right mouse, save the model into a .cif file (uncheck "Use untransformed coordinates"), and then type the following python script in the Shell in the session performed the rotation and in a new session/launch of ChimeraX and opening of the saved file, the results are different, see the attached screenshots. ======= from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] mol.atoms.scene_coords ======= For 6ARA, if I do not change the camera setting before rotation (drag the left mouse), only rotate in the original camera setting, this is not reproduced. But if I change the camera setting, this is reproduced. For 6MEO, I always reproduce the described behavior. From https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi… , *property *scene_coords <https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi…> Atoms’ coordinates in the global scene coordinate system. This accounts for the Drawing positions for the hierarchy of models each atom belongs to. Either I misunderstood the whole scene and camera system, or this should not have happened. Why is this the case? How can I access from the session performed the rotation the coords as in a new session? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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license for university students
by Angel David Montijo Valdés 10 Sep '24

10 Sep '24

Good afternoon, I am writing to you in the kindest way to request a free use license for the chimera X program. Because I am a student at the National Autonomous University of Mexico (UNAM), within the Faculty of Sciences, and it would be a great opportunity to use your tool in different molecular biology analyses. If you need a proof of my identity as a student, you can ask me for it without any problem. I look forward to hearing from you. Best regards.

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Select multiple rotamer conformations for a single amino acid
by Alexander Lee 09 Sep '24

09 Sep '24

Hi! I was able to select and use multiple rotamer conformations simultaneously for a single amino acid using the Rotamers tool, saved as alternate locations within a pdb file. Is there a way to do that using swapaa or from the command line?

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Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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Re: [Chimera-users] morph command in chimerax
by Elaine Meng 09 Sep '24

09 Sep '24

Hi Bryan, Since this is a ChimeraX question, I've CC'd chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> --- in the future please use that mailing list for ChimeraX questions, because we don't want to confuse users between the two programs, for which the answers may be different. This answer is for ChimeraX: The "morph" command is for atomic structures, not maps. That's why it keeps saying you need structures! This is mentioned in the first sentence of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> To instead morph maps, see the "volume morph" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 9, 2024, at 7:29 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I’m using ChimeraX v 1.8 (2024-06-10) and I’m having a problem with the morph command. No matter how I format the command I’m getting the same error message of “Require at least 2 structures for morph” I’ve tried > morph #3,4 core 0.1 frames 75 wrap t > and > morph #3#4 core 0.1 frames 75 wrap t > These are 2 electron density maps so there’s no sequence info docked in yet. Thanks for any tips or advice on what I’m doing wrong. > Bryan Hansen

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MD Trajectory
by Mcguire, Kelly 07 Sep '24

07 Sep '24

What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories? Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego

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colored stl file for 3d printing
by Haydar Witwit 06 Sep '24

06 Sep '24

Dear ChimeraX team, I'd like to know if it is possible to save a colored file of pdb into stl, because when I save the file as stl, chemierax saves it as a monocolor structure. Actually, my intention was to 3d print a hydrophobic structure of small protein but labeled with one letter code label and position of the amino acids. Something similar to the following image: [cid:4c34bc91-300a-456c-8583-ab4de7f1b1d9] Kind regards Haydar

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Re: Optimizing ChimeraX Performance for Multiple Subtomo Maps
by Tom Goddard 06 Sep '24

06 Sep '24

Hi Wang, Glad to hear ArtiaX helps showing your subtomogram averaged particles. An important feature of that extension written by Utz Ermel optimizes the display of thousands of particles by not using a separate ChimeraX model for each one. I tried opening 1500 maps of size 20 x 20 x 20 grid points in ChimeraX 1.8 on a Mac Studio M2 Ultra with much less powerful graphics than an Nvidia 4090, displaying all as surfaces, full lighting, and they rotated, zoomed and translated usably fast at 9 frames per second. So I am surprised you had a problem and I don't know why it is slow for you. Tom > On Sep 6, 2024, at 3:01 AM, 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> wrote: > > Hi Tom, > > > Thank you for your prompt response. > > It seems that the performance issue was caused by the excessive number of subtomo maps. In my case, I loaded approximately 1,500 subtomo maps using the subtomo2chimera script, and displayed them in surface mode. This led to ChimeraX freezing for several seconds after any rotation or zoom of the view. Loading an extra tomograph did not affect performance. > > I tried using AriaX to load the subtomo maps, and now the scene runs smoothly. Thank you for your advice! > > Thanks, > > Wang GuangLei > > > > -----原始邮件----- > 发件人:"Tom Goddard" <goddard(a)sonic.net> > 发送时间:2024-09-06 03:34:59 (星期五) > 收件人: 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> > 抄送: chimerax-users(a)cgl.ucsf.edu > 主题: Re: [chimerax-users] Optimizing ChimeraX Performance for Multiple Subtomo Maps > > Hi Wang, > > I think your Nvidia 4090 should handle the large tomogram fine, and probably the slowdown is because having 1000-2000 open model of any kind, even if they are small like your subtomo maps, is more than ChimeraX was designed to handle. I am surprised though that rotating the view becomes slow because that should just move the camera which should not depend on the number of models shown. Do I understand correctly that you just open the tomogram and 1000-2000 subtomograms, display them all, and rotate and it updates slowly? How slowly, like 1 frame per second, or does it freeze for ten seconds? What display style do you use for the subtomograms, surface or volumetric? > > You might be interested in the ArtiaX ChimeraX extension which is for looking at particles in tomograms. You would get it using ChimeraX menu Tools / More Tools.... > > Tom > > >> On Sep 5, 2024, at 1:15 AM, 王光磊 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> >> >> Hi, >> >> I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. >> >> My system specifications are as follows: >> >> Dual Intel Xeon 5317 processors(a)3.00GHz >> RTX 4090 GPU >> 128GB RAM >> Operating System: CentOS Stream 9 >> GNOME Version: 40.4 >> GPU Driver Version: 550.54.15 >> I would greatly appreciate any suggestions. >> >> Thanks, >> >> Wang GuangLei >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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error in the documentation?
by Bourguet,Pierre 06 Sep '24

06 Sep '24

Dear ChimeraX support, First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX! I have noticed the following inconsistency in the documentation. https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts "If one set of entities is higher-confidence (lower in pLDDT<https://alphafold.ebi.ac.uk/faq#faq-12>) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set." My understanding is that it should say "(higher in pLDDT)". Hopefully that helps! Best, Pierre Pierre Bourguet Postdoc Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet(a)gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png]

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Optimizing ChimeraX Performance for Multiple Subtomo Maps
by 王光磊 05 Sep '24

05 Sep '24

Hi, I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. My system specifications are as follows: Dual Intel Xeon 5317 processors(a)3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions. Thanks, Wang GuangLei

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Discrepancy: plDDT laphafold3 and ChimeraX version 1.9.dev202405310031 (2024-05-31)
by Khawar Siddiqui 03 Sep '24

03 Sep '24

Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence). Thanks again for the help. sohail Dr Khawar Sohail Siddiqui, [cid:3f847f24-9a1b-47bc-bb56-1704e8bd8ac3] [cid:2c952f1f-e76e-458e-a444-8242f6bdab3a] [cid:0089dce1-a9be-4009-93b9-d158c31cee29]hoo.com

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I found that the phosphodiester bond has broken.
by Yan ZHANG 张艳 03 Sep '24

03 Sep '24

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible. [cid:image001.png@01DAFDEC.77532DA0]

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Purchase license
by Lili Ye 03 Sep '24

03 Sep '24

Hello, I am from Sironax(Beijing)Co.,Ltd. We want to buy two licenses now, how to buy? Thanks! Lili Ye 叶丽丽 Sironax (Beijing) Co., Ltd. 维泰瑞隆（北京）生物科技有限公司 Add: Building 2, No.9 Yike Road, Zhong-Guan-Cun Life Science Park, Changping district, Beijing, China 102206 北京市昌平区生命科学园医科路9号院2号楼8层 Tel: （+86）15201581663 Email: Lili.Ye(a)sironax.com<mailto:Lili.Ye@sironax.com> [1534753277(1)]

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Inquiry About Building Molecular Structures in ChimeraX
by 化工化工 02 Sep '24

02 Sep '24

Dear Professor, I hope this message finds you well. I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library. At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work. I would greatly appreciate any guidance or suggestions you might have. Thank you very much for your time and assistance. Best regards, Youcai Zhu 化工化工 1366924572(a)qq.com  

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Re: color bfactor by alphafold palette
by Elaine Meng 02 Sep '24

02 Sep '24

To summarize for users, the ChimeraX alphafold coloring to show pLDDT values is continuously shaded, whereas the coloring shown at the AlphaFold database is similar but discontinuous, and differences may be evident. The reasoning behind the ChimeraX alphafold coloring palette is that it may be more informative about the specific values. However, it may be confusing that it looks similar, yet not the same, as the AlphaFold database pLDDT coloring. A few months ago, Abnieszka Obarska (thank you!) helpfully provided a command to match the coloring shown at the AlphaFold database. Since it was in an image, however, it is not convenient for cut and paste, so I have copied it here: color bfactor palette 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 Although I did not check if the color hex codes exactly match the AlphaFold database colors, I tried it on a couple of examples at least to my eye, it reproduced the coloring of structures shown at the database. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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AlphaFold PAE plot not generated
by Catrin McHugh 30 Aug '24

30 Aug '24

Good morning Having successfully generated a PAE plot (and coloured the model accordingly) with data generated by AF3, I am getting an error message when I try to do the same using a JSON file generated by ColabFold for AF2. The error message is: 'is not AlphaFold predicted aligned error data, expected a top level list". I attach the JSON file, and the relevant structure PDB. Many thanks in advance Catrin

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Random residue colors?
by Daniel Asarnow 30 Aug '24

30 Aug '24

Hi all, In the color command documentation, it says 'color random' can per atom or per residue. How can random residue colors be specified? I can only get random atom colors. Thanks! -da

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CIMERAX 64BIT FOR WIN 10
by Lee, Yong Sok (NIH/NIAID) [E] 29 Aug '24

29 Aug '24

I AM LOOKING A FOR A 64BIT VERSION OF CHIMERAX FOR WINDOWS 10. TRED DOWLOANDING AND INSTALLING CHIMERAX 1.8 BUT IT WOULD NOT LAUNCH ON MY WINDOWS 10 64 BIT SYSTEM. LET ME KNOW IF YOU HAVE A SOLUTION FOR THIS ISUUE. LOOKING FORWARD TO HEARING FROM YOU.

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Invitation to conduct a UCSF Chimera Workshop at Purdue University
by Ferdausi, Nourin 29 Aug '24

29 Aug '24

Dear Team, I hope this email finds you well. My name is Nourin Ferdausi and I am a graduate student at the Department of Biological Sciences in Purdue University. My colleague, Priyanka Naik (cc’d here) and I are writing to you on behalf of the Structural Biology and Biophysics Club (SBBC). We are hoping to organize a virtual workshop focused on UCSF Chimera, and we would be honored if one of your team members could conduct this workshop. The graduate students and researchers of our structural biology group use a wide variety of experimental approaches like cryo-electron microscopy and X-ray crystallography for determining molecular structures. Consequently, the Chimera software is integral to our research, and we believe your insights would be of great impact to our community. We are flexible with the format of this virtual workshop, which is tentatively scheduled for mid-September; however, we are open to adjusting the date based on your availability. Your participation will provide our members with a unique opportunity to learn directly from a developer of UCSF Chimera. Please let me know if we can have a quick Zoom call to discuss the event in detail. We look forward to your reply at your earliest convenience! Thank you, Nourin Ferdausi Ph.D. Candidate, Noinaj Lab Supporting officer, Structural Biology and Biophysics Club Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology West Lafayette, IN-47907-2054

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Re: [Chimera-users] Finding SASA for individual residues
by Elaine Meng 29 Aug '24

29 Aug '24

Hi Ale, In the future please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I'll reply to this post for my question cause the title seems appropriate. > I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. > > This is the log: > measure sasa /A > Solvent accessible area for /A = 22276 > measure sasa /A:trp & aromatic-ring > Solvent accessible area for /A:trp & aromatic-ring = 1824.9 > measure sasa /A:phe & aromatic-ring > Solvent accessible area for /A:phe & aromatic-ring = 3339.6 > measure sasa /A:tyr & aromatic-ring > Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 > > But the I tried to get the sum: > > measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe > Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 > Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 > > Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... > Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. > You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? > Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. > > Thank you!! > Best, > Ale

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Re: Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk> mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk>mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:46, mjfssmr <http://mark.rosenberg@manchester.ac.uk> wrote: Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <http://guillaume.gaullier@KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…>

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Re: Command line interface saving
by Guillaume Gaullier 26 Aug '24

26 Aug '24

Not that I know, sorry. But maybe somebody else knows, so it is better to keep the list in CC. 😊 Cheers, Guillaume ________________________________ From: Mark Rosenberg <mark.rosenberg(a)manchester.ac.uk> Sent: Monday, August 26, 2024 1:46:29 PM To: Guillaume Gaullier Subject: Re: Command line interface saving Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <guillaume.gaullier(a)KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ [uu.se]<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy [uu.se]<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

1 1

Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark

1 0

molmap command question
by Grigory Mechetin, Ph.D. 23 Aug '24

23 Aug '24

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one? When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid. [cid:3853c8fe-0ccd-4133-ba08-4732e3be8905] Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

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Data handling / privacy policy information?
by Frumolt, Brian 23 Aug '24

23 Aug '24

Hi, We are looking at ChimeraX for commercial use. I was looking on the site for information related to data use and privacy policies. I understand the app runs locally, but was wondering whether it leverages any web services, or passes any data outside the local installation? We have strict data handling policies in place for our clients, so would need to be aware. If there is a policy document I missed, that would be ideal. Thanks! Brian This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

2 2

Morphing two GPCR conformations
by Enrico Martinez 23 Aug '24

23 Aug '24

Dear Chimera-X users! I try to use the morph command to model the conformational change of GPCR related to its activation. Having two superimposed conformations of the receptor, which are different in the position of the internal part of the transmembrane helix VI, I try to visualize the displacement of this helix using morph #2,1 frames 250 Unfortunately the produced trajectory looks very unnatural (one helix overlaps with another one). Would it be possible to improve the accuracy of such morphing e.g. providing some restraints? Many thanks in advance ! Enrico

2 4

Mol 2.0 desktop version
by Nicholas Koylass 22 Aug '24

22 Aug '24

Good day, I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property. However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels. Can anyone assist me with this? Thanks, Respectfully, Nicholas Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1(a)jh.edu

2 3

Restoration of missing helical fragments of the structure
by Enrico Martinez 22 Aug '24

22 Aug '24

Dear Chimera-X users ! Suppose I have a pdb structure with a missed C-terminal fragment corresponding to the transmembrane helical part that should anchor the protein in the membrane. Is it possible to use some built-in utilities (modeller?) to predict this missing fragment based on the full length sequence of the entire construct? Many thanks in advance Enrico

2 5

results swiss dock
by Aurélie Hoeffel 21 Aug '24

21 Aug '24

Dear Chimeras members, I obtained some docking results from swiss dock, unfortunately my result.dock4 document is not readable in chimerax, I did not achieve to open it. Is it something special I have to do? Because, on the website it is written that we can directly upload it and it will work but for me chimerax did not recognize my .dock4 document. What should I do? Thank for the answer, Aurelie Hoeffel

2 1

ChimeraX docker arm64
by Daniel Diaz 20 Aug '24

20 Aug '24

We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture. We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines. We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips. We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64. How do you recommend we proceed? Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages. -- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin

4 7

Protein backbone representation
by Alex Henley 20 Aug '24

20 Aug '24

I was wondering how I can achieve this structure representation. The papers I read cite Chimera, but I cannot figure it out. Any help is appreciated.

2 1

Per-Model Lighting Options
by ygilron＠asu.edu 20 Aug '24

20 Aug '24

I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this? I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..." I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console: >lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image. P.S. full output command when I loaded the molecule: open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...] Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets

3 4

Thanks Elaine, Tom, Eric and team
by Artie Kushner 20 Aug '24

20 Aug '24

Apologies for an off-topic message. I'd like to express my gratitude to Elaine Meng in particular and the rest of the RVBI team who are tirelessly killing it in the Users mailing list with questions. On top of the amazing software, I appreciate the consistency, informativeness and thoughtfulness of each individual response. I learn a lot about ChimeraX and the community by reading other people's questions and answers. Thanks and kind regards from BC and Manitoba, Canada Artem

4 3

Assistance Required: Visualizing Complete Amino Acid Residue with Cartoon Transparency in ChimeraX
by Amandeep Sharma (P24BB0001) 19 Aug '24

19 Aug '24

Dear ChimeraX users, I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result. To provide context and illustrate the issue, I am enclosing images of the current visualization: - *Image 1:* Shows the current state where part of the residue is obscured by the cartoon structure. - *Image 2:* Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms. I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency. Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX. Best regards, Amandeep -- Amandeep Sharma PhD Student (2024-25) Dept. of Bioscience & Bioengineering Indian Institute of Technology Jodhpur Karwar 342037, Rajasthan

3 3

Alligning a trajectory
by ygilron＠asu.edu 19 Aug '24

19 Aug '24

Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai

4 4

2D labels colored by chain color
by NG, Cheukhei Jackie [Student] 19 Aug '24

19 Aug '24

Dear sir/madam, I am trying to generate publication-quality images with chimeraX with appropriate 2D labels. 1. Is there a variable I could use to represent the coloring of my current chain so i can apply in the command where the selection is multiple chains: label sel color (the variable)? 2. is the an offset parameter or any relevant parameters in the 2D label command that are recommended for publication use? Thank you very much for your time. Thanks, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

2 3

Feature of chimera
by Arpita Nandy 19 Aug '24

19 Aug '24

Hi, I am a PhD student from Germany and would like to make a figure where I can highlight specific proteins of interest in the mitoribosome complex of yeast. Could you please assist me to use ChimeraX in this context. Best regards Arpita Nandy

2 1

Usage and Distribution of ChimeraX at our Upcoming Max Planck Institute Summer School
by SantaLucia, Daniel 15 Aug '24

15 Aug '24

Hello ChimeraX team, My name is Dan SantaLucia; I'm a research scientist working under Prof. Frank Neese and Prof. Serena DeBeer at the Max Planck Institute for Chemical Energy Conversion. One thing we do every year is to organize a summer school for students from all over the world, where they get to learn in-depth about many different spectroscopic techniques as well as quantum chemical calculations to help them in their interpretations of these datasets. You can find more information here, if you're curious: https://summerschool.cec.mpg.de/en/home thing that would be really nice would be to offer students the ability to use ChimeraX alongside our tutorial/practical sessions. We use ORCA to do calculations (considering, of course, that Frank invented it), and we've found that ChimeraX has a lot of really nice features that would be perfect for helping the students to learn. What I wanted to ask was this: do we have permission to distribute the download files at: https://www.rbvi.ucsf.edu/chimerax/download.html to the students? They would be distributed on flash drives that we give to the students, and we would distribute the Windows, Mac, and Linux versions so that we could cover all users. The internet connection is not the best, unfortunately, at our venue, which is why they can't just go to the link to download it themselves. To be clear: this is a non-commercial use event, where we simply have international students coming to attend the summer school, and this is an event that is for learning purposes only. Nonetheless, I want to have your explicit permission for distribution of ChimeraX to the students as well as your permission for them to use your software at our summer school? Thanks so much, and looking forward to hearing back from you, -Dan [1668779311055] [1668779979115] Dr. Daniel J. SantaLucia MPI-KoFo/CEC Joint Workspace Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany Tel.: +49 208 306 3724

2 2

problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

2 1

ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

4 6

AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

3 2

Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

2 1

Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

1 0