- ChimeraX-users - RBVI Mailing Lists

ChimeraX linux binaries too inconvenient
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, Can you provide ChimeraX linux binary as useful as the Chimera linux binary ? - without all of the dependencies being outside of the package. Also, can the package simply install in the /home/username/.local/CHIMERAX... directory, just as Chimera or in a similar path ? (makes uninstallation easy, saves disk space). Many distros do not have package managers as convenient as those of Red Hat or Debian. For example I use Clear Linux (for the performance) and the dependencies are not even in the package manager. There is also no explicit list of dependencies and according to your web site there are about 50 of them, anyway. Basically whatever I do there is always a missing library I cannot easily find / compile / have no time for it, etc., so ChimeraX for me is out of reach. I tried Chimera from the linux binary and it ran just fine, but it lacks something in the GUI, which ChimeraX does not. The visualization settings fields can be scrolled up and down, so if I load let's say 12 molecular orbitals - I can easily hide / show the ones I need, instead of having them all on the screen and using the "Data set list" to manually show / hide each one. Best Regards, Dobromir

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Re: [chimerax-users] color
by Elaine Meng 19 Dec '22

19 Dec '22

Hi Guan, To ensure you get an aswer, we recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here). You can click the square "color well" for each model listed in the Model Panel to open your system color browser, which will show the code. See also this page for the names of the initial model colors... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> ...and then this page which shows the codes for the names <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2022, at 5:46 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine: > I like the color usage in chimeraX. I wonder if we could know the color code for the color auto-painted when we open it. > Thanks, > Lan

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Aligning atoms
by Noriega, Heather 18 Dec '22

18 Dec '22

Hello, I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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ChimeraX Alphafold Multiple jobs
by Rayees Mattoo 16 Dec '22

16 Dec '22

Hi, I was wondering if I could run multiple Alphafold jobs via ChimeraX using my Colab Pro. Also, very often Alphafold job submitted gets disconnected after some time (15 min or so) without completing the job, any solution to that? Best Rayees

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help please - electrostatic potential units and fit in map correlation
by Leslie Bridges 15 Dec '22

15 Dec '22

Dear All What are the units for electrostatic potential in ChimeraX? Is it possible to say whether the fit in map correlation represents a "good" fit for the atoms (e.g. if my correlations are above 0.75, can I conclude all the fits are good?) All the best, thanks Dr Leslie R Bridges Hon Snr Lecturer in Neuropathology St George's University of London

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no conformation comparison category in ChimeraX1.5 and ChimeraX-daily
by Jiang Xu 14 Dec '22

14 Dec '22

Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu

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Analysis of docking results
by Luigi Marongiu 14 Dec '22

14 Dec '22

Dear sir or madam, I am new to docking analysis. I obtained a model from SwissDock but there are some commands that do not work on ChimeraX. 1. I can load the molecule, which is composed by 4 homo-chains. I can select one chain (A); how can I delete or hide chains B-D. I can select chain A using select>chain`; is there a way to hide the others? 2. The model (saved in the file clusters.dock4.pdb) shows several ligands: [cid:c289e47f-ca49-4f27-9ad6-acef069f976e][cid:728d8f47-8cfb-445c-9476-ebb8a9d54ef9] Is there a way to show only the ligands with the highest docking score? 3. the tools>binding analysis>ViewDockX` says that "No suitable models found for ViewDockX". But is not this the "clusters.dock4.pdb"? How can I load the model into ChimeraX? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Morphing structures with ligands (glycans)
by Nebojsa Bogdanovic 13 Dec '22

13 Dec '22

Hello, I am looking into morphing several protein structures that contain glycans important form the function. The structures are all the same protein, in different states so the sequence info is good. Is there any function that retains the glycans visible once the command* morph #1-5 same true* produces a new model? I can just show them from origin structures but this does not look the best. Thank you and best regards Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Primer in chimeraX
by Luigi Marongiu 13 Dec '22

13 Dec '22

Dear sir/madam, I am new in the use of ChimeraX (for Linux). I would like to use ChimeraX for two jobs: 1. calculate the volume of a molecule (namley: maltose). I have uploaded the pdb of the molecule, selected the tools>volume>volume viewer, but I don't see any actual output. How can I get the value for the volume of this molecule? 2. show the docking of a ligand. I have obtained a docking model with swissdock, which I have loaded; how can I show the bonds between target and ligand? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Isolde loading issue
by Dmitry Semchonok 13 Dec '22

13 Dec '22

Dear colleagues, Is there any alternative for ISOLDE installation? >From ChimeraX 1.5 it doesn't load on my Mac - it stops. Kind regards, Dmitry

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using chimerx on unix
by Barak Yariv 11 Dec '22

11 Dec '22

Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak

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Specify unmodelled residues
by Jaremko, Matt Joseph 09 Dec '22

09 Dec '22

Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?: [cid:image001.png@01D90BDD.3983D7C0] I’d like to have this information in my own PDB files. Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Perframe and distance
by Simonson, Benjamin Thomas 09 Dec '22

09 Dec '22

Hello! I am trying to measure the distance between two atoms in my trajectory in every 10th frame. My approach was to use the perframe command paired with the distance command. Below was my attempt: perframe "distance /D:15@NH1 /B:42@OD1;distance save dist$1.txt;~distance /D:15@NH1 /B:42@OD1" interval 10 However, it instead simply outputs the distance of the currently displayed frame over and over again. Any help would be appreciated! Ben ......................................... Benjamin Simonson MCIBS PhD Candidate Penn State University

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How do I NOT "show disjoint surfaces"?
by Sungwook Woo 06 Dec '22

06 Dec '22

Hi I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel! One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version. Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time. Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks! Best, Sungwook

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swapna in ChimeraX
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Hi all, Does ChimeraX have swapna functionality? I can find the swapaa command but not swapna. Is there another way to achieve its effects? If not, I think it would be useful addition. Kind regards, Taha

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ChimeraX 1.5 release not visible on website
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Dear ChimeraX Team, I would like to update, but can't see either the ChimeraX 1.5 release candidate or production release on the USCF ChimeraX download page (only ChimeraX 1.4 and the daily build are available). Many thanks, Taha Dr Taha Shahid Postdoctoral Research Associate Leicester Institute of Structural and Chemical Biology Henry Wellcome Building | University Road | Leicester | LE1 7RH | UK e: ts387(a)leicester.ac.uk<mailto:XXXX@leicester.ac.uk> w: https://www2.le.ac.uk/institutes/liscb Follow us on Twitter<https://twitter.com/leicstructbio> [cid:D64185E6-9A9E-47F3-98A6-A33685D0B03A]

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chimerax freezing
by HOH Francois 30 Nov '22

30 Nov '22

Hi I had to change my hard drive and reinstall everything. When launching chimerax, it starts but freeze. Have to kill it. OS ubuntu 22.04. No special message in the log when using chimerax --debug Any idea ? Thank's FH ________________________________________ Hoh François, PhD Research Engineer Team BSME: Biologie structurale multi-échelles Centre de biochimie Structurale de Montpellier CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 29

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ChimeraX 1.5 release
by Elaine Meng 30 Nov '22

30 Nov '22

UCSF ChimeraX version 1.5 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ Updates since version 1.4 (Jun 2022) include: - AlphaFold search/fetch uses database v4 (fixes ~4% of v3 entries) - show AlphaFold residue-residue errors (PAE) with colored lines - Axes/Planes/Centroids tool to define objects, use in measurements - transform surface models (scale, shift, rotate) - add hydrogens GUI - calculate and assign charges, including for nonstandard residues - dock prep command - renumber residues, change chain IDs - crosseye and walleye stereo - cleaner close session (reverts more settings) - UniProt sequence fetch updated to work with UniProtKB's new API - DICOM browser shows patient-study-series hierarchy in medical image data For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Ribbon coloring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Re: [chimerax-users] Placing a ligand in a protein structure from PDB
by Elaine Meng 30 Nov '22

30 Nov '22

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler(a)kemi.uu.se> wrote: > > Hej Elaine, > > I found you on the ChimeraX website, and I have a question. > > I have a PDB file of my protein, but not showing a ligand. > > I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX? > > Best regards, > Amit > Hi Amit, We recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) to make it more likely you get a response. Not sure what you mean by add a ligand. Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save. But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program. ChimeraX does not do docking. You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX. Moving models by hand, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Or maybe you don't have a structure of the ligand. If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command open pubchem:12120 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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font size on the task bar
by Krishnan Raman 29 Nov '22

29 Nov '22

Is it possible to change the font size(larger) on the first line of the of the taskbar file…edit select etc… For viewing at from a distance on a big screen? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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tile and 2dlabels
by Krishnan Raman 29 Nov '22

29 Nov '22

Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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chimerax hbonds batch analysis
by Visvaldas K. 28 Nov '22

28 Nov '22

Dear ChimeraX wizards, I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc", where in the script I put the following commands: open /Users/visvaldas/temp0000.pdbselect /B hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true quit However, something is wrong with hbonds line since I am getting this error:Executing: runscript myscript.cxc Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script code = compile(data, stream.name, 'exec') File "myscript.cxc", line 4 hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true ^ SyntaxError: invalid syntax What I am doing wrong? (Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent truefrom the GUI does not work either) Best wishes, Visvaldas

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Cα distance per residue in alignment
by Michael Habeck 28 Nov '22

28 Nov '22

Dear ChimeraX forum, I'm interested in getting the distance between Cα for all residues in an alignment. I've noticed that the Cα RMSD values in the txt file obtained from the header of the sequence alignment created by matchmaker via sequence header rmsd save are different from the distances measured using the rmsd or distance command. The Cα distance measured is approx. 41% higher across the entire alignment than in the saved output. When selecting a pair of aligned residues from the alignment viewer, the distance shown does not match the one in the output file but the distance measurement. I've attached a file with the respective distances for the alignment of chains A in 3c4f and 3gqi as an example. Not sure if this is a misunderstanding from my side or a bug, yet I'd greatly appreciate a clarification of the differences. With thanks in advance and best regards, Michael

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Align with specific atoms (but against all other molecules)
by Kim, Doo Nam 28 Nov '22

28 Nov '22

Hi, I’ve used align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N … to align #2 molecule against #1 molecule with backbone atoms #3 molecule against #1 molecule with backbone atoms #4 molecule against #1 molecule with backbone atoms etc… However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule with backbone atoms at once in chimeraX? I’ve used align all toAtoms #1 matchAtomNames true align all toAtoms #1 matchNumbering true to align all molecules to #1 molecule at once. However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning. I think that there should a 1 line command that aligns all molecules with specific atoms only or there is chimeraX equivalent python script as from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages Best, Doo Nam

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input delay on one computer and only for ChimeraX
by Barbara S Holme 28 Nov '22

28 Nov '22

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Re: [chimerax-users] [Chimera-users] Writesel command in chimeraX
by Elaine Meng 27 Nov '22

27 Nov '22

Hi Prathvi, Please use the chimerax-users(a)cgl.ucsf.edu address to ask ChimeraX questions (instead of chimera-users(a)cgl.ucsf.edu) so that users will not be confused about which program we are discussing. In ChimeraX you can use the "info" command to report the selection to the Log, as detailed in this previous post. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/003963.html> "info" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> It does not have an option to save a file. Instead you have to save the ChimeraX Log in another step. You can use "log clear" before you use "info" and then "log save" to save to HTML file. "log" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 26, 2022, at 5:04 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is the writesel command available in chimeraX because I could not find it in the Actions menu? > If not, then is any equivalent available apart from the command which saves selection as a new PDB file? > > Thanks once again in advance

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how to remove axes?
by Francisco Murphy Pérez 26 Nov '22

26 Nov '22

After loading a mtz file, 3 axes appear in the middle of the screen. How do I remove them? Thanks

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Display sequence alignment from structure alignment
by James H Naismith 25 Nov '22

25 Nov '22

In Chimera I can sort of print out a sequence alignment based on structural superposition. (Match-align) I can make a very nice structural superposition of very unrelated proteins with matchmaker, all I want to do is print out the resulting sequence alignment (where residues are with y A of each other) Any help gratefully received. With best wishes Jim Division of Structural Biology, Roosevelt Drive, Oxford, OX3 7BN james.naismith(a)strubi.ox.ac.uk Pronouns: he, him, his

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Opening .xyz file in ChimeraX
by Carina Luo 23 Nov '22

23 Nov '22

Hello, I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info." Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl Errors may have occurred when running pip: pip standard error: --- [notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip --- pip standard output: --- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0 Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX? Sincerely, Carina

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How do you submit a sequence text file to BLAST/Modeller in ChimeraX?
by Ralph Loring 23 Nov '22

23 Nov '22

Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Developing a ChimeraX bundle - accessing programmatically ChimeraX(GUI open) session
by Stylianos Iliadis 23 Nov '22

23 Nov '22

Hello, I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so. Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX. Kind regards, Stel Iliadis

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suggestion
by Hassan, Sergio (NIH/NIAID) [E] 22 Nov '22

22 Nov '22

Hello, I recently requested via Phil Cruz the 'tile' command, which I learned it was recently introduced. I have been using it successfully. However, there are two points I would like to bring to your attention (I asked Phil to ask you, but not sure he reached out) 1) when a session is saved as .cxs and I quit the program, after opening it again, the most important feature of the 'tile' command (rotations around each own axis) is lost. The tile distribution is still there, but now the entire thing rotates around a common axis. I need to apply 'tile' again to make it work, but this resets all the modifications I made in the saved session (these modifications include those in point 2 below). 2) any chance to add an argument to the 'tile' command so that the default spatial distribution, which assigns a 'distance' between near neighbors, can be adjusted with, say, 'zoom in" or "zoom out" or crowd in/out? I noticed the default puts each panel too far away from its neighbors for my taste, so I need to "move" them to make them look closer to one another. thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Re: [chimerax-users] Export pLDDT scores
by Tom Goddard 22 Nov '22

22 Nov '22

Hi Asmahan, The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file. Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1. ATOM 1 N ASP B 1 -0.818 -36.026 -12.912 1.00 85.53 N ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 3 C ASP B 1 0.706 -34.352 -13.882 1.00 85.53 C The bfactor is assigned to every atom. But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines. $ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 10 CA CYS B 2 1.983 -32.130 -13.721 1.00 95.45 C ATOM 16 CA PRO B 3 3.029 -30.770 -17.151 1.00 93.20 C ATOM 23 CA SER B 4 6.629 -31.094 -18.066 1.00 93.36 C You can also write the values into a ChimeraX attribute file using ChimeraX commands select #1@CA save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true and that file looks like the following attribute: bfactor recipient: atoms match mode: 1-to-1 /A:1@CA 56.150001525878906 /A:2@CA 53.33000183105469 /A:3@CA 53.59000015258789 /A:4@CA 59.380001068115234 documentation here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes Tom > On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Dear Tom, > I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)? > > Thank you very much. > Asmahan

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Zoom over frames
by Krishnan Raman 21 Nov '22

21 Nov '22

Hi , Can I have the zoom command execute over several frames? Thanks Krish

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Re: [chimerax-users] [Chimera-users] Coloring the unit cell box
by Elaine Meng 21 Nov '22

21 Nov '22

(switching to chimerax-users address since this is all about ChimeraX, not Chimera) Sorry no, there is no linewidth setting on the unit cell outline box. However, you can "fake it" by selecting that model so that there are green outlines to show the selection, and then changing the selection-outline color and width: (1) select the outline box model, e.g. as described in the previous message by checking the selection box in the Model Panel (2) use "graphics selection" command to change the selection-outline color and thickness <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot, Elaine, this worked indeed! > Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. > I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up. > > On 18/11/22 17:49, Elaine Meng wrote: >> Hi Xavier, >> As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now: >> >> - open your structure that has unit cell information, e.g. 1fav >> >> - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box >> >> - if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot: >> >> <Screen Shot 2022-11-18 at 8.48.02 AM.png> >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> P.S. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu >> >>> On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Elaine, >>> I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions >>> I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. >>> Am I missing something? >>> Thanks a lot in advance, >>> Xavier >>> >>> On 26/10/22 17:45, Elaine Meng wrote: >>>> Hi Xavier, >>>> You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> >>>>> On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? >>>>> This forces the background to be dark.... >>>>> Thanks a lot in advance, >>>>> Xavier >>>>> >>> >> > > -- > <fxgr_signanew.jpg> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] [Chimera-users] Alphafold
by Tom Goddard 20 Nov '22

20 Nov '22

AlphaFold prediction is running fine in ChimeraX, just tested a monomer and heterodimer prediction in the ChimeraX release candidate. AlphaFold prediction is not available in the old Chimera software. You would have to give details such as the exact pasted error, the input you were running on, the ChimeraX version, and best to do that with ChimeraX menu Help / Report a Bug.... Tom > On Nov 19, 2022, at 11:38 PM, Kornelius Zeth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear all – > > I’m using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? > > Thanks and have a nice day > > Kornelius > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Chimerax Error
by Natalie Loui 20 Nov '22

20 Nov '22

Hi all, I’m trying to visualize a capsid by using the sym command but I keep getting this error ”Assembly "1" not found, have" If you have any advice, please let me know. Natalie Loui PhD Student | Skaggs Graduate School of Chemical and Biological Sciences Email: nloui(a)scripps.edu | Phone #: (808)221-8270 Scripps Research Institute | 130 Scripps Way, Jupiter, FL 33458 | https://education.scripps.edu

2 1

ChimeraX Render by Attribute tool
by Elaine Meng 18 Nov '22

18 Nov '22

Hi Prathvi, There is a different address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see the currently available tools listed in the ChimeraX User Guide, and links to their pages: <https://rbvi.ucsf.edu/chimerax/docs/user/index.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/render.html> ... and the dates that they were added in the ChimeraX Change Log <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> ... so yes, we just started adding Render by Attribute to ChimeraX, but you have to get a recent daily build of version 1.6, and it does not have many options yet. Only ChimeraX (not Chimera) has a command to save attributes to a file. In Chimera you have to use the GUI. In ChimeraX we are specifically trying to make commands for all or nearly all actions you can perform with the GUI. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 18, 2022, at 4:23 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks once again Eric. > I have two more questions. > Is the "Render by Attribute" tool available in chimeraX because I get nothing when I run the command: ui tool show "Render by Attribute". If it isn't available, can I expect it to be added to chimeraX in the future? > Is there a command to save attributes of a residue in chimera (not chimeraX; that you covered in the previous reply) >

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cif writer broken in ChimeraX
by Pranav Shah 18 Nov '22

18 Nov '22

Hi Team, I am trying to save my coords in mmcif format to keep up with the times and I am running into the following error - ///////////////////////////////////////////////////////////////////////////////////////////////////////// AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets' File "/Users/ps/software/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/gui.py", line 130, in options_string if self.compute_sheets.isChecked(): See log for complete Python traceback ////////////////////////////////////////////////////////////////////////////////////////////////////////// Admittedly I am on a nightly build of the program details of which are - version 1.6.dev202211090831 (2022-11-09) 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

2 1

Distance between two atoms
by McClean, Phillip 17 Nov '22

17 Nov '22

Hi Everyone, I have a two chain model. I would like to determine the distance between the CD1 atom of residue 77 in chain B and the CD1 atom of residue Leu 150 in chain C. What would be the proper distance command. Thanks for the help again. Phil McClean

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Re: [chimerax-users] [Chimera-users] Finding SASA for individual residues
by Elaine Meng 17 Nov '22

17 Nov '22

On Nov 17, 2022, at 8:01 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > The methods you suggested for calculating SASA for residues saved me so much time. Thank you once again for it. > But I have noticed an ambiguity. > When I calculate the SASA for the same residue using chimera and chimeraX, I am getting different values. > For ex: in the PDB file 1TY4, the SASA value for residue 174.a is 2.55 when calculated using chimera and it is 292.44 when calculated using chimeraX. The same is true for other amino acids in other PDB files as well. > Why is there such a difference? > On which of the two software should I rely on? > Also, what is the unit of SASA calculated by these two softwares? > > On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > [...] > In Chimera, they are automatically calculated when you show a molecular surface. It creates an attribute named areaSAS, as explained here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfa…> > > See also this previous chimera-user post on using Chimera to get a list of residue SASA values > <http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html> > > (If you use this page <https://www.rbvi.ucsf.edu/chimera/docs/feedback.html> to search chimera-users by "sasa", that was the top hit) > > In ChimeraX, you would use the command "measure sasa" > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> > ... then save attribute "area" to file > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> > Hi Prathvi, The atomic coordinates are in angstroms so the surface areas are in angstroms squared. Since this answer is mostly about ChimeraX, I'm also CCing the chimerax-users list. Regarding the differences in value: The programs are both right but based on different surfaces. By default, Chimera encloses all of the protein chains together into one surface (and chain A residue 174 is buried by some interactions with chain C, which you can probably see if you look at the structure). In ChimeraX, the default for display is to make each chain a separate surface, but for SASA calculation, it only depends on what you wrote in the "measure sasa" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> As mentioned in my earlier answer, the important part of what you get from "measure sasa" is not (in your case) the total reported in the Log, but instead the "area" attribute value that you will get for each residue. If you just use this ChimeraX command: measure sasa /A:174 ... 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. If you wanted to enclose all the protein chains of a model in a single surface (like Chimera default), then measure sasa protein If you wanted to make a separate surface for chain A only, then something like measure sasa /A & protein (the & protein part is still needed so that it won't enclose ligands, water, etc. that also happen to have chain ID A) Using "measure sasa" gives the residue "area" attribute that you could save to file, show in labels, etc. as explained in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> <https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html> For your example structure 1TY4, using these ChimeraX commands: measure sasa protein info residues attribute area ...gives 2.55 for residue 174 in chain A, the same as in Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Multiplying the model around the helical cryo-EM map
by Dmitry Semchonok 16 Nov '22

16 Nov '22

Dear colleagues, I am trying to multiply the model subunit into the helical density. I found some command for Chimera sym #1 group c2*h,4.328,23.27,120,1 center 191.99,191.99,191.99 coord #0. Probably I have to somehow find the centre - perhaps with this command, right? Measure center #1 But not for ChimeraX. So my question is, how to do that in ChimeraX? Could you please provide the usage - it would be most helpful. Thanks in advance! Kind regards, Dmitry

2 1

Bond Rotation Questions
by FUNG Chun Po 15 Nov '22

15 Nov '22

Hello I have recently tried to use the bond rotation feature of Chimera X (Windows 10), and I have not been able to get it to work. I have tried the Bond rotation button on the toolbar, and the torsion command to no avail. The bond rotation button does not seem to do anything even when I click and drag with right click. The Torsion command states that my bond “is part of a ring/cycle and cannot be rotated” or “To set torsion, middle two atoms (/A ARG 543 N C) must be bonded;they aren't” I want to ask how do I use this function to rotate upon a simple amide bond. I am not sure am I just selecting the wrong atoms/bonds or is the function just locked for this PDB. The PDB file I am using is 7Y4P and I am trying to rotate about residues 543-544. I have also tried to do it in normal Chimera’s rotation command with no results. Thank you any advice would be welcome. Regards, Chun Po Fung

2 1

create chain as a new model from exiting PDB model
by tim smith 15 Nov '22

15 Nov '22

Hi All, I would like to create chain A as a separate model from the existing model. Could you please help me. Thank you. Best regards Tim

2 1

Question about pad parameter
by Thu Nguyen 14 Nov '22

14 Nov '22

Hello, I am using the volume cover command to crop the chain from the protein map. Here is what I did: > open 12554 from emdb > open 7ns0 > volume cover #1 atomBox #2/A1 pad 1.0 Suppose I want to add extra 17 voxels on each size of the chain, what value of pad should I add? Also, could you tell me the unit of pad in this command? Thank you very much. Best regards, Thu

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Re: [chimerax-users] Google colab sign in inquiry
by Tom Goddard 14 Nov '22

14 Nov '22

Hi Alejandro, On Windows the QtWebEngine Google Colab authentication info is in C:\Users\<username>\AppData\Roaming\ChimeraX\QtWebEngine\AlphaFold You can delete that directory and try using ChimeraX AlphaFold prediction again. Tom > On Nov 14, 2022, at 5:38 PM, Abraham, Alejandro <alejandro.abraham(a)icahn.mssm.edu> wrote: > > Hi Tom, > > Thank you for your email. I cannot see the login page anymore, and uninstalling ChimeraX to later reinstall it does not work. > Is there a folder where sign in is saved like in Macs ? I am using a Windows 10 PC. > Thanks again. > > Best, > > Alejandro > > > On Mon, Nov 14, 2022 at 12:59 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Alejandro, > > ChimeraX remembers your Google Colab sign-in. I don't understand why it would not let you sign in. A screenshot showing what you see would help understand the problem. > > If you signed in and ran AlphaFold previously but you want to change the account you sign in with, that should also be possible by clicking the image in the upper right corner of the AlphaFold Run panel which is just a web browser -- that button which shows the icon for your Google account will pull down a menu and let you sign out. And then you can also use it to sign in to another account. > > If somehow the ChimeraX remembered Google sign-in is causing problems you can delete that remembered sign-in info. On Mac you would delete the directory > > ~/Library/Caches?/UCSF ChimeraX/QtWebEngine/AlphaFold > > This is described further in this ChimeraX bug report > > https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7654#comment:2> > > Tom > > >> On Nov 14, 2022, at 7:36 AM, Abraham, Alejandro via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear ChimeraX Support Team, >> >> Before all, congratulations on such awesome software. >> On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? >> >> Thanks again. >> >> Best, >> >> Alejandro >> >> _______________________________________________ >> 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> >

1 0

stretching protein?
by Noriega, Heather 14 Nov '22

14 Nov '22

Hello, I hope this email finds everyone well. I was wondering if ChimeraX had a function specific to "stretching" the protein. I am going to attach a picture, for reference. Is it possible to stretch the monomer to build a larger capsid? Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883 [image: image.png]

3 5

Export PAE plot
by Clara Jegousse (TSL) 14 Nov '22

14 Nov '22

Dear ChimeraX team, After watching the YouTube tutorial on “how to show AlphaFold error estimates with ChimeraX”, I was wondering how to export the plot as an image (pdf, png?). Kind regards, Clara

3 2

Google colab sign in inquiry
by Abraham, Alejandro 14 Nov '22

14 Nov '22

Dear ChimeraX Support Team, Before all, congratulations on such awesome software. On another note I wanted to contact you because I am not able to connect to Google sign in when trying to predict with alpha fold. Is there a way to reset login ? Thanks again. Best, Alejandro

2 1

ChimeraX 1.5rc running on Nvidia RTX Titan [ubuntu 22.04]
by HONG ZHAN 11 Nov '22

11 Nov '22

Dear, I recently installed a Nvidia RTX Titan GPU card, and ChimeraX 1.5rc, it is a bit wired. I can open the window using intergrated GPU but if I just clicked on Chimerax or try to open it in terminal, it failed to open the program... Is ChimeraX only working on integrated GPU? Also, I cannot install the chimerax using apt install as in the website description, but dpkg -i works... is this the right way to install? many thanks! Hong

2 2

.pdb from Protein Data Bank has more chains than expected
by McClean, Phillip 10 Nov '22

10 Nov '22

Hi Everyone, I downloaded the 7FDL .pdb from the Protein Data Bank. I was expecting just two chains (it is a heteromeric complex), but I found 12 chains in the file (A-L). I was expecting two chains because the manuscript suggested they were just modeling protein fragments of the two protein. It appears that chains that A,C,E,G,I,K are multiple models of one fragment, while chains B,D,F,H,J,L are multiple models of the second fragment. Two questions. Why are multiple structures reported, and how to I visualize just two fragments at the same time, for example A and B. I have attached the .pdb file. Thanks for any advise. Phil McClean

3 5

Density extraction
by Dmitry Semchonok 09 Nov '22

09 Nov '22

Dear colleagues, I have a 3D map of the helix. 1. Do you know how can I extract 1 subunit? 2. Also, if there is no x-ray structure available. Thanks in advance. Kind regards, Dmitry

3 2

Fast Archive Search
by Kazan Ramy 09 Nov '22

09 Nov '22

Greetings to all, How can one search the archive with given keywords? Like for example, Ctrl + F search. I can only find the manual search by subject, thread ... and limited by month. Cheers, Ramy

3 2

Problem with the addcharge command
by svle＠tiscali.it 09 Nov '22

09 Nov '22

Hi all, for Chimerax version 1.4 (2022-06-03) when in the command line I use addcharge or addcharge #1 I receive in the Log panel the following: Unknown command: addcharge or Unknown command: addcharge #1. Where I'm wrong? Thanks. Saverio VOUCHER CONNETTIVITÀ per P.IVA e PMI: internet a canone 0 per 48 mesi. ATTIVA ORA https://casa.tiscali.it/promo/?u=https://promozioni.tiscali.it/voucher_busi…..

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Re: [chimerax-users] [Chimera-users] MD simulation movie in chimeraX
by Elaine Meng 09 Nov '22

09 Nov '22

Hello! For ChimeraX questions you may want to use the other address, chimerax-users(a)cgl.ucsf.edu CC'd here. You can see what formats ChimeraX reads by using command "open formats," or view this User Guide page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> ChimeraX can read .trr trajectory coordinates, but it cannot read .tpr trajectory topology. If your MD program can output a single PDB snapshot you can use that for the topology. First you would open the PDB file. Then to open the .trr file you would need to use the "open" command and also specify the already-open PDB file with the "structureModel" option. For example, if you open the PDB file as model #1, then something like: open myfile.trr structureModel #1 See details and more examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#structureModel> When you open the trajectory in ChimeraX, I believe that a playback slider will automatically appear. However, if it does not you can use "coordset slider" to show it. The "coordset" command can also be used to play the trajectory frames directly (not using the interactive slider): <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 8, 2022, at 6:17 PM, Shivam Gupta via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Support Team, > > I am a commercial license user of chimeraX. I have .trr and .tpr files from the Gromacs MD simulation. I am not getting any option to create an MD movie. I know how to do it in chimera but couldn't find a similar GUI/option in chimeraX. Literature/tutorial of chimeraX didn't help me much. > > Please help me out by guiding me to generate MD movies. > Please reply to this email inline. > > I am Looking forward to hearing from you. > Thanks > > -- > With Regards > Gupta　Shivam グプタ　シヴァム > E-mail: shivam-gupta(a)pharmafoods.co.jp > Biomedical Department > Pharma Foods International, Kyoto Japan > 株式会社ファーマフーズ > 〒615-8245　京都市西京区御陵大原1-49 > TEL:075-748-9811 > FAX:075-948-9818 > URL: http://www.pharmafoods.co.jp/

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side view window : lines are too thin
by Valerie Biou 08 Nov '22

08 Nov '22

Hello, I am a Chimera user slowly adapting to ChimeraX. I find that the moving lines in the Side view window are very thin, almost invisible when a cryoem map is displayed. is there a way to make them thicker ? thanks, kind regards, Valérie

2 1

RMSD Problem
by Timothy JM Clayson 08 Nov '22

08 Nov '22

Hiya, I am currently having a problem when trying to use RMSD on 2 sequences. *I am using the command: * *rmsd #1:149,264 to #2:469,553* (where a.a. on chain 1 are 149-264 and on chain 2 they're 469-553) *It is coming up with the error:* *'Number of atoms from first atom spec (21) differs from number in second (10)'* I was wondering if there is a fix to this problem? Thanks, Tim

2 1

Re: [chimerax-users] Applying symmetry operations to generate an oligomeric model
by Tom Goddard 07 Nov '22

07 Nov '22

Hi Rob, Hopefully you are using ChimeraX, not Chimera -- we have only done maintenance on Chimera for the past 6 years. The ChimeraX commands all work in physical coordinates (Angstroms), not grid index units (pixels), and usually they use scene coordinates, not local model coordinates which makes a difference if you have moved individual models relative to one another in the scene. Your Dn symmetry problems are because the two-fold symmetry that flips one Cn ring to the other stacked Cn ring needs to be aligned on the x-axis. In your map apparently it is not aligned with the x-axis. In general it is helpful to have your map aligned in a standard way if you will be applying symmetry. For dihedral symmetry the z-axis is the cyclic symmetry axis, the origin should be on that cyclic symmetry axis mid-way between the two rings, and the x-axis should be a two-fold symmetry axis. If you don't use standard map orientations for symmetric maps it is going to be very painful to make symmetric copies of atomic models in those maps. Tom > On Nov 6, 2022, at 12:58 PM, Robert Harkness <r.harkness(a)utoronto.ca> wrote: > > Hi Tom, > > Thank you for your detailed response! > > I think I am using an older version of chimera. When I use the center <map> command, I just get one line of output that corresponds to the center of the map in grid coordinates. I have been converting these into angstrom coordinates using the pixel size and applying those in sym. > > Sometimes when I open a model and a map, I have to rotate and translate the model into a reasonable position inside the map and then do a “fit in map” to get the initial placement for sym, so this means that the model’s coordinates will now be different relative to the scene and the map. If I save the fitted model to a new PDB and then re-open it, will it now have the same coordinates of the scene (and map if I haven’t moved the map at all)? I think that way I can use scene coordinates for all maps and models. > > I am finding for other cages I am working on that have Dn symmetry, in some cases they work beautifully if I just fit the model into the portion of the map that corresponds to one unit of the cage, then save that model as a PDB relative to the map, then open it and use sym <model> group <Dn> center <map center in angstrom units> coordinateSystem <map>. In other cases doing this same procedure, the first half of the cage units are made perfectly as sym goes from the initial model around the Cn axis placing copies in the density, but when it flips over the 2-fold axis to do the other half, the model units are out of alignment with the density. So I have been adding the axis option to get it closer but find it requires a little tweaking. I guess the axis command doesn’t always give the perfect axis of rotation because the map is not perfect. Will this also be alleviated by just using everything in scene coordinates? > > Best, > > Rob > >> On Nov 5, 2022, at 7:55 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Rob, >> >> It sounds like you did everything right. Using "measure center #1" where model #1 is the map should give the right center of the tetrahedron. When you use that command it reports the center in map grid index units and also in scene coordinates, for example, >> >> measure center #1 <cxcmd:measure center #1>Center of mass grid index for emdb 15560 = (279.52, 279.92, 253.25) >> Center of mass xyz coordinates for emdb 15560 = (289.20, 235.85, 185.32) >> >> >> In the sym command were you use that center to copy your atomic model with tetrahedral symmetry you should use the scene coordinates (the second line of output) not the grid index coordinates. The "sym" command expects scene coordinates for the "center" option and you should not use the "sym" command coordinateSystem option. The coordinateSystem option is used only if the center coordinates are given in the coordinate system of a specific model rather than the whole scene. The models start out with the same coordinate system as the whole scene, but if you move a model in the scene (e.g. when you fit an atomic model into the map) then that model has different local coordinates than the scene. >> >> I see another potential problem in your sym command. The "axis" option is supposed to be a 3-fold symmetry axis of the tetrahedron. You are giving it the symmetry axis of the asymmetric unit trimer which may or may not be a symmetry axis of the tetrahedron. To determine the symmetry axis of the tetrahedron open two copies of the map and rotate one copy by hand using the "Move Model" mouse mode (which moves only the selected model) to roughly align two different trimeric subunits then optimize the alignment with "fitmap #2 in #1", then use measure rotation #2 to #1 and it will report a symmetry axis of the tetrahedron. Another way to go about this is if you density map already has a standard orientation, such as tetrahedron 2-fold symmetry axes along x,y,z then you don't need to specify the axis in the sym command, just use "t,222" in the sym command. Or if it has a symmetry axis along z use "t,z3" with no axis specification. You can probably see if it has a standard symmetry using "measure symmetry #1". >> >> Sorry for the delayed answer. I was at a workshop all last week and did not have time for email. >> >> Tom >> >>> On Nov 3, 2022, at 4:35 AM, Robert Harkness via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do >>> >>> sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) >>> >>> And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! >>> >>> Best, >>> >>> Rob >>> >>> _______________________________________________ >>> 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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error saving session in v 1.5
by Yoda Muppet 07 Nov '22

07 Nov '22

Greetings. We're having an issue savings session with ChimeraX 1.5. Trying to save a session file results in the following error: [save] (help: user/commands/save.html) /data/processed/staggers/cryofib- tryps/process/YTAT9-1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs [save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs] (cxcmd: save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs) Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm. take snapshot (obj session, self.-state flags) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/log/tool.py", line 542, in take snapshot "contents': self.page source, AttributeError: *Log' object has no attribute 'page source' The above exception was the direct cause of the following exception: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process (obj, parents) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError (msg) from e RuntimeError: Error while saving session data for "tools' -> ‹chimerax.core. tools. Tools object at 0x7f90efeb0310> => <chimerax.log. tool. Log object at 0x7f90ee2b3c10> During handling of the above exception, another exception occurred: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 896, in save session. save (output, version=version, include maps=include maps) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 625, in save mgr.discovery(self. state containers) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError ("error processing: %S: %S" % ( obj stack(parents, obj), e)) ValueError: error processing: "tools' <chimerax.core. tools. Tools object at 0x7 f90efeb0310> <chimerax.log. tool.Log object at 0x7f90ee2b3c10>: Error while saving session data for 'tools' -> <chimerax.core. tools. Tools object at 0x7f90efeb0310> <chimerax.log. tool. Log object at 0x7f90ee2b3c10> BUG: ValueError: error processing: 'tools' for "tools => -> ->: Error while saving session data File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 266, in discovery raise ValueError ("error processing: %S: %5" % (obj stack(parents, obj), e)) See log for complete Python traceback.

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Change luminance in color palette
by Scott, Brandon L. 07 Nov '22

07 Nov '22

I am coloring surfaces using palettes (purples or a custom green-white-magenta). These both have a single luminance value, is it possible to generate a color palette that also has changing luminance. The ideal palette would be green -> white -> magenta along the color axis, and 0 - > 255 scaling the luminance of the rgb. We would effectively have a color bar matrix that goes from dark green to black to dark magenta if the values are low and bright green to white to bright magenta if the values are high. Thanks for your insights! -Brandon Brandon Scott, PhD CZI Imaging Scientist, Assistant Professor Nanoscience & Biomedical Engineering South Dakota Mines EEP 229 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/>

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Create command for subunit model
by tim smith 06 Nov '22

06 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Applying symmetry operations to generate an oligomeric model
by Robert Harkness 05 Nov '22

05 Nov '22

Hello, I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! Best, Rob

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Create subunit model
by tim smith 05 Nov '22

05 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Re: [chimerax-users] [Chimera-users] Jagged edges in chimera X
by Elaine Meng 03 Nov '22

03 Nov '22

Hi Prathvi, For ChimeraX questions, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu CC'd here. As per this recent post, ChimeraX does not have multisampling, but if you are saving an image you can use supersampling: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-September/004310.ht…> ChimeraX also has a "graphics quality" command to increase the number of facets used to draw atoms, bonds, and cartoons (ribbons), although I don't know if that is going to help your issue very much: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 3, 2022, at 4:59 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Elaine, > > Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? > The jagged edges can be removed in UCSF chimera by setting the subdivision value to 20 and enabling multisampling but I do not see these features in chimeraX. > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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How to discover hydrophobic between two chains
by McClean, Phillip 02 Nov '22

02 Nov '22

Hi Everyone, I ran AF2 multimer and have a two-chain complex. I ran the mlp command on the two chains separately and together. The two chains seem to interact via hydrophobic residues where chain B fits into a pocket on chain C. Here are the chain residues: /b:72-124 /c:1-190 Is there any way to determine which residues (hydrophobic) in each of these two regions are interacting via hydrophobic interactions. Thanks for any help you can provide. Phil McClean

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Copy attribute value from one attribute to another
by Sean Connell 02 Nov '22

02 Nov '22

Hello, I have a question with a probably obvious answer but I cannot figure it out. Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value. Sorry in advance if I miss something obvious.

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Get atom from selection string in script
by Thibault TUBIANA 02 Nov '22

02 Nov '22

Hi! I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in [ https://rbvi.github.io/chimerax-recipes/ | https://rbvi.github.io/chimerax-recipes/ ] to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?". Here's my current script from chimerax.core.commands import run def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg atoms = AtomsArg(selection) from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms]) torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}") def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger) register_command(session) Thank you for your help :) Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

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Re: [chimerax-users] [Chimera-users] xyz axis indicator
by Elaine Meng 01 Nov '22

01 Nov '22

Hi Xiang, I am guessing you are using ISOLDE with ChimeraX (not Chimera) so I am cross-posting this question to the chimerax-users(a)cgl.ucsf.edu list. I am not expert with ISOLDE so I am not sure about the answer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 10:58 PM, Xiang Zhang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi all, > > I was wondering how I could hide the xyz indicator in the center of window when I was viewing the X-ray density from mtz file? It only appears in crystal unit view mode but disappears in EM projection side view. > > Best, > Xiang > <1667192316818.png>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 3

Co-centering maps and pub models
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Dear ChimeraX users I have a density map and a pdb model opened in ChimeraX. How to move one of them to have a common axis (for both) , without disturbing the other. Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] AlphaFold Prediction
by Tom Goddard 31 Oct '22

31 Oct '22

Hi Raihan, The maximum sequence length that can be predicted by AlphaFold is limited by GPU memory. The following table says that paid Google Colab services only offer at most 16 Gbytes of GPU memory (from https://blog.paperspace.com/alternative-to-google-colab-pro/ <https://blog.paperspace.com/alternative-to-google-colab-pro/>). Not sure if it is correct since the table is from a Google competitor. You can run sequence length 1000, sometimes 1200, with 16 GB of GPU memory as shown here https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html Various cloud compute services offer modern GPUs like Nvidia A40, A100, A6000 with 48 GB, or 40 or 80 GB of GPU memory usually charging about $2-3 per hour. But ChimeraX can only currently use Google Colab for AlphaFold predictions. Tom > On Oct 31, 2022, at 2:45 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com> wrote: > > Thank you. I saw the run times. Is it possible to run sequences of around 1200 in Google Colab pro plus paid service through ChimeraX? In the website link you shared, I only saw about Google Colab pro paid service. Please let me know. > > Regards, > Raihan > > On Mon, 31 Oct 2022 at 14:33, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > ChimeraX only runs AlphaFold on Google Colab. Because Google Colab provides 5 year old GPUs with little memory (16 GB) it can only run sequences of length about 1000 or less. With better equipment and your own AlphaFold installation you can run sequences up to length 3000 or 4000 although that can take 30 hours. Here are example run times > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Tom > > >> On Oct 31, 2022, at 2:28 PM, S.M. RAIHAN RAHMAN <smrrbtgeiu(a)gmail.com <mailto:smrrbtgeiu@gmail.com>> wrote: >> >> Thank you so much. Is there any alternative to Google Colab for running AlphaFold through ChimeraX? Please let me know. >> >> Regards, >> Raihan >> >> On Mon, 31 Oct 2022 at 14:22, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Raihan, >> >> The ChimeraX AlphaFold prediction produces 5 models but it only automatically opens the best model. All 5 models are in the ~/Downloads/ChimeraX/AlphaFold/prediction directory after the job completes. There is no option to run fewer models. Running AlphaFold not through ChimeraX also produces 5 models. This is because AlphaFold works by running 5 slightly differently trained neural networks and the best is chosen. If you install your own AlphaFold (a somewhat difficult task, needs Linux and an Nvidia GPU and a few Tbytes of disk for databases) then you can modify the AlphaFold Python code to predict only one or a few models by choosing which of the 5 networks it should run. >> >> Tom >> >> > On Oct 31, 2022, at 1:39 PM, S.M. RAIHAN RAHMAN via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi! >> > Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. >> > >> > Regards, >> > Raihan >> > _______________________________________________ >> > 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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AlphaFold Prediction
by S.M. RAIHAN RAHMAN 31 Oct '22

31 Oct '22

Hi! Good Afternoon. I hope that you are doing well. I am facing a problem in running structure prediction of large protein sequence in AlphaFold prediction. Is there any way of predicting only 2 models of a given sequence in lieu of 5 models before providing the final model in AlphaFold prediction? Please let me know. Thank you. Regards, Raihan

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Copy a part of a model ?
by mailman-bounces＠cgl.ucsf.edu 31 Oct '22

31 Oct '22

Hi :) I wanted to duplicate only one part of a model and I haven't found a copy function (I found this old thread tho https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-January/000783.html>) For now my strategy is to duplicate the model with "combine #1 close false" and then delete what I don't want on the new model like for example (to delete helices) "delete ~helix & #2" I know you are always super busy with ChimeraX dev, but I thought this could be a good "quick way" to create a "copy" function of example (if there are no alternative that I missed of course). Have a great day! Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @IMAPP <https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism…> Institute for integrative biology of the cell (I2BC <https://www.i2bc.paris-saclay.fr/>) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: http://www.tubiana.me/gallery <http://www.tubiana.me/>

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Re: [chimerax-users] [Chimera-users] Question regarding protein-protein interactions in ChimeraX
by Elaine Meng 31 Oct '22

31 Oct '22

Hi Camille, ChimeraX does not move the proteins to predict how they might bind each other, although you could move one relative to the other "manually" (with the mouse) yourself, or use some other program to do protein-protein docking. ChimeraX is just showing the coordinates in the Protein DataBank data files that you opened, i.e. whatever the authors deposited. If you are using ChimeraX, for future questions you may want to use ChimeraX mailing list chimerax-users(a)cgl.ucsf.edu CC'd here instead of the Chimera one. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 30, 2022, at 3:26 PM, Lake, Camille (NIH/NIAID) [C] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, > > My name is Camille Lake and I have used ChimeraX to model proteins. I was wondering - if I load two completely separate proteins from PDB, what is the nature of their interaction as shown by ChimeraX? The two proteins I'm interested in, TIM-3 (5f71) and CEACAM1 (5dzl), are predicted to interact in the literature, but if I load them separately into ChimeraX, is this predicted interaction what displays automatically? It seems that they are, but I can't find anywhere on the web whether this is automatically done in ChimeraX. Other proteins I randomly add in generally keep far away from each other in space. > > Thank you, > > Camille

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can not download
by keqing yin 29 Oct '22

29 Oct '22

Hello, There is no reaction after I clicked the save as the CSV when I want to download the clipper from tools/more tools . I would be very appreciate if you could solve this problem. [cid:image003.png@01D8EAFB.ECAB74A0] 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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How do I visualize an amber nc file in ChimeraX?
by Yasmene Wang Elhady 28 Oct '22

28 Oct '22

Hello, I'm new to molecular modeling, and new to Chimera. I'm trying to visualize an AMBER .nc output file from an AMBER tutorial ( http://ambermd.org/tutorials/basic/tutorial0/) and I have a topology file that in VMD is the type AMBER7 Parm. How can I visualize this in ChimeraX? I saw another thread suggesting to use the MD movie tool, but I don't see that option in ChimeraX. Is this something I need to add? If so, where can I get it from, and how do I add it? Thanks in advance, Yasmene

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Selection by segid
by CUNIASSE Philippe 28 Oct '22

28 Oct '22

Dear all, Is there a way in ChimeraX to make a selection by segid (column 73-76 in pdb format from CHARMM of XPLOR)? Thanks in advance. Philippe Cuniasse. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_700846419][signature_2907812893][signature_966493179] -----------------------------------------------

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Re: [chimerax-users] ChimeraX sequence alignment score?
by Elaine Meng 27 Oct '22

27 Oct '22

> On Oct 27, 2022, at 4:46 PM, Budayr, Omar Mahdi <obudayr(a)vols.utk.edu> wrote: > > Dear Dr. Meng, > > I looked through the documentation for ChimeraX and I still cannot figure out what the value for sequence alignment score indicates. I aligned two b-adrenergic receptors from PDB (2RH1 and 3NH8) and it gives a value of 2423.9. What does this value actually represent? The documentation refers to it but never gives specifics besides the parameters in the table that matchmaker generates > > Sincerely, > Omar Budayr Dear Omar Budayr, The value itself is not at all important. The reason to have a score is that the alignment process tries to maximize it for the pair of sequences that it is given. By changing parameters for scoring you can change the relative importance of the different parts of the score, and thus what is most important for the alignment method to align. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. we recommend sending questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here) so that others can benefit from the answers and/or help to answer the questions - thanks!

1 0

Selecting residues in two chains
by McClean, Phillip 27 Oct '22

27 Oct '22

Hi Everyone, I have a .pdb file created using AF2 Multimer. It consists of two chains, B and C. Chain B is a protein with 315 residues, while Chain C is a protein with 662 residues. Each chain is modeled with structured and unstructured regions. I would like to only show residues 19-24 of Chain B and residues 1-190 of Chain C in the display window. I have tried using the information provided on the "Command-Line Target Specification" page, but I have not had any success with just displaying those ranges of residues in the display window. My goal is to highlight specific features of those ranges of residues to display their interaction. Thanks for any information you can provide. Phil McClean

2 4

segmented tomogram density in chimeraX
by Jesse HANSEN 25 Oct '22

25 Oct '22

hi all, I have segmented a tomogram in Amira and exported to chimera for visualization. I first opened the .rec file in chimera and re-saved as .mrc. Okay, the segmentation output gives a fully filled volume cube except for the regions of segmentation. Obviously things are inverted. Also, the volume viewer shows clear sharp peaks (delta functions) rather than continuous density, as volume slider moves to the right new segmentation features appear. So I used volume filter with "scale" to -1, and I turned off "displayed subregions only". This fixed the inversion problem and now as I slide toward the right I see more segmented densities. However the threshold values are all negative (-250 on the far left to -240 on the far right). This, combined with the densities being sharp peaks, makes it impossible to use this volume like a regular volume for surface coloring, filtering, segger, etc. Any suggestion on how to go from this step to a usable density would be appreciated. thanks! Jesse ================================= Dr. Jesse Hansen Schur Group Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg Austria

3 4

Useful tools ideas/requests
by Shayne Quinn 21 Oct '22

21 Oct '22

Hello, I have been using ChimeraX for a few years now for multidimensional cell bio-imaging and cannot thank the team and developers enough for such an amazing program. I am not sure where to ask for other useful tools so I am starting here. These may already exist but I was unsuccessful in finding them in the user guide so my apologies if I missed them. 1) Is there an option to color the different axis for the 'showOutlineBox' feature for volumes? For example box lines in x-blue, y-green and z-red to help keep orientation (I have included a mock version in the attachment) 2) I work specifically with Lattice Light Sheet Data which requires our 3D cells to be placed on glass coverslip that do not show up in the captured data but are useful for referencing orientation. Is there a feature in place already that would allow me to create a mock coverslip. So far I resorted to importing a throwaway volume (Volume 4 in attachment) and made the threshold for a surface ~0, set it to grey, and made it fill the bottom 5 pixels or so, shown in the attachment. 3) Is there a time stamp feature similar to the scale bar function that has already been implemented? Thank you so much for all the time and effort that has been put in and for creating such an amazing visualization tool! Cheers, Shayne Quinn

3 4

Installing ChimeraX on Ubuntu 16.04 or openSuse Leap 15.2
by Miguel 19 Oct '22

19 Oct '22

Hello, I am trying to install ChimeraX on Ubuntu 16.04 or openSUSE Leap 15.2 without success. Is it possible? If so, what would be the procedure? Thanks, Miguel

3 5

Center of the erase sphere
by Tianming Qu 19 Oct '22

19 Oct '22

Hi ChimeraX developers, Is there any way I can know the center of the erase sphere in CHimeraX? Best, Tianming

2 1

Generate surface from a model using user defined color
by HONG ZHAN 17 Oct '22

17 Oct '22

Dear all, I would like to generate surface using my model but I want to keep the color as I defined. My protein contains only one chain so that when I ran Surface command, it generated surface with one color... Is there a way to generate surface to keep my defined color? Super thanks! Hong

3 3

chimeraX clipper install
by Gutierrez, Dominique 17 Oct '22

17 Oct '22

Hello, I tried to install clipper with the popup window but it takes forever. I downloaded it directly from the website. Where do I put it .whl file? Best Regards, Dominique Gutierrez

2 2

Re: [chimerax-users] [chimera-dev] ChimeraX pyhton script
by Elaine Meng 17 Oct '22

17 Oct '22

> On Oct 17, 2022, at 7:26 AM, Jan Hofmann via Chimera-dev <chimera-dev(a)cgl.ucsf.edu> wrote: > > To whom it may concern, > I want to write a python script to open a pdb file, then load a .xplor file in as well. After one rotation which I also want to do via the script I want to export the output file as a .png file. > Could you provide any advice to me on how to write such a script? I am having troubles loading any python script into ChimeraX. Eventually I want to use this script to batch wise output structures including guest adsorption where the guest species is introduced via the .xplor from previous analysis and the structure is provided by a .pdb file. I really would need some advice/tutorial at this stage so I would be more than happy to hear back from you. > Many thanks and kind regards, > Jan Hofmann, M.Sc. > PhD Student, Department of Chemistry > Chapman Group > Stony Brook University > jan.hofmann(a)stonybrook.edu > Office: Room 563, Chemistry Hi Jan, This is the Chimera list, maybe you wanted to send to chimerax-users(a)cgl.ucsf.edu instead? (Cc'd) Maybe it can be done at least partly with ChimeraX command script instead of a python script. If you do these steps interactively in ChimeraX, it should show the corresponding commands in the Log . A ChimeraX command script is just the same commands you would enter in the Command Line, except in a plain text file named something.cxc as explained here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc…> There is also a "forEachFile" option of the "open" command to read a ChimeraX command file and apply it to a series of input files, e.g. all the .pdb files in some folder. If you name the .xplor files to match the corresponding .pdb files, maybe you can use the $ mechanism described for that option, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#forEachFile> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 2

How to hide a chain and overly the shown chain with another model
by McClean, Phillip 13 Oct '22

13 Oct '22

I have a .pdb file obtained from ColabFold. The model was developed with AlphaFold2 Multimer. It has two chains. How can I 1) hide only one chain and then 2) add a second model. The second model will be the visualized chain developed only on its own. I am looking for regions that might be different between the model with a second protein and by itself. I tried hide /c but that didn't work. Phil McClean

2 1

Loading density files
by Tianming Qu 12 Oct '22

12 Oct '22

Dear Chimerax developers: I have a lot of density files, is there anyway I can load them at the same time and view then like a protein traj? Best, Tianming

2 3

Problem reading ccp4 maps
by Luca Pellegrini 11 Oct '22

11 Oct '22

When I try to read ccp4 maps from Phenix Resolve_cryoEM into ChimeraX, I’ve started getting the following message: "MRC file is truncated. Failed reading 1 values, type int32” It’s ChimeraX version 1.5.dev202210110346 (2022-10-11)/ macOS Monterey/MacBook Pro 2021, M1 Pro. Best wishes, Luca

2 1

Can you do convex hull on ChimeraX?
by Tianming Qu 10 Oct '22

10 Oct '22

Hi dear ChimeraX-Users and developers, Is ChimeraX available for drawing the convex hull of protein structures? Best, Tianming

4 4

Fit in map, save new coords of map
by Nebojsa Bogdanovic 10 Oct '22

10 Oct '22

Hello, I open two maps and I fit #2 into #1. I need to save map #2 at it's new position, but there is no option "relative to model or map". By doing "volume resample #1 onGrid #1, I match the box sizes but the new position is not maintained after saving that new map. Is there any command/function I could do that with? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

3 3

Re: [chimerax-users] alphafold contacts between 3 and more subunits
by Tom Goddard 10 Oct '22

10 Oct '22

Hi André, I added two options "replace" (default true) and "name" (default "PAE Contacts") to the alphafold contacts command. The replace option determines if existing contact pseudobonds (in the group with the specified or default name) are deleted. If replace is false the new contacts are just added to any existing ones. The name option gives the pseudobond model the specified name. So you could use alphafold contacts /A to /B alphafold contacts /B to /C replace false alphafold contacts /A to /C replace false to put all the contacts in one pseudobond submodel. If instead you wanted them in 3 different models you could use alphafold contacts /A to /B name "AB contacts" alphafold contacts /B to /C name "BC contacts" alphafold contacts /A to /C name "AC contacts" This will be in tomorrow's (Oct 11) ChimeraX daily builds. Tom > On Oct 10, 2022, at 12:38 PM, Michaelis, Andre Clemens <michaelis(a)biochem.mpg.de> wrote: > > Awesome, > Thank you so much! > > Best > André > > > —————————————————— > > >> Am 10.10.2022 um 20:50 schrieb Tom Goddard <goddard(a)sonic.net>: >> >> Hi André, >> >> The "alphafold contacts" command creates a submodel of the atomic structure containing pseudobonds with the submodel named "PAE Contacts". If you rename that submodel then it won't replace it when you do the second alphafold contacts command on the same structure. For instance, if the structure is model #1. >> >> alphafold contacts /A to /B >> rename #1.1 "AB contacts" >> alphafold contacts /B to /C >> rename #1.2 "BC contacts" >> alphafold contacts /A to /C >> >> This should be easier to do. I should add an option to the alphafold contacts command "replace false" that automatically uses new names for each group of pseudobonds. I've made a request for this. >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770 <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7770> >> >> Tom >> >>> On Oct 10, 2022, at 5:47 AM, Michaelis, Andre Clemens via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hi, >>> >>> Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? >>> e.g.: >>> alphafold contacts /A to /B >>> AND >>> alphafold contacts /B to /C >>> AND >>> alphafold contacts /A to /C >>> >>> Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those >>> >>> Thank you very much! >>> >>> Best André >>> >>> >>> _______________________________________________ >>> 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>

1 0

alphafold contacts between 3 and more subunits
by Michaelis, Andre Clemens 10 Oct '22

10 Oct '22

Hi, Is it possible to draw contacts (PAE, alphafold) between more than just 2 subunits? e.g.: alphafold contacts /A to /B AND alphafold contacts /B to /C AND alphafold contacts /A to /C Righ now, a new command deletes the old contacts. Not sure about a syntax that would combine/add those Thank you very much! Best André

2 1

mrc to pdb
by Tianming Qu 07 Oct '22

07 Oct '22

Hi, is there any way I can convert a .mrc file to .pdb file in chimera? Best, Tianming

5 5

A question about the level option in volume viewer
by Qu Tianming 06 Oct '22

06 Oct '22

Hi ChimeraX-developers, I got a question about the level option in volume viewer. I think the level represent the isovalue for the density map. So when I set the level as 0.03, I got a density map as following : [?? ???????] When I set the level as 0.01, the density map as following: [?? ???????] So my question is that, does level 0.03 or 0.01 means, all grids with a density value lower than 0.03 or 0.01 will be present? Means when I set the level as 0.01, everything left in the density map is the density value lower than 0.01? Best, Tianming

2 1

Moving molecules in VR
by Dr. Eddie 06 Oct '22

06 Oct '22

Hello, I'm trying to move some waters away from a ligand (and eventually some lipids as well) as they overlap too much for minimization to fix it. I can't seem to figure out how to select an entire (water) molecule. The select atom lets me select one atom, but I cannot chain or add more atoms. Some atoms seem to refuse to move even when I try to move one at a time using the "Move atoms" right mouse option. Any help would be appreciated as I can't find much about translating molecules (the bond rotation works perfectly!). Thanks! Eddie

3 2

Problems with Qt6
by Hoover, David (NIH/CIT) [E] 06 Oct '22

06 Oct '22

Hi, I'm trying to create a Ubuntu 22.04 container for ChimeraX v1.4 and no matter what I do I get this error message: NOTE: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1021, in <module> exit_code = init(sys.argv) File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 573, in init from chimerax.ui import initialize_qt File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/__init__.py", line 21, in <module> from .gui import MainToolWindow, initialize_qt, menu_capitalize File "/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/ui/gui.py", line 130, in <module> from Qt.QtWidgets import QApplication File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in <module> from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory BUG: ImportError: libQt6Core.so.6: cannot open shared object file: No such file or directory File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/Qt/__init__.py", line 64, in from PyQt6.QtCore import PYQT_VERSION_STR as PYQT6_VERSION _See log for complete Python traceback._ I am attempting to install into Ubuntu 22.04 with ever Qt6 package available, but nothing seems to help. The library in question definitely exists at /usr/lib/x86_64-linux-gnu/libQt6Core.so.6, along with a multitude of other libQt6* libraries. Is there something additional that needs to be done or installed to enable ChimeraX v1.4 to run? I have tried export LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH but this does not help. Any insight would be appreciated. David -- David Hoover, Ph.D. Computational Biologist High Performance Computing Services, Center for Information Technology, National Institutes of Health 12 South Dr., Rm 2N207 Bethesda, MD 20892, USA TEL: (+1) 301-435-2986 Email: hooverdm(a)hpc.nih.gov

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Re: [chimerax-users] usage for multimer
by Tom Goddard 05 Oct '22

05 Oct '22

Hi Dennis, Are you asking about fetching AlphaFold database models? Those are only of monomer proteins. With AlphaFold predictions energy minimization is done using OpenMM and the Amber force field -- it has nothing to do with binding affinity. I don't know what you mean by a contact map. Maybe you are interested in the ChimeraX interfaces tool that shows contact residues at an interface. Please give enough details in your questions so they are clear, otherwise we will not be able to spend the time to answer. Tom > On Oct 5, 2022, at 7:41 PM, Dennis Poh <pohdennis90(a)gmail.com> wrote: > > Hi Tom > > Thanks, also in the chimerax GUI software, I can fetch my separated sequences delimited with a comma, but does the overall structure that appears the most energy-minimized model or just a superimposition simply based on sequence similarity? > > How is the energy-minimization done (is it based on deltaG = G(bound complex) - G(protein1) -G(protein2)) ? > Could a contact map be produced (if 2 sequences are compared pairwise) too? > > -Dennis > > On Thu, 6 Oct 2022 at 01:43, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Dennis, > > AlphaFold on Google Colab will only work for total sequence length of about 1000 because the old Google Colab GPUs only have 16 Gbytes of memory. Modern GPUs for machine learning like an Nvidia A40 (48 GB) or A100 (40 or 80GB) or A6000 (48 GB) can handle more than 3000 residues but those GPUs cost $5000-$15000. A consumer Nvidia RTX 3090 (24 GB, $1500) can manage up to 2000 residues. Setting up AlphaFold on your own machine is a bit of work. I see from your output file name "af1848" you tried to run total sequence length 1848 which certainly will fail on Google Colab. For examples of AlphaFold runs at different sequence lengths see > > https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> > > Also AlphaFold has a minimum sequence length for each individual sequence is 16 so your example ACCCC and ALLPAAAA will not work. This minimum length is because AlphaFold uses a sequence alignment made by searching a billion database sequences and searching shorter sequence produces millions of hits that are not evolutionarily related. > > The sequence length limits are described in the ChimeraX documentation > > https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#caveats> > > Tom > > >> On Oct 5, 2022, at 9:35 AM, Dennis Poh via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hi Eric >> >> 1. It seems that I don't have sufficient GPU memory in colab. >> >> I have the following error message: >> INFO:colabfold.batch:Running model_1 >> /usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:195: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> leaves, structure = jax.tree_flatten(mapping) >> /usr/local/lib/python3.7/dist-packages/haiku/_src/data_structures.py:203: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> self._mapping = jax.tree_unflatten(self._structure, self._leaves) >> /usr/local/lib/python3.7/dist-packages/haiku/_src/stateful.py:457: FutureWarning: jax.tree_leaves is deprecated, and will be removed in a future release. Use jax.tree_util.tree_leaves instead. >> length = jax.tree_leaves(xs)[0].shape[0] >> /usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:136: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> flat_array_like, inner_treedef = jax.tree_flatten(array_like) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/geometry/struct_of_array.py:210: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> inner_treedef, data[array_start:array_start + num_array]) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:50: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> values_tree_def = jax.tree_flatten(values)[1] >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:54: FutureWarning: jax.tree_unflatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_unflatten instead. >> return jax.tree_unflatten(values_tree_def, flat_axes) >> /usr/local/lib/python3.7/dist-packages/alphafold/model/mapping.py:129: FutureWarning: jax.tree_flatten is deprecated, and will be removed in a future release. Use jax.tree_util.tree_flatten instead. >> flat_sizes = jax.tree_flatten(in_sizes)[0] >> ERROR:colabfold.batch:Could not predict af1819. Not Enough GPU memory? INTERNAL: cublas error >> INFO:colabfold.batch:Done >> Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold >> cp: cannot stat '*_relaxed_rank_1_model_*.pdb': No such file or directory >> cp: cannot stat '*_unrelaxed_rank_1_model_*_scores.json': No such file or directory >> >> 2. Would it be possible to run this in jupyter? Or are there alternatives? >> >> 3. " Prediction may fail with total sequence length over 1000 residues due to limited GPU memory." - this total sequence length meaning all the sequences in the list to be concatenated? >> >> 4. I seem to also have some pdbxx.m8 and afxxxx.csv files - may I know what these files are for? >> >> Thanks! >> -Dennis >> >> On Thu, 6 Oct 2022 at 00:25, Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >> Also, if you are copying the sequence from a text editor, make sure the editor is displaying the sequence as plain text or that you are copying as plain text, otherwise invisible formatting characters may be embedded in what you paste. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> > On Oct 5, 2022, at 9:14 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Well, the message says there is an invalid character, so all I can say is to make sure that you are pasting plain text, and check to see that you have only standard amino acid codes and commas. >> > >> > WIthout seeing exactly what you pasted, we can't tell which part caused the problem. >> > >> > Elaine >> > >> > >> >> On Oct 5, 2022, at 9:09 AM, Dennis Poh <pohdennis90(a)gmail.com <mailto:pohdennis90@gmail.com>> wrote: >> >> >> >> Hi Elaine, >> >> >> >> Thanks, I was trying to predict a multimer or the overall structure of many subunit chains using individual sequences, each separated with a comma in colab. >> >> But it seems that there was some error and no pdb file was generated; the error message is as follows: >> >> >> >> ERROR:colabfold.batch:Could not generate input features af1848: Invalid character in the sequence: >> >> Traceback (most recent call last): >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1357, in run >> >> model_type, >> >> File "<ipython-input-1-d6881d38b934>", line 122, in generate_input_feature_wrapper >> >> (input_features, domain_names) = batch.generate_input_feature_orig(*args, **kw) >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1018, in generate_input_feature >> >> sequence, input_msa, template_features[sequence_index] >> >> File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 869, in build_monomer_feature >> >> sequence=sequence, description="none", num_res=len(sequence) >> >> File "/usr/local/lib/python3.7/dist-packages/alphafold/data/pipeline.py", line 43, in make_sequence_features >> >> map_unknown_to_x=True) >> >> File "/usr/local/lib/python3.7/dist-packages/alphafold/common/residue_constants.py", line 580, in sequence_to_onehot >> >> raise ValueError(f'Invalid character in the sequence: {aa_type}') >> >> ValueError: Invalid character in the sequence: >> >> INFO:colabfold.batch:Done >> >> Downloading structure predictions to directory Downloads/ChimeraX/AlphaFold >> >> cp: cannot stat '*_relaxed_rank_1_model_*.pdb': No such file or directory >> >> cp: cannot stat '*_unrelaxed_rank_1_model_*_scores.json': No such file or directory >> >> >> >> -Dennis >> >> >> >> On Wed, 5 Oct 2022 at 23:36, Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >> >> Hi Dennis, >> >> Your sequence input is wrong - it should contain only the sequences pasted as plain text, with only a comma between them (NOT the ">description" line because it is not supposed to be in fasta format). How to input sequence(s) is explained in the AlphaFold help page. >> >> >> >> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>> >> >> >> >> "For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains), or individually within a comma-separated list of UniProt identifiers or pasted-in amino acid sequences." >> >> >> >> E.g. something like >> >> >> >> ACCCC,ALLPAAAA >> >> >> >> I hope this helps, >> >> Elaine >> >> ----- >> >> Elaine C. Meng, Ph.D. >> >> UCSF Chimera(X) team >> >> Department of Pharmaceutical Chemistry >> >> University of California, San Francisco >> >> >> >>> On Oct 5, 2022, at 4:12 AM, Dennis Poh via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >>> >> >>> Sorry, I couldn't generate the pdb from chimera colab - is there anything that i may have missed? >> >>> >> >>> -Dennis >> >>> >> >>> On Wed, 5 Oct 2022 at 17:11, Dennis Poh <pohdennis90(a)gmail.com <mailto:pohdennis90@gmail.com>> wrote: >> >>> Hi >> >>> >> >>> I encounter a problem in multimer prediction with the sequences I use as input. >> >>> It's always indicating: >> >>> "Missing or invalid "sequences" argument: Sequences argument" >> >>> and " is not a chain specifier, alignment id, UniProt id, or sequence characters" >> >>> >> >>> The input format is always something like a fasta format: >> >>>> seq_id >> >>> ACCCC >> >>> >> >>>> seq_id2 >> >>> ALLPAAAA >> >>> >> >>> May I know how I can rectify this? >> >>> >> >>> Thanks! >> >>> - Dennis >> >> >> > >> > >> > _______________________________________________ >> > 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> >> >> _______________________________________________ >> 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> >

1 0

combining executable html commands
by Krishnan Raman 05 Oct '22

05 Oct '22

I have large presentation with several html executable commands . is there a way I can run them with one click single command for all of them? thanks Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

usage for multimer
by Dennis Poh 05 Oct '22

05 Oct '22

Hi I encounter a problem in multimer prediction with the sequences I use as input. It's always indicating: "Missing or invalid "sequences" argument: Sequences argument" and " is not a chain specifier, alignment id, UniProt id, or sequence characters" The input format is always something like a fasta format: >seq_id ACCCC >seq_id2 ALLPAAAA May I know how I can rectify this? Thanks! - Dennis

4 7

Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
by Tan, Wei Ren 05 Oct '22

05 Oct '22

Dear Sir/Mdm, Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King's College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command: alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest) Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead? Thank you very much and sorry to disturb you! Sincerely Yours, William Tan

3 4

ligand not showing up
by Dr. Eddie 05 Oct '22

05 Oct '22

Hi all, I've got a pdb and I can't seem to get ChimeraX to recognize the ligand (resname STR) at the end of the pdb. I've modified the ATOM to be HETATM but it still does not show up. I hide solvent and the lipids and I know where it should be (from seeing it in vmd) but only a void is there. Any ideas what is wrong with the pdb? Thanks, Eddie

3 6

alphafold contacts output file
by McClean, Phillip 04 Oct '22

04 Oct '22

Hi Everyone- I used the following command to obtain a file with the contacts between two chains: alphafold contacts /B to /C output contact_pae.txt I cannot seem to find where the output file is located. Thanks for any help. Phil McClean

3 7

ChimeraX for multimeric prediction
by Dozic,Abdul-Vehab 03 Oct '22

03 Oct '22

Greetings, Firstly, I wanted to say that ChimeraX is excellent software, and it can definitely be helpful to enhance our research experience. I wanted to ask about using ChimeraX to predict whether a protein occurs in a multimeric form. I ran Alphafold for multimeric simulations and I have analyzed the predicted aligned error qualitatively, but I was wondering if ChimeraX had some built-in package for fast error analysis such as that it can tell us automatically whether it is likely to find a protein in a particular multimeric state that was modeled by Alphafold. Thanks, Best, Abdul-Vehab

2 1

morph question
by Krishnan Raman 29 Sep '22

29 Sep '22

The morph creates a new model; when i display this new model the last(frame) with final conformation shows up on the screen. is there a way to show the first frame when i play the morph using an executable command? i do have to show the model to play the morph using coordset command. thanks Krishnan CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

Question about resfit command
by Mary Liu 28 Sep '22

28 Sep '22

Dear Chimera X users, Is it possible to show the fit of each nucleotide (not amino acid residue) in density using the resfit command or something like that? Thanks

2 2

Re: [chimerax-users] alphafold contacts output
by Elaine Meng 28 Sep '22

28 Sep '22

> On Sep 27, 2022, at 1:59 PM, McClean, Phillip <phillip.mcclean(a)ndsu.edu> wrote: > > Hi Elaine, > > I am using output data from alphafold2 multimer as provided by Colabfold. Following the video (https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s) I use the following command: > > > alphafold contacts /b to /c distance 8 > > For my complex, the links at the distance are all blue (good results). What is confusing is that the distance of some of the contacts are greater than 8 angstroms. Those distances are between backbone carbon atoms, I assume. The fact that the command asks for amino acid pairs that are less than 8 angstroms apart suggest that other atoms than those in the backbone are less than 8 angstroms. Is my conclusion correct. > > Thanks as always for the advise. > > Phil Hi Phil, Yes, your conclusion is correct - the distance cutoff applies to any atom in the residue within any atom in the other residue, whereas the pseudobond is drawn between alpha-carbons, as mentioned here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts> We generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) since many heads are better than my one, unless you are including some data that needs to remain private. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Fitmap on a subvolume?
by vincent Chaptal 27 Sep '22

27 Sep '22

Hi, I'd like to compare 2 maps, and would like to superposse them on specific portions of the map. Is there a way to do this? I was thinking to assign a pdb to each map, and apply a superposition of pdb1 onto pdb2 and have the maps follow the movement? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

3 2

transparency
by Krishnan Raman 26 Sep '22

26 Sep '22

How to set transparency on surfaces during morphing? I start out with 95% but end up with 0%. The morphing works well though. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

3 2

mseries slider
by Krishnan Raman 26 Sep '22

26 Sep '22

The mseries slider appears inside chimerax main screen. Is there a command to make it appear outside the main screen(undock it automatically in a command line? thanks Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

3 2

Website downtime starting Tuesday, Sep 27
by Elaine Meng 26 Sep '22

26 Sep '22

Dear users, The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tuesday, Sep 27 9pm PDT, through Wednesday, and possibly extending to Thursday, Sep 29 5pm PDT. PDT = Pacific Daylight Time. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Sorry for the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Combining chain #1 and residue #2: naming issue
by Dmitry Semchonok 26 Sep '22

26 Sep '22

Dear colleagues, I would like to add the residues to the secondary structure (residues come from similar structures and are aligned for the position). For that I use combine tool. When I combine the secondary structure with the residues (combine #1 #2), in the new model the residues (#2) get arbitrary names and no longer belong to each of the main chains (#1). That creates a mass. Could you please advise how to change the names of the residues so that each will belong to the corresponding main chain? (In the combined model I have chan A and residues G…ect ) I tried to use Renumber Residues tool but it did not work (renumber /A-F,I-M,X seqStart 1. 0 residues renumbered) Thanks in advance. Kind regards, Dmitry

2 1

view saves/move commands
by Krishnan Raman 26 Sep '22

26 Sep '22

I tried to play a morph including a flyin of a ligand. It worked fine exceopt for the fly-in and out part The session file did not save the views with ligand away and ligand in the active site. Is there a way around it? How do I estimate a the move coordinates for a ligand to position it where I want it using move command? Thanks again for all the quick and timely help for all my queries. Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 1

define contour level range when molmap
by Yanhe Zhao 25 Sep '22

25 Sep '22

Dear developer, I have docked several pdb to my reference map, there are still large area of density have not assigned any models. Right now I am doing molmap onGrid of reference map, the contour range of new generated became pretty narrow and start from 0. I was wondering which option I can use to define the contour range? Thanks and best regards, Yanhe

2 2

Orientate models
by Yanhe Zhao 23 Sep '22

23 Sep '22

Dear Developer, I have aligned all my models to one reference model, What is the right way to orient all models based on reference model's xyz axis? (They have different coordinate system) Thanks and best, Yanhe

2 2

(no subject)
by Tianming Qu 23 Sep '22

23 Sep '22

Dear ChimeraX group, My name is Tianming Qu and I am currently a phd candidate in Florida State University working on MD simulation study about enzyme proteins. I am currently trying to use chimeraX to show a water density map calculated from an MD trajectory and I got the following fig as result: [cid:image001.png@01D8CD9D.17E4A690] I wonder if the ChimeraX can grab the “red region”out of the whole map, since this the “pocket region”I want. Looking forward to your reply! And it will be my great pleasure if I can have a chance to talk (maybe zoom?) to one of the developers in ChimeraX group! Thanks a lot for the help. Best, Tianming

4 14

Website downtime starting Tuesday, Sep 27
by Elaine Meng 23 Sep '22

23 Sep '22

The RBVI website (Chimera, ChimeraX, etc.) and RBVI-hosted web services will be down for maintenance from Tue, Sep 27 9pm PDT, through Wed, possibly extending to Thu, Sep 29 5pm PDT. RBVI-hosted web services called from Chimera and ChimeraX include Blast Protein, Modeller, and multiple sequence alignment with Clustal Omega or MUSCLE. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Fixing the PDB
by Dmitry Semchonok 23 Sep '22

23 Sep '22

Dear colleagues, I tried renaming the residues. When I did so in chimeraX the file opens just fine but in pymol - it looks as a green hedgehog. I suppose that the pdb file is corrupted somehow. Is there a way to fix it? Kind regards, Dmitry

2 2

Only retrieving the first predicted model in AlphaFold?
by Yao-Chi Chen 22 Sep '22

22 Sep '22

Hi: By ChimeraX, I am using AlphaFold to predict several protein-protein complexes. These complexes totally comprised about 600-800 amino acids. To have the predicted results as soon as possible, I would like to ask: 1: Is there a way to predict only one model(the best one)? 2: what's the advantage of using the Energy-minimized structures? Could I just not use it? Thanks for your help. backy

2 1

AlphaFold July 2022 update to PAE json file - cannot open PAE file with ChimeraX.
by Brandon Payliss 21 Sep '22

21 Sep '22

Hi there, I’m having some issues loading the PAE JSON file from a recent AlphaFold multimer prediction into ChimeraX, generated using a Colab notebook. The warning message is as follows: JSON file "./predicted_aligned_error.json" is not AlphaFold predicted aligned error data, expected a dictionary with keys "residue1", "residue2" and "distance" It appears that AlphaFold reduced their JSON file size by 4X on July 28th 2022 (https://alphafold.ebi.ac.uk/faq) and it no longer uses “distances”, “residue 1” and “residue 2” keys. Just curious, will there be an update coming to ChimeraX to support the new JSON file format from AlphaFold? Thanks for your time! Best, Brandon

2 1

fitmap command in chimerax
by Yanhe Zhao 21 Sep '22

21 Sep '22

Greeting there developer, I am using fitmap command of chimerax to fit pdb to map, the command as below: fitmap #2,3 inMap #1 seq 2 res 3.7 #2 and #3 are copy of each other and I manually placed them in different positions in map, #2 and #3 come to same position after the command running, I had shift option false, but come to same result. I remember it works in chimera. Could you please point me out? Thanks and have a nice day, Yanhe

3 3

tips for large 180kda protein for morph
by Krishnan Raman 20 Sep '22

20 Sep '22

I morphed a 180kda protein. Trying to view it in stereo with surface. Works good but slow. Any tips/ideas to make the morph faster? Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

3 2

comparison of 2 similar models
by Dmitry A. Semchonok 18 Sep '22

18 Sep '22

2 1

clickable commands
by Krishnan Raman 16 Sep '22

16 Sep '22

How do I make an html file for chimerax with clickable(executable) commands? Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 2

Feature request: combine while keeping chain IDs
by mailman-bounces＠cgl.ucsf.edu 15 Sep '22

15 Sep '22

From: Vorländer,Matthias Kopano <matthias.vorlaender(a)imp.ac.at <mailto:matthias.vorlaender@imp.ac.at>> Subject: Feature request: combine while keeping chain IDs Date: September 14, 2022 at 9:10:48 AM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear ChimeraX team, With the addition of Isolde, ChimeraX is now such a powerful modelling tool that I would like to suggest a new option for the “combine” command. It would be great if it were possible to specify that chain IDs are kept rather than being renumbered if both input models have the same chain ID (ideally this would only work if there were no overlapping residue numbers). This is very helpful if separately refined domains of proteins are put together in one PDB. Thanks a lot in advance, Matthias

2 1

save symmetry information to cif header
by Pranav Shah 15 Sep '22

15 Sep '22

Hi Team, Is it possible to insert BIOMT like fields into the asymmetric unit of a symmetric molecule when saving the coordinates as a cif file? 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

3 7

Why is this happening
by Noriega, Heather 15 Sep '22

15 Sep '22

Hello, Hi Elaine and Tom. I appreciate your help on the inner volume from before both methods with blob and shape, I think I have been able to tailor it for my usage. I also have been using the icosahedron surface in Chimera, and have not had any issues until this capsid, why is it not forming inside the capsid? Did I do something? Thanks in advance. icos_why.py <https://drive.google.com/file/d/1AozCkS-zpp1M9h3ZtXIxNZUhN420WeJB/view?usp=…> Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 1

cuboid eraser?
by Walton, Travis Steven 14 Sep '22

14 Sep '22

Greetings everyone, I was wondering if there is a way to change the shape of the eraser tool for manually deleting map densities. By default, it is a circle, but a flat surface could be really useful in many circumstances. Thanks, Travis

3 2

closest to playing animation chimer to chimerax
by Krishnan Raman 14 Sep '22

14 Sep '22

What is best way to play a series of frames(images)with changing representation/colors, zooming in on regions of interest etc. in chimerax? In chimera I used to create them as individual frames and play them using the animation tool/player. I do not want to encode a movie as I want them to be in stereo3d to play them within the chimerax . All suggestions welcome... Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 2

Multi-sampling in ChimeraX
by Chen, Zhen 14 Sep '22

14 Sep '22

Hi all, May I ask is there a super-sampling option in ChimeraX to turn on so that the edges of maps are smoother? Somethiing equivalent to Tools - Viewing Controls - Effects, there is a Graphics quality, you can choose subdivision and whether to turn on multisample. Thanks! Best, Zhen

3 3

Recall the color code from a previously defined color
by HONG ZHAN 14 Sep '22

14 Sep '22

Dear all, I checked through old archive mails, I may iterate this question again about the color code. Is there a command/option to retrieve the color codes in the Reply log from previously used in the ChimeraX session? I saved my session when I defined the Grey scale for one of my surface model in the palette GUI… When I clicked on the other structure I want to know what color I previously used, the RGB code changed to grey as well… Would be a way to retrieve the color code in the Log I defined previously? Thanks, Hong

3 2

Re: [chimerax-users] 2D plots and graphs for protein-ligand interactions
by Tom Goddard 13 Sep '22

13 Sep '22

So the chimerax-daily command is installed in a separate location from the production releases. So if you install both, you will have a /usr/bin/chimerax and a /usr/bin/chimerax-daily. The bug in the installation process was in the post-install script, so the command is already there. That particular bug has to with with integrating ChimeraX in the system menus and no effect on starting ChimeraX from a terminal. You might see a similar error when installing the next chimerax-daily -- that will not have that bug :-). -- Greg On 9/9/2022 10:41 AM, Tom Goddard wrote: > Greg Couch our Linux expert would have to answer that question. > > Tom > >> On Sep 9, 2022, at 1:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> P.S. Are there other possibilities to install chimera-daily in a distinct directory from the chimerax stable release not to overlap between the both ? >> >> Il giorno ven 9 set 2022 alle ore 10:07 Enrico Martinez <jmsstarlight(a)gmail.com <mailto:jmsstarlight@gmail.com>> ha scritto: >> Thank you Tom! >> Actually I faced the problem with the installation of the chimerax-daily on the ubuntu-20.04 >> (currently I am using the 1.4 version realized in june 2022). Here is the error of the installation: >> >> root@Perfetto-7920-Tower:/home/enrico/Downloads# dpkg -i ./chimerax-daily.deb >> (Reading database ... 322925 files and directories currently installed.) >> Preparing to unpack ./chimerax-daily.deb ... >> Deregister desktop menu and associated mime types >> Remove Python cache files >> Unpacking ucsf-chimerax-daily (2022.09.08ubuntu20.04) over (2022.09.08ubuntu20.04) ... >> Setting up ucsf-chimerax-daily (2022.09.08ubuntu20.04) ... >> Install desktop menu and associated mime types >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__main__.py", line 724, in init >> run(sess, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/cmd.py", line 23, in linux_xdg_install >> install(session, verbose=verbose, system=system) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 428, in install >> generate(session, info, system, verbose) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/linux/_xdg.py", line 421, in generate >> from chimerax.core import localized_app_name >> ImportError: cannot import name 'localized_app_name' from 'chimerax.core' (/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/chimerax/core/__init__.py) >> dpkg: error processing package ucsf-chimerax-daily (--install): >> installed ucsf-chimerax-daily package post-installation script subprocess returned error exit status 70 >> Processing triggers for man-db (2.9.1-1) ... >> Errors were encountered while processing: >> ucsf-chimerax-daily >> >> >> Il giorno ven 9 set 2022 alle ore 00:07 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> ha scritto: >> Hi Enrico, >> >> As Elaine says, ChimeraX isn't a plotting package, so it doesn't let you set colors, sizes, scales, ..., of plots. You could save the plot ChimeraX makes with Python, but I don't think it is very useful to do in an automated way because the aspect ratio of the plot will probably be poor and you cannot control it in a script. At any rate, for reference here is Python that would save the image >> >> from chimerax.core.commands import run >> plot = run(session, 'crosslinks histo #1.1') >> plot.save_plot('histogram.png') >> >> This will need a September 9, 2022 or newer daily build because I just made the "crosslinks histogram" command return the plot, before it did not return it. >> >> The figures in the paper were made interactively in ChimeraX on a high resolution display and just a screen capture was used to save an image. Although as Elaine notes the right-click context menu on those plot windows has a "Save Plot As..." menu entry that will save at 300 dots per inch resolution. >> >> Tom >> >> Example histogram of hydrogen bond lengths for pdb 7qfc saved with the context menu entry "Save Plot As..." >> >> <histogram.png> >> >>> On Sep 8, 2022, at 9:10 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> The main advantage of these plots inside ChimeraX is that they are interactive with the 3D structure (e.g. you click something on the plot, it does something in the 3D window). They weren't meant for making figures for hundreds of molecules in scripts. >>> >>> So, there are no options to customize plot appearance, and the only way to save the histogram currently is by interactively using the context menu on that window, as mentioned in the help: >>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>> >>> If you wanted to make your own plots with everything about the appearance customized, currently you would have to write python scripts to dump the data and then use your own favorite plotting program to generate images. >>> Best, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Chimera(X) team >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>>> On Sep 8, 2022, at 1:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Thanks a lot, Elaine! >>>> Actually crosslink hist #1 works very well! >>>> Could you please specify would it be possible to plot the histogram >>>> (using batch chimera-x execution) or alternatively add it directly to >>>> the produced png image? >>>> I did not find any possibility to save the plot or to customize its >>>> appearance (color of the bars etc). >>>> Cheers >>>> Enrico >>>> >>>> Il giorno mer 7 set 2022 alle ore 17:52 Elaine Meng >>>> <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto: >>>>> >>>>> Hello! >>>>> The chain contacts diagram shown in Fig 4b is made with the "interfaces" command. Then you can use context menu on that contacts diagram to make the interface-residue plot in Fig 4d. Please see the "interfaces" help for details on both of those. >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>> >>>>> >>>>> The histogram plot in Fig 5b is made with the command "crosslinks histogram" but first you have to have some crosslinks, or other pseudobonds such as from finding H-bonds or contacts. Then in the "crosslinks histogram" command you specify the pseudobond model to plot their distances. See "crosslinks histogram" help: >>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram <https://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram>> >>>>> >>>>> Also for a more detailed example see the "Interactive H-bond Histogram" feature highlight, which includes a script (.cxc file): >>>>> <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram <https://www.rbvi.ucsf.edu/chimerax/features.html#hbond-histogram>> >>>>> >>>>> I hope this helps, >>>>> Elaine >>>>> ----- >>>>> Elaine C. Meng, Ph.D. >>>>> UCSF Chimera(X) team >>>>> Department of Pharmaceutical Chemistry >>>>> University of California, San Francisco >>>>> >>>>> >>>>>> On Sep 7, 2022, at 2:18 AM, Enrico Martinez via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>>> >>>>>> Dear ChimeraX users! >>>>>> I am dealing with the analysis of protein-ligand interactions in a >>>>>> single PDB structure. I am looking for any tools implemented in >>>>>> Chimera-X, which could be used to analyse the interactions (besides >>>>>> the hbond and contact tools giving info in the log files). >>>>>> I wonder to know which commands and corresponded ChimeraX tools could >>>>>> be used to produce the 2D contact diagrams shown on the Fig.4 as well >>>>>> as python graphs demonstrated on the Fig.5 in the Chimera-X article: >>>>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/> >>>>>> >>>>>> Many thanks in advance! >>>>>> Cheers >>>>>> Enrico >>> >>> >>> _______________________________________________ >>> 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> >>> >> >> _______________________________________________ >> 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> >

2 3

Saving obj files
by Daniel VillanuevaAvalos 12 Sep '22

12 Sep '22

Hello, I am exporting molecules in the backbone view from chimera x as obj files, but only the points are saving and not the faces. When I import the file to another 3D software, only points show up. How can I save the faces too? Thank you, Daniel.

2 4

Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
by Tom Goddard 12 Sep '22

12 Sep '22

Hi Asmahan, Ok, probably you used ChimeraX 1.3 since 1.4 was not released in December 2021. So of course Model_1_multimer_pae.json goes with Model_1_multimer_unrelaxed.pdb. And Model_5_multimer_relaxed.pdb is the energy minimized version of Model_5_multimer_unrelaxed.pdb and in that older ChimeraX it only energy minimized the best scoring model so model 5 is the best scoring one. The best_model.pdb file is a copy of Model_5_multimer_relaxed.pdb. Tom > On Sep 12, 2022, at 1:07 PM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Hi Tom, > Thank you very much for your time and help. > > I used ChimeraX 1.4 December 2021 on my laptop. The type of files I have got are as follows: > > Best model file , then three files for each model except model 5 in this particular prediction > > Model_1_multimer_pae.json > Model_1_multimer score > Model_1_multimer_unrelaxed > > The same for model2,3,4 > > But 5 with extra file that is: model_5_relaxed > > After that, a list of sequence files > > Best regards > Asmahan > > Get Outlook for iOS <https://aka.ms/o0ukef> > From: Tom Goddard <goddard(a)sonic.net> > Sent: Monday, September 12, 2022 8:03:22 PM > To: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) > > Hi Asmahan, > > I'm not sure how you ran your AlphaFold prediction. Currently ChimeraX AlphaFold predictions creates JSON PAE files that match the 5 predicted models > > af111_unrelaxed_rank_1_model_4.pdb > af111_unrelaxed_rank_1_model_4_scores.json > af111_unrelaxed_rank_2_model_5.pdb > af111_unrelaxed_rank_2_model_5_scores.json > af111_unrelaxed_rank_3_model_3.pdb > af111_unrelaxed_rank_3_model_3_scores.json > af111_unrelaxed_rank_4_model_2.pdb > af111_unrelaxed_rank_4_model_2_scores.json > af111_unrelaxed_rank_5_model_1.pdb > af111_unrelaxed_rank_5_model_1_scores.json > > The file names have both the scoring order (rank 1 best, rank 5 worst). If you ran AlphaFold on your local machine it might put out > > relaxed_model_1_multimer.pdb > relaxed_model_2_multimer.pdb > relaxed_model_3_multimer.pdb > relaxed_model_4_multimer.pdb > relaxed_model_5_multimer.pdb > result_model_1_multimer.pkl > result_model_2_multimer.pkl > result_model_3_multimer.pkl > result_model_4_multimer.pkl > result_model_5_multimer.pkl > > where the .pkl files contain the PAE data. These are not in score ranked order but you can find the score ranked order from another file AlphaFold writes > > ranking_debug.json > > There are other ways to run AlphaFold that give different output files. You'd have to show your list of output files to advise further. > > Tom > > >> On Sep 12, 2022, at 2:37 AM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> Dear ChimeraX users support, >> Thanks for making AlphaFold such accessible and user friendly tool that has added a great deal to my protein-protein investigations. >> >> I have modelled a number of protein complexes a long while ago effortlessly. However, i need to get the PAE for the best model only, so I managed to know which model is the best because from file name but the pae.json file does not. >> >> Just I am wondering if there is a way to know which json file is associated with the best model? >> >> Thanks a lot. >> Asmahan >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Sent: Thursday, June 23, 2022 9:39:46 AM >> To: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Thank you very much, I will try that and see how it goes. >> >> your help is much appreciated. >> Asmahan Alghamdi >> >> >> Get Outlook for iOS <https://aka.ms/o0ukef> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Thursday, June 23, 2022 12:52:50 AM >> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>>; Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> >> Cc: Asmahan Alghamdi <stxamalg(a)exmail.nottingham.ac.uk <mailto:stxamalg@exmail.nottingham.ac.uk>> >> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?) >> >> Hi Asmahan, >> >> I added an outputFile option to the "alphafold contacts" command so the pairs of close residues and their PAE value can be written to a file. This will be in tomorrow's ChimeraX daily build. >> >> alphafold contacts /B to /C output contact_pae.txt >> >> and the output_pae.txt file looks like >> >> /B:24 /C:30 4.30 >> /B:56 /C:9 9.84 >> /B:68 /C:32 1.48 >> ... >> >> with chain identifier and residue number for both residues and their PAE value. >> >> Elaine is right that the PAE values are in a file produced by AlphaFold. For ChimeraX AlphaFold predictions using Google Colab the file is JSON format (text) like >> >> ~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json >> >> If you run your own installation of AlphaFold with multimer or monomer_ptm presets the PAE data is in Python pkl format (binary) like >> >> alphafold_output/result_model_1_multimer_v2_pred_0.pkl >> >> Each of these files have a matrix of all residue by all residue PAE values. It is not too convenient to get the values for specific residues out of such a file unless you write some code. That is why I made ChimeraX do it for you. >> >> Tom >> >> > On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear Asmahan Alghamdi , >> > I am guessing you are talking about the AlphaFold PAE values. These are output by the AlphaFold calculation into a file. What you see as a plot using ChimeraX was already read from that file. So you don't need to export it, you just need to find the file that already exists. >> > >> > I am not sure where this file is stored, or whether it is in some "temp" location. We will get back to you on that. >> > >> > I should also clarify that a PAE value by itself is not a measure of how likely the residues are in contact. It is the predicted error in the relationship between the two residues in the Alphafold-predicted structure, where some pairs of residues are close together like a contact, but many more are far apart and not in contact. Although the "alphafold contacts" command does draw lines between residues that are close together based on a cutoff value, the presence of a line does not mean a contact is predicted with high confidence unless its coloring also shows a favorable PAE value. >> > >> > I hope this helps, >> > Elaine >> > ----- >> > Elaine C. Meng, Ph.D. >> > UCSF Chimera(X) team >> > Department of Pharmaceutical Chemistry >> > University of California, San Francisco >> > >> > >> >> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> >> >> Dear Chimerax team, >> >> >> >> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. >> >> >> >> Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. >> >> >> >> Your help would be much appreciated in this respect. >> >> >> >> Thanks in advance >> >> Asmahan Alghamdi >> >> The university of Nottingham >> > >> > >> > _______________________________________________ >> > 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> >> > >> >> This message and any attachment are intended solely for the addressee >> and may contain confidential information. If you have received this >> message in error, please contact the sender and delete the email and >> attachment. >> >> Any views or opinions expressed by the author of this email do not >> necessarily reflect the views of the University of Nottingham. Email >> communications with the University of Nottingham may be monitored >> where permitted by law. >> >> >> >> _______________________________________________ >> 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 > > > This message and any attachment are intended solely for the addressee > and may contain confidential information. If you have received this > message in error, please contact the sender and delete the email and > attachment. > > Any views or opinions expressed by the author of this email do not > necessarily reflect the views of the University of Nottingham. Email > communications with the University of Nottingham may be monitored > where permitted by law. > > >

2 1

Export list of contacts
by Asmahan Alghamdi 12 Sep '22

12 Sep '22

Dear Chimerax team, Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. Your help would be much appreciated in this respect. Thanks in advance Asmahan Alghamdi The university of Nottingham Get Outlook for iOS<https://aka.ms/o0ukef> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

3 5

inquiry about label the residues of pseudo bonds
by Jiaqiao Zhou 12 Sep '22

12 Sep '22

Dear Chimerax users, I am trying to analyze the results of AF2 predictions. I used the "alphafold contacts" command to the interfacing residues, then several pseudobonds are displayed. "label sel pseudobonds" shows the length of the bonds, but I want to show the residue name the number that makes the pseudobonds. Actually, I found that in the label mode of right mouse, it shows the residue name and the number. However, I have to do it one by one. So I am wondering if there are any easier ways. Another question is about the "alphafold contacts" command itself, I want to know the definition of "distance of residues". Is it the distance of the centroid, the average distance of heavy atoms of the residues. or some other ways of determining the distance between two residues? Thanks in advance.

2 1

How to update the bonding status in a molecular trajectory?
by 洪冉 12 Sep '22

12 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

2 2

Failure in installing daily build version
by jq 10 Sep '22

10 Sep '22

2 1

morphed model
by Krishnan Raman 09 Sep '22

09 Sep '22

How do we get the morph player after reopening the saved session with a prexisting morphed model ? thanks Krishnan Raman CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

5 7

2D plots and graphs for protein-ligand interactions
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ Many thanks in advance! Cheers Enrico

3 9

Create Complete Oligomers
by Samuel Kyobe 09 Sep '22

09 Sep '22

Dear ChimeraX We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6). Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. We would like to use the complete structure for MD studies. Thank you Samuel

2 1

Visualization of the carbon - Cl bond in a small molecule
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I have an issue with the visualization of the small molecule obtained from the tleap module of the amber tools. First of all in vmd and pymol everything looks OK. In the ChimeraX there is no bond between atom CL of the ligand and the aromatic C atom. I've tried to change atom type for the CL: setattr :lig@CL1 atoms idatm_type CL show :lig@* but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico

3 11

How to update the bonding status in a molecular trajectory?
by 洪冉 08 Sep '22

08 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

1 0

image
by 洪冉 08 Sep '22

08 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

1 0

Moving one map in a session while keeping the other/s inactive
by mailman-bounces＠cgl.ucsf.edu 08 Sep '22

08 Sep '22

Dear All, This question might have been answered before but could you let me know how to move 1 map from one position to another without disturbing the other map/s (as we inactivate the maps in Chimera). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

2 1

Re: [chimerax-users] [Chimera-users] How to caluculate buried surface area
by Elaine Meng 07 Sep '22

07 Sep '22

Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users(a)cgl.ucsf.edu (different than chimera-users(a)cgl.ucsf.edu) The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> So, maybe something like command: measure buriedarea protein with ligand ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead: measure buriedarea protein with :UNK You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera > > I am sorry to interrupt your busy schedule. > > My name is Matsui, and I am a second-year master's student at a Japanese university. > Thank you for taking time out of your busy schedule to respond to my question the other day. > > We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. > > For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. > > What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. > > In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. > > I tried to check and tried , but it did not work. > > 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html > > 2.Try to use measure blob using chimera X. > Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea > > However, I didn't know how to solve this command. > Command ;ui mousemode right "pick blobs > > Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology　M2 > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > > <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

2 3

Structure editing
by Niklas Laenger 06 Sep '22

06 Sep '22

Good afternoon, Here is Niklas Laenger. I am a graduate Student at Saint Joseph University. I am trying to modulate conformational changes due to mutation in a protein. In a YouTube tutorial I watched, they used a “minimize structure” tool under the structural editing menu. I could not find this tool, is this not there anymore? With good wishes, Niklas Link to video: https://www.youtube.com/watch?v=eJkrvr-xeXY&t=221s

2 1

AlphaFold prediction template structures
by Tom Goddard 06 Sep '22

06 Sep '22

Hi Hernando, When you run an AlphaFold prediction using the sequence of a structure you have open in ChimeraX, for instance, it shows "Sequence #1/A" to use the sequence of model #1 chain A, it only uses the sequence. It does not use the atomic coordinates in any way. AlphaFold can use structure templates but it is rather inflexible and finds them itself from the Protein Data Bank. If you get a ChimeraX daily build and press the Options button in the AlphaFold panel it will show a checkbutton "Use PDB templates when predicting structures" (default false). This checkbutton is not in ChimeraX 1.4. You can turn that on an AlphaFold will find up to 4 templates from the Protein Data Bank. AlphaFold does a really horrible job finding templates and it does not even report the templates it used. Also in my tests trying to get AlphaFold two different structure conformations by running it with different template structures, it always found just one conformation. It seems that the sequence alignment has much more influence on the final prediction than a template structure. Still if you want to try forcing AlphaFold to use your templates, the ColabFold notebook web server (not in ChimeraX) has an option to use custom templates. https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/Alph… ChimeraX uses this same improved method (called ColabFold) of running AlphaFold but does not offer all of the options that the web server does. Tom > On Sep 4, 2022, at 7:45 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > Hi Tom, > > Not sure is I've been accepted yet in the ucsf-chimeraX list but perhaps I can ask you another Alphafold related question:. > > When specifying the sequences to predict structures they van be pasted into the input sequence window, but they can also be taken from the structures/models already opened in chimera. In this second case does these 3D structures are used as templates or in any way (other than the sequence) in the Alphafold prediction? > > Thanks > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Sent: Sunday, September 4, 2022 10:59 AM > To: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [chimerax-users] AlphaFold > > By the way I find a bit disconcerting the way ChimeraX arranges the windows. For example, when the new window with the Alphafold run is hovered a bit over the ChimeraX window, ChimeraX grabs it and all windows inside ChimeraX gets rearranged. It takes a while to put things back the way they were. Is there a button to reset the windows display ? Perhaps like other programs that have a view menu ? > > Thanks again > > Best > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Friday, September 2, 2022 5:17 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] AlphaFold > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > I have not seen that problem. Does that always happen when you run an AlphaFold prediction? What operating system are you on? Mac? I have seen Mac ask for permission to download from a web site the first time you download from that site. It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask. But it doesn't make much sense because I do not observe this. Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine. If it is sleeping you might want to set your machine not to sleep during the run. This can also be important to avoid Google Colab dropping your job entirely due to inactivity. I guess another possibility is that it could be a firewall problem where your network firewall blocks the download. Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem. > > At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes. There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file. Try that. ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N. It may also hang if there is some issue that prevents the downloads. Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem. > > Tom > > >> On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera/ChimeraX, >> >> I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? >> >> Thanks >> >> Hernando >> >> <image.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…>

2 1

Re: [chimerax-users] What to do if chimerax encounters a problem that cannot be opened？
by Tom Goddard 06 Sep '22

06 Sep '22

Glad you got it to work! Sounds like either the original installation was corrupted or the ChimeraX preferences were corrupted. Tom > On Sep 5, 2022, at 7:36 PM, 胡玉霞 <18111510056(a)fudan.edu.cn> wrote: > > Thanks for all your suggestions, I tried updating the system version to macOS 12.5 and it didn't work. Because I had deleted the corresponding program (as well as the ChimeraX preferences setting file) when the software error occurred previously, changing the system preference did not apply, but I found that trying to install it a few more times and moving the ChimeraX preferences after a new error file was generated was able to install it successfully and open it normally. Thanks again! > > >> -----Original Messages----- >> From: "Tom Goddard" <goddard(a)sonic.net> >> Sent Time: 2022-09-02 03:21:47 (Friday) >> To: "胡玉霞" <18111510056(a)fudan.edu.cn> >> Cc: chimerax-users(a)cgl.ucsf.edu >> Subject: Re: [chimerax-users] What to do if chimerax encounters a problem that cannot be opened？ >> >> One further suggestion is you might try if your Mac has an M1 CPU, try the native M1 Mac version of ChimeraX which is under the Technology Preview section at the bottom of the ChimeraX download page. >> >> Tom >> >> >>> On Sep 1, 2022, at 12:16 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>> Hi Yuxia, >>> >>> That crash report says the Mac graphics driver crashed. I've never seen that on an M1 Mac in the past 2 years since they have been out. The error also says texture descriptor has width zero. I'm not sure if means it was trying to create a 0 width window image, in any case that should not crash. >>> >>> First think I would suggest is updating your macOS 12.1 to the current macOS 12.5. The graphics driver comes with macOS and maybe a newer graphics driver will fix this. >>> >>> The second thing is that maybe the trouble is caused by some ChimeraX preferences setting. You can try moving your ChimeraX preferences so that ChimeraX starts with factory defaults. >>> >>> mv ~/Library/Application\ Support/ChimeraX ~/Library/Application\ Support/ChimeraX.previous >>> >>> then try starting ChimeraX. >>> >>> I've made a ChimeraX bug report so we can follow up on this problem. >>> >>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/7544 >>> >>> Tom >>> >>> >>>> On Sep 1, 2022, at 2:34 AM, 胡玉霞 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>> >>>> Greetings. >>>> >>>> Thank you for the great work you have done for ChimeraX development to meet the research needs of the majority of researchers. Recently, I have encountered a problem with the ChimeraX, when I open the software I have the following prompt and then the software does not work properly. So I would like to ask if there is an update for ChimeraX (the version I am using is macChimeraX-1.4.dmg, my computer system is macOS Monterey 12.1) or if I need to download the appropriate plugins and where can I download the plugins? >>>> >>>> Thanks for reading the email and I look forward to hearing from you. >>>> >>>> Yuxia Hu >>>> Fudan University >>>> >>>> >>>> >>>> <Screen Shot 2022-09-01 at 15.47.03.png> >>>> >>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list >>>> ChimeraX-users(a)cgl.ucsf.edu >>>> Manage subscription: >>>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >>> > > > > > >

1 0

ChimeraX slower than Chimera at loading maps?
by Brian Hudson 06 Sep '22

06 Sep '22

Hi, I have a question about map-loading performance in ChimeraX. We use Chimera for the visualization of EM maps, and have recently loaded ChimeraX 1.3 on our Centos 7 workstations. We frequently run a script that opens Chimera (or ChimeraX) and loads one or more maps. Running the script for the same 2 Gb CCP4-format map in three different programs, I get the following times for program startup + map loading, i.e., the time from when I run the script at the command line to when the map appears onscreen: Chimera 1.12 13 seconds ChimeraX 0.1 25 seconds ChimeraX 1.3 66 seconds This isn't exactly the direction I had hoped performance would trend, and was wondering if there was anything that could be done within ChimeraX 1.3 to speed the process along a little. Thanks, Brian -- BRIAN HUDSON, Ph.D. Biocurator, RCSB Protein Data Bank Assistant Research Professor, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08854 P: 848.445.4941 | E: brian.hudson(a)rcsb.org

3 4

Assistance
by Priyanka Abeyrathne 06 Sep '22

06 Sep '22

Hi, Could you let me know the command to color only the side chain not the backbone of amino acids in ChimeraX, please? Thank you. Kind regards, Priyanka

2 2

ChimeraX docked panels
by Tom Goddard 06 Sep '22

06 Sep '22

Hi Hernando, ChimeraX panels can be docked into the main window or can float freely. I agree the behavior is pretty annoying when you are trying to move a free floating panel like the AlphaFold pane and it accidentally docks it. Panels can be told not to dock -- you right click on a blank space on the tool and it shows a popup menu with an entry "Dockable Tool" and you uncheck that. Unfortunately the AlphaFold Run pane is a web browser and it takes over the right click popup so it doesn't have that menu entry. But you can make the AlphaFold Run panel not dockable with this command ui dockable false "AlphaFold Run" This will be remembered for all future sessions so you only would need to do it once. I'll look at making that the default setting for the AlphaFold Run panel. I figured out that command by right clicking on another panel and unchecking "Dockable Tool" and it logs the command that does it in the Log panel. A useful feature of docking panels is they can be stacked on top of each other as tabs. This can help save screen space. The docking system is provided by the Qt window toolkit that ChimeraX uses -- we did not write it. I am not sure if it is a blessing or curse, some of both. Tom > On Sep 4, 2022, at 7:59 AM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > By the way I find a bit disconcerting the way ChimeraX arranges the windows. For example, when the new window with the Alphafold run is hovered a bit over the ChimeraX window, ChimeraX grabs it and all windows inside ChimeraX gets rearranged. It takes a while to put things back the way they were. Is there a button to reset the windows display ? Perhaps like other programs that have a view menu ? > > Thanks again > > Best > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Friday, September 2, 2022 5:17 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] AlphaFold > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > I have not seen that problem. Does that always happen when you run an AlphaFold prediction? What operating system are you on? Mac? I have seen Mac ask for permission to download from a web site the first time you download from that site. It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask. But it doesn't make much sense because I do not observe this. Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine. If it is sleeping you might want to set your machine not to sleep during the run. This can also be important to avoid Google Colab dropping your job entirely due to inactivity. I guess another possibility is that it could be a firewall problem where your network firewall blocks the download. Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem. > > At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes. There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file. Try that. ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N. It may also hang if there is some issue that prevents the downloads. Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem. > > Tom > > >> On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera/ChimeraX, >> >> I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? >> >> Thanks >> >> Hernando >> >> <image.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…>

1 0

Re: [chimerax-users] AlphaFold predictions
by Tom Goddard 06 Sep '22

06 Sep '22

Hi Hernando, It is hard to explain how a 400 residue AlphaFold prediction downloads automatically, but a 1500 residue prediction hangs downloading. It only downloads once the job finishes. But that is a bit suspicious because I have never seen Google Colab succeed with 1500 residues. The GPUs it offers are just too old, even with Colab Pro (which is what I use) -- I only get GPUs with 16 GB memory that can handle about 1200 residues -- larger runs don't have enough GPU memory. Here are some test runs of AlphaFold prediction on Google Colab Nvidia P100 (16 GB) and on a desktop PC Nvidia RTX 3090 (24 GB) and on a server Nvidia A40 (48 GB). The A40 can handle over 3000 residues. https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html <https://www.rbvi.ucsf.edu/chimerax/data/alphafold-jan2022/afspeed.html> I think your download problem is a Google Colab issue. Unfortunately Google Colab is an erratic service, although the price (free) is right. Tom > On Sep 4, 2022, at 6:51 AM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > Thanks Tom, > > I've run successfully other predictions but of smaller sequences (~400 residues). This happened with a larger but not huge complex ( ~1500 residues total). I've tried others runs but they crashed with an error message saying that RAM was insufficient, even though the goggle account was upgraded to pro (not pro+). > > I am using a windows 10 computer and it was not in screen saving mode, but I was using the multiple desktop feature. It is likely that when the run finished the desktop with chimera and the google colab window was not the one that was on display. Would this be an issue ?? > > Best > > Hernando > > ___________________________________ > Hernando Sosa > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Friday, September 2, 2022 5:17 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] AlphaFold > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > I have not seen that problem. Does that always happen when you run an AlphaFold prediction? What operating system are you on? Mac? I have seen Mac ask for permission to download from a web site the first time you download from that site. It may be that the browser in ChimeraX showing the Alphafold run does not know how to ask. But it doesn't make much sense because I do not observe this. Another idea -- if your machine is sleeping when the job finishes maybe Google Colab gives up trying to download the results to your machine. If it is sleeping you might want to set your machine not to sleep during the run. This can also be important to avoid Google Colab dropping your job entirely due to inactivity. I guess another possibility is that it could be a firewall problem where your network firewall blocks the download. Since the download seems to succeed for most users, there seems to be something specific about your computer setup that causes the problem. > > At any rate, to get the results you should be able to click on Files in the left column of the AlphaFold google colab panel and among the files you should see results.zip which is what ChimeraX downloads when the job finishes. There should be a vertical "..." if hover over that file that pops up a menu that allows you to download the file. Try that. ChimeraX is receiving the download and putting it in ~/Downloads/ChimeraX/AlphaFold/prediction_N. It may also hang if there is some issue that prevents the downloads. Possibly you could connect to Google Colab through a standard web browser and try downloading the results.zip file and maybe you would at least get an error that would help diagnose the problem. > > Tom > > >> On Sep 2, 2022, at 1:26 PM, Hernando J Sosa via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Dear Chimera/ChimeraX, >> >> I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? >> >> Thanks >> >> Hernando >> >> <image.png> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.…>

1 0

protonation of small molecule
by Enrico Martinez 05 Sep '22

05 Sep '22

Dear ChimeraX users! I need to protonate a small molecule from the input pdb file producing another pdb with the protonated ligand. I use the following batch script: open 'ligand_without_H.pdb' addh hbond false save ligand_with_H.pdb displayedOnly true exit Depending on the complexity of the input 3D structure of the ligand some protons could not be added so the final protonation state is not correct. Is there a possible way to fix this issue? Many thanks in advance Enrico

2 1

AlphaFold
by Hernando J Sosa 02 Sep '22

02 Sep '22

Dear Chimera/ChimeraX, I've been running Alphafold through UCSF ChimeraX and sometimes the procedure gets stuck indefinitely at the last step, downloading the results files (see screenshot). Is this a known issue? is there a workaround ? Thanks Hernando [cid:fec1a7e2-7922-44b8-b86e-eb2401cd211c]

2 1

What to do if chimerax encounters a problem that cannot be opened？
by 胡玉霞 01 Sep '22

01 Sep '22

Greetings. Thank you for the great work you have done for ChimeraX development to meet the research needs of the majority of researchers. Recently, I have encountered a problem with the ChimeraX, when I open the software I have the following prompt and then the software does not work properly. So I would like to ask if there is an update for ChimeraX (the version I am using is macChimeraX-1.4.dmg, my computer system is macOS Monterey 12.1) or if I need to download the appropriate plugins and where can I download the plugins? Thanks for reading the email and I look forward to hearing from you. Yuxia Hu Fudan University

2 2

Proposal to an add on
by Noriega, Heather 31 Aug '22

31 Aug '22

Hello, I hope everyone is doing well. I know I have asked this before about the molmaps and have been trying to work around the "holes", in order to create a solid map for the inner volume calculation. It works very well with the AAVs, however with the other subfamilies because of their larger pores it makes it to where it is an inconsistent volume contour, and I believe it throws off the inner volume calculations. I propose to add an element to only cover the pores as a means to make the contour thinner to create a more realistic inner volume calculation. I would like to help with this feature, as my skills have improved within the last year since I first started using Chimera and ChimeraX for my project. I am unsure how I go about this and your response. I have reached out before and most of the time it ends in maybe trying another software. There is no other software that is remotely comparable to this molmap feature that is as user-friendly as it is in ChimeraX. I would really like to continue the use of ChimeraX. I have also thought of possibly trying to create a way for the molecular surface to work with the volume blob feature, but it still comes down to the pores creating the holes. A mechanism to create a feature of only covering the pores could be useful for not only my project but others that may have similar issues. Please let me know what your thoughts are as I would like to contribute to this resolution, but would also need some direction on how to start it. Thank you and I hope to hear from you soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

3 2

Displaying the main chain of residues
by Diksha Parwana 31 Aug '22

31 Aug '22

Hello, I want to display the main chain as well as the side chain of my selected residues. The main chain is only displayed when I use the hide cartoon feature. Is there some way I can see the backbone of my residues without deleting the chain as I don't want to break the continuity? I want to study both backbone and side chain interactions of my residues. Please let me know if there's a way. I'll highly appreciate it. Thanks & regards,

2 1

Help with Zone features
by Binh Nguyen 31 Aug '22

31 Aug '22

Dear ChimeraX developers, Would you please show me how to make this following figure? [cid:01baf593-38aa-4ef0-8392-146a9fb2e78d] I have learned that this is a feature in zone feature and probably solvent accessible surface, but I do not know how to make it. Any hint is much appreciated. Warm regards, B _____________________________________________ Binh A. Nguyen, Ph.D. @ Saelices's Lab Center for Alzheimer’s and Neurodegenerative Diseases Peter O’Donnell Jr. Brain Institute UT Southwestern Medical Center ________________________________ UT Southwestern Medical Center The future of medicine, today.

4 7

Color atoms by kdHydrophobicity
by Daniel Gurnon 30 Aug '22

30 Aug '22

Hi all, I use Chimera mostly for teaching purposes, and while Chimera X is definitely more user friendly for students, there are occasionally things I like from the legacy version that I can't find on a menu in the new program. One such feature is "Render by attribute". While the mlp command can create a lipophilicity surface, when I teach protein folding I like to have students visualize all atoms, with residues colored by kdHydrophobicity. Is there a simple way to implement this? Thanks Dan ____________________________ Daniel Gurnon, Ph. D. Associate Professor of Chemistry and Biochemistry DePauw University Greencastle, IN 46135

4 6

Moving/aligning/ modifying the model
by Dmitry Semchonok 30 Aug '22

30 Aug '22

Dear colleagues, Is there a way I can move(rotate) the chain/residue within a model in ChimeraX? If yes, then how? Thank you in advance. Kind regards, Dmitry

2 1

Zooming into the areas on click
by Dmitry Semchonok 29 Aug '22

29 Aug '22

Dear colleague, For presentation purposes: I would like to show the full map/model structure, then I would like to zoom in on particular areas: area 1, then area 2, then…. (preferably in motion). How is it possible to do in chimeraX? Probably as a movie? How? Thanks in advance! Kind regards, Dmitry

2 1

Can I change the curved cylinder into a straight one?
by 王超(Chao Wang) 28 Aug '22

28 Aug '22

Dear All,After displaying helix in cylinder mode, I found that it is curved by default. I would like to ask whether it can be changed to a straight shape with two ends as fulcrums or other straight way?Thanks,Chao.

3 2

Questions on job status
by Will Grubbe 26 Aug '22

26 Aug '22

Hello, I've submitted a few jobs using ChimeraX and am wondering how to check the status of them. I just need to fill in a few residues in a protein complex with known sequence - where can I find the results when they are done? Thank you for your help, Will

5 7

Imod map values
by HONG ZHAN 26 Aug '22

26 Aug '22

Dear all, It might be not a good question regarding chimeraX. I have a PEET generated averaged map and output of PEET is reversed vs. single particle maps. What is a good function to change the density of PEET output? I used newstack -multadd -1,0 function in imod, however it gave -137 level… Thanks! Hong

2 2

3d-SNFG representation of glycans
by Varga Julia 26 Aug '22

26 Aug '22

Dear All, I am trying to visualize glycans in ChimeraX, however I cannot find the possibility to use either the 3D-SNFG, nor the filled planar representation. Am I overlooking something? Is there a possibility to do this? [image: image.png] Thank you very much! Best regards, Julia Varga

2 1

Job or output file name when running Alphafold in ChimeraX?
by Rayees Mattoo 23 Aug '22

23 Aug '22

Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX? Best Rayees

3 4

Segment Maps In ChimeraX
by Myers, Jonathan 22 Aug '22

22 Aug '22

Dear ChimeraX User Group, I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system. Is there a better way to do what I am trying to do or am I out of luck? Thank you. Shosholoza, Jonathan Myers

3 3

request for true transparency support in .bild files
by Francois Berenger 22 Aug '22

22 Aug '22

Dear chimera hackers, In the old Chimera (not X), if I put two transparent spheres in a .bild file: one sphere can completely hide the other (e.g. a small one inside of a bigger one). While, if there was true transparency, no sphere should completely hide another. Is this better handled in ChimeraX? I _love_ .bild files, because it is so easy to generate them in order to annotate a 3D molecular system then view all of it (molecules + annotations) in Chimera. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Thanks a lot, F. PS: here is an example problematic .bild file for the old chimera --- .color green .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .color orange .transparency 0.750000 .sphere 0.611100 -2.324200 -0.346200 1.250000 .sphere 1.108100 2.092000 0.140700 1.250000 .sphere -3.097400 0.651000 0.062700 1.250000 .color grey .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .sphere -1.453700 2.784800 0.269900 1.500000 .sphere 3.272900 0.026100 -0.134900 1.500000 .sphere -2.354000 -1.959600 -0.245900 1.500000 ---

3 2

Morph map parts transformation in a complex
by HONG ZHAN 22 Aug '22

22 Aug '22

Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong

3 4

Measure volume at multiple threshold levels not function
by Christian Tüting 22 Aug '22

22 Aug '22

Dear ChimeraX-Team, I have an issue with the volume measure tool. I would like to measure the volume at different thresholds. Using the gui mode, I can type the following: volume #1 level 1 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 2.144e+06 So this is functional in principle. But I would like to run this in no gui mode, so the commands are ";" seperated. But, even in gui mode, I got the following: (threshold was set to 1 before executing) volume #1 level 1; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 So the threshold level is not applied, prior to the measurement of the volume. And this is the same in the no-gui mode. I would like to check the volume at 5 different levels, but I got always the same value when executing: "/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX --nogui --cmd 'open cryosparc_P42_J241_002_volume_map_sharp.mrc; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1' --exit" Is there any command, that the threshold level is somehow applied, and the measure volume is executed correctly? The problem is present in UCSF ChimeraX version: 1.4.dev202202240543 and UCSF ChimeraX version: 1.5.dev202207221833 Best Christian

3 4

AlphaFold prediction of complex - results not downloaded
by Erik Werner 22 Aug '22

22 Aug '22

Ladies and Gentlemen, This weekend, I did an AlphaFold prediction run of the human Troponin complex (Troponin C, T and I, UniProt-Ids P63316, P45379, P19429, respectively) via a freshly installed ChimeraX (v 1.4)/Google Colab on macOS Catalina (10.15.7). It completed successfully after 8 hrs (see screenshot below) but I failed to locate the results. According to your tutorial (https://www.youtube.com/watch?v=6lXeCPuTePs and https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html) I was expecting the results in a Prediction#-folder within the Downloads folder, but ChimeraX had only saved the UniProt xml files there. Also, the notebook code indicated the download of a "results.zip" folder but that also cannot be found anywhere on the computer. What have I done wrong? Would I have to edit the notebook? Specify a folder, and where? And: can I still recover the results from Google Colab servers? I copied the notebook to my GoogleDrive but was unable to identify a run-id or anything specific to my run. I would really like to get this working as the prediction of complexes is such a fantastic resource! Many thanks for your help, Erik Werner, Berlin /--// //Dr. Erik Werner// //Paulstr. 36// //10557 Berlin// //Germany/

4 3

Re: [chimerax-users] writing names of models as a text file
by Rangarajan, Amith 19 Aug '22

19 Aug '22

Dear Chimerax team, I want to access the names of the models in a individual chimerax session , i am not able to find a way to write them out as a txt file or to the log . please help me find a way to do this. thanks again for all your help, best amith

2 1

Sym #1 command not executing
by John O'Brien 18 Aug '22

18 Aug '22

Hello, I am a new user to ChimeraX, and was doing the examples in the Quick Start Guide as practice. While following the Atomic Structure Commands, the "sym #1" command did not appear to produce the full table of symmetries, as described in the guide. Could you please help me with this? I have attached a screenshot of what I see to this email, hopefully that helps. Best, John O'Brien

2 1

Re: [chimerax-users] Question about Coulombic scale bar in ChimeraX
by Elaine Meng 18 Aug '22

18 Aug '22

Hi Guipeun, This is the usual situation: The Color Key is not saying that -10 to +10 are the entire range in your structure, it is just showing how the color changes between -10 and +10. You would not change the values on the color key unless you also change the coloring. Any areas of the surface that have values beyond the range just get the same color as that end of the Color Key. I.e., all surface points with values below -10 (all the way down to the minimum for your surface -13.11) are the pure red shown at one end of the Color Key, and all surface points with values above 10 (up to the maximum for your surface +21) are the pure blue color shown at the other end. In between -10 and +10 the color gradually changes, and showing that change is the purpose of the Color Key. The tutorial uses "coulombic" with the default coloring, and the "key true" option in that command shows the values for that default coloring which are red for -10, white for 0, and blue for 10. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k…> If you used different value/color settings in the command, then the key would appear with those different settings. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. it is recommended to send questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data that needs to remain private > On Aug 18, 2022, at 12:14 PM, Guipeun Kang <Guipeun.Kang(a)UTSouthwestern.edu> wrote: > > Dear Dr. Elaine Meng, > > My name is Guipeun Kang, a postdoctoral researcher in Dr. Ryan Hibbs at UT Southwestern medical center. > > I have a silly question about scale bar of Coulombic surface. > > I displayed Coulombic potential of 3eeb, which is an example on ChimeraX tutorial page. > https://www.rbvi.ucsf.edu/chimerax/features.html > > In the Log, Coulombic values are minimum -13.11 and maximum 20.86 for chain A, but the scale bar is ranged from -10 to 10 when I add color key as shown in the instructions. > https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k… > > My question is: > When I type command "coulombic protein key true", the range of Coulombic surface of 3eeb is automatically reflected from -10 to 10? Or, should I manually change the scale bar range from -13 to 21 as shown in Log? > > I'm attaching a screenshot of ChimeraX Log and Color Key panel related to my question. > > I really appreciate your help, > Guipeun > > <image.png> > > UT Southwestern > Medical Center > The future of medicine, today.

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How to get back to original view after running resfit
by Rayees Mattoo 17 Aug '22

17 Aug '22

Hi, I am using resfit command. Is there a command or way to go back to the original view? Best, Rayees

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Rotate image on screen by 6 degrees?
by Robert Stroud 15 Aug '22

15 Aug '22

Is there a command that would rotate the image on screen (model and em map) by 6 degrees around the y axis? Im trying to make crossed eye stereo image for a paper, so I can then put the two images together in illustrator - as I see it Chimerax does not do crossed eye stereo, - and in stereo mode the center of rotation is not in the center of the image for me, so that the half images appear windowed differently on left and right? Thank you Robert Stroud stroud(a)msg.ucsf.edu <mailto:stroud@msg.ucsf.edu> 415 987 7535

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command question
by Kwangjun Lee 15 Aug '22

15 Aug '22

Hello, How can I adjust the position of the distance label? I figured out how to adjust the label for the residues. Thanks!

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Alternative locations
by Michael Bruist 15 Aug '22

15 Aug '22

In a demonstration page for students, I wish to show how the presence of the 2’OH on a ribonucleotide creates a clash at the active site of DNA polymerase. We are also trying to see if 2’OH’s create clashes within the primer. I have created a PDB file with deoxyribose as alternative location A and ribose as alternative location B. This works in original Chimera, but I am not getting it to work in ChimeraX. I am not able to specify the alternative atoms by their A and B designations. I do not see alternative locations in the hierarchy under target specification in the documentation. My PDB file is attached. Residues 106-113 have alternate locations included. The command “altlocs change A :113" does not seem to change anything, nor does changing the selection buttons in the Altexplorer. Mike Bruist mbruist(a)sju.edu

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docked UI
by Pranav Shah 13 Aug '22

13 Aug '22

Hi Team, Is there a way to make sure that some UI elements (eg. the chimerax python console) that I have enabled by calling from a custom startup script are pinned into the main window instead of appearing as floating windows? 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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ISOLDE download
by Jason Mears 12 Aug '22

12 Aug '22

I am trying to download the ISOLDE bundle for my ChimeraX software. I have been unsuccessful thus far. The download starts, but it never completes the download. I have tried a number of times and logged in using my university credentials thinking that this might help. Nothing yet. I am running OS Monterrey (v 12.5). Any advice is appreciated. Thanks. - Jason Mears -- Associate Professor of Pharmacology Graduate Program Director, Pharmacology Center for Mitochondrial Diseases Case Western Reserve Univ SOM 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

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Drag select blanks view window
by Daniel Asarnow 09 Aug '22

09 Aug '22

In ChimeraX 1.3 and now 1.4 releases, I have an issue where control-click dragging to select causes the 3D viewer frame to black out. Everything else functions normally, including the select itself, although it is very difficult to use since the structure can't be seen. The select box *is* visible, but it's magenta instead of green. Afterwards things go back to normal if something was box selected, but if nothing was boxed then the 3D viewer remains blacked out until an interaction like moving the models/camera takes place. I'm on a 2021 M1 MacBook Pro with macOS 12.4. I was wondering if others have experienced this and if it's an M1 issue as this is the only machine I've seen exhibit the problem. Best, -da

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Distance between two residues
by Kwangjun Lee 07 Aug '22

07 Aug '22

Hello, Do you have a command that measures the distance between two residues? For example, I have a dimer model, and I want to measure the distance between /A:100 and /B:200 Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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maps not on same grid in new ChimeraX?
by Moritz, Michelle 05 Aug '22

05 Aug '22

Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle

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Find Residues From Specified Residue Numbers Help
by Myers, Jonathan 05 Aug '22

05 Aug '22

Dear ChimeraX Users, I'm learning how to use the Python API and I found the set of ChimeraX recipes and am trying to use the code featured on the "Find Residues From Specified Residue Numbers" page. I've run into the following issue: NameError: name 'structure' is not defined. I'm not sure what I should be using as an input for the "structure.residues" argument so I have not changed that input. What "structure" should I be specifying? Any help would be greatly appreciated. Shosholoza, Jonathan Myers

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Color by Chemical Shift Perturbations
by Nadun Chanaka Karunatilleke R Wasala Mudiyanselage Vihare 05 Aug '22

05 Aug '22

Hi admin, I am trying to color the protein surface based on the chemical shift perturbations. As mentioned in the example published on March 15th, 2021, I was able to color the surface. However, I needed to add 6 levels, and I failed to do so. It was possible to define the levels and colors in chimera but I failed to do so in chimerax. Is there a way to solve this? Thank you Nadun Nadun Karunatilleke Ph.D. Candidate Dr. James Choy's Lab Department of Biochemistry Schulich School of Medicine & Dentistry Western University London, Ontario, Canada N6A 5C1

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Use different distances for several marker sets
by SHIQING LIAO 04 Aug '22

04 Aug '22

Dear community, I'm wondering if there is any way for me to color a volume density with different distances from several marker sets. Thank you for your help! Best, Shiqing

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Time-efficient python code for obtaining coordinates of atoms
by Shubham Devesh Ramgoolam 03 Aug '22

03 Aug '22

Hi all, I hope you are doing well. I am looking for a time-efficient way of obtaining the coordinates of specified residues. I cannot use the command getcrd as I need these coordinates in a python script for defining geometric objects (getcrd prints the output to the log). My attempt at this consisted of selecting all of the specified residues via run(session, ‘sel ...’), accessing that selection using selected_residues(session), and then, extracting the coordinates using .atoms.coords. The issue here is that run(session, ‘sel ...’) slows down if there are lots of specified residues. I tried bypassing the command ‘sel’ by first importing AtomSpecArg from chimerax.core.commands.atomspec and then using AtomSpecArg.parse('my residue_ID', session)[0].evaluate(session).atoms[0]. However, this is even slower. Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Error message
by Kwangjun Lee 02 Aug '22

02 Aug '22

Hello, I was trying to find residues within the dimerization interface. I have watched the video https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s [https://i.ytimg.com/vi/TMcjEecFHaI/maxresdefault.jpg]<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> Evaluating AlphaFold protein-protein binding with ChimeraX<https://www.youtube.com/watch?v=TMcjEecFHaI&t=17s> We show how to display AlphaFold predicted aligned error for residues at the binding interface between two proteins, encapsulin and ferritin, using ChimeraX.... www.youtube.com and follow the instructions but I got an error message and it seems others have the same issue with me. Is it a bug or did I do something wrong?? Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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ChimeraX change chain IDs tool not available
by Rish, Anthony 02 Aug '22

02 Aug '22

Hello, I created a protein model with 9 separate chains and fit it to my experimental cryo-EM map. However, once I saved the new model, relative to the map, the chains were renamed to 1.1/A, 1.2/A… 1.9/A. This is no good since all chains now are labeled as A in the PDB file and programs like PyMol can’t tell the difference between the chains. I checked the ChimeraX user guide and there is supposed to be a tool for this exact problem called change chain IDs under the Tools->Structure Editing tabs, using the command changechains, but the tool is nowhere to be found. I’m running the current build of ChimeraX as of 8/2/22. How can I change the chain IDs of my model? Thanks, Anthony

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Sorting the required molecules in cvc file
by Dmitry Semchonok 02 Aug '22

02 Aug '22

Dear colleagues, I would like to find out about the possibilities. I have a model that contains apart from the other data, the pigment molecules – chlorophylls, carotenoids etc. Is there a way sort certain types of molecules in a *.cvc file by chimeraX so that the following information will be shown? Mol,Label,Element,X,Y,Z CHL,n 606,NC,267.342,151.989,253.363 CHL,n 606,MG,266.202,151.941,255.073 CHL,n 607,NB,275.512,153.952,252.428 CLA,n 610,MG,273.005,139.807,270.918 CLA,n 611,NB,288.916,127.885,266.725 Thank you! Kind regards, Dmitry

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Superposing protein structures
by Alicia Gardiol 01 Aug '22

01 Aug '22

We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD

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Re: [chimerax-users] Model panel for multi-state objects of dimeric protein
by Elaine Meng 01 Aug '22

01 Aug '22

Hi Enrico, I haven't figured out why this doesn't work on your example (omitted since mailing to the list): close #1 & ~ #1.5 However, this works: delete #1 & ~ #1.5 Also if you didn't have other models (#2 etc.) that you were trying to keep you could just use delete ~#1.5 I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 1, 2022, at 6:39 AM, Enrico Martinez <jmsstarlight(a)gmail.com> wrote: > > Hello Elaine, > I just faced the same problem that has been indicated in this topic > Thi time I am dealing with the monomeric multi-model complex obtained > from docking. > Here is the example of a pdb file consisted of 80+ docking poses. To > keep only the 1.5 sub-modeli've tried to use > close #1 & ~ #1.5 > but this produced nothing, while for other pdbs it works fine. Could > you tell me what's wrong with it? > Many thanks in advance > Cheers > Enrico

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Reduce figure size for export for publication
by Fossati, Andrea 01 Aug '22

01 Aug '22

Hi, How to best export figure at high-ish resolution to then add it to an already made illustrator panel? After some googling seems vector-based export is not possible so what is the recommended format and which resolution is best for 3x3 inch illustrator panel? At the moment I am exporting as TIFF with transparent background and size 5000 and supersampled 4 times to keep high res but the file has like 15Mb per structure which is not feasible/handy to modify. What is the suggested solution for paper figures? Best, Andrea Fossati, Ph.D Krogan Lab

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How to estimate 2dlabels fading?
by Edoardo D Imprima 01 Aug '22

01 Aug '22

Hi, Could you please explain more how the frames option works when changing 2dlabels? Let’s say I have 100 frames and I wish to have an arrow to appear at frame 10 for 5 frames? Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

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

31 Jul '22

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

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ChimeraX on Mac
by Lisa Käshammer 30 Jul '22

30 Jul '22

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

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command inquary
by Kwangjun Lee 29 Jul '22

29 Jul '22

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

2 1

Re-scaling maps
by Nebojsa Bogdanovic 29 Jul '22

29 Jul '22

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

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

28 Jul '22

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

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