- ChimeraX-users - RBVI Mailing Lists

Define axis along z?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center. Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so. Cheers Oli

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Difficulty with Z-translation - bug?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. Watch the selected yellow marker in the side view here on the right hand side: https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… 1. Initially I translate in x-y using Alt-drag - works fine. 2. I try to translate in z using alt-ctrl-drag - nothing happens 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? Cheers Oli

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*.mdb files from MOE (chemcomp)
by Krishnan Raman 29 Mar '24

29 Mar '24

how to convert docking poses from MOE software to be read into chimerax? thanks Krish 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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pTM and ipTM Score Access
by Haley V Goodwin 27 Mar '24

27 Mar '24

Hello! I am using ChimeraX to use AlphaFold Multimer. I have read from a couple of places that AF provides pTM and ipTM scores to evaluate the quality of the models. I was wondering how I access these values from ChimeraX. I have looked through the results zip file, but can’t seem to find where these values may be stored. Thank you so much for your help! Best, Haley Goodwin

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Re: isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 27 Mar '24

27 Mar '24

Hi Tristan, That worked perfectly - many thanks for your help! Phenix.metal_coordination didn’t like for_phenix.cif file created by Isolde write phenixRsrInput, but I was able to create the edits file by saving the model file as a PDB from ChimeraX directly. Cheers and happy Easter, Taha On 25 Mar 2024, at 16:15, Tristan Croll <tcroll(a)altoslabs.com> wrote: You don't often get email from tcroll(a)altoslabs.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. Hi Taha, I'm very glad you find ISOLDE useful! Regarding magnesium (and metal ions in general): ISOLDE itself doesn't currently try to write extra Phenix restraints for these, but you can use the program phenix.metal_coordination to generate an edits file that you can add to the phenix.real_space_refine input. That should automatically create a set of bond and angle restraints for all metals in the model. Best, Tristan On Mon, Mar 25, 2024 at 3:46 PM Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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change chain description
by Joshua Arribere 27 Mar '24

27 Mar '24

Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J

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Apple's cpus for trajectory visualisation
by Enrico Martinez 26 Mar '24

26 Mar '24

Dear ChimeraX users ! I wonder about the performance on the modern Apple CPUs: using several Apple's models as a benchmark, I tested Chimera-X on the 2015 and 2017 iMacs equipped with the i7 8 cores and then on the 2023 Macbook Pro equipped with the Apple m2pro chip. In the end, although the modern hardware was much more stable (never mind when loading large netcdf trajectories, as I reported in the case of the 2015 iMAC), I only noticed a slight increase in performance during film editing. As a benchmark, I took a very large model containing the membrane with an embedded oligomer and loaded a trajectory of 5500 frames in Chimera-X. I used surface rendering with 0.4 grid spacing for everything. While everything worked fine, I was able to produce a short 30-second film of 750 frames in about 1h30 on the m2pro, which was almost the same as on my imac 2015. Is there any way to improve the performance of film-making on modern Apple CPUs? Many thanks in advance Enrico

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ChimeraX_question
by 杜博文 26 Mar '24

26 Mar '24

hello,  Chimerax will have an error when we want to use the ribbon inside color white command, please guide me to correct this mistake,Thx. 杜博文南方科技大学/研究生/研究生2021级广东省深圳市南山区学苑大道1088号  

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Re: Chimera X Matchmaker RMSD
by Elaine Meng 25 Mar '24

25 Mar '24

(CC-ing chimerax-users(a)cgl.ucsf.edu since that is the recommended address for ChimeraX questions as long as they do not include private data. Email sent to me directly has more chance of falling through the cracks.) Dear Dr. Sharyn Endow, The Matchmaker algorithm in ChimeraX is the same as in Chimera. So everything I said before about Chimera's Matchmaker is also the case in ChimeraX. If you have the "iteration" option turned on it doesn't use all aligned columns but instead prunes residue pairs for a better fit of the core. If you are showing the sequence alignment, it shows what set of positions were used for the final fit as a light orange colored box. As before, it uses only the CA-CA pairs within those columns, not the side chains. These overall RMSD values are reported in the Log. "pruned" refers only to the fit iteration process, where iteration prunes away some pairs so that they are not used in the final fit. See "Fitting" at the bottom of the "Matchmaker" help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#fitting> Or, if you are using the "matchmaker" or "mmaker" command, see the "cutoffDistance" option for the description of iteration and pruning: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> If you mean the RMSD header across the top of the sequence alignment, that is a different thing calculated per column (not for the whole structures overall), and you can control in the Sequence Viewer Settings whether this RMSD histogram is calculated CA-only or backbone-only. Neither of them uses the sidechains. If a pairwise alignment, "CA RMSD" boils down to just the CA-CA distance. Simply selecting some range of residues on the sequence alignment doesn't change anything. See help for Sequence Viewer, its header lines, and its Settings: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings> Finally as mentioned in my previous answer about Chimera, you can use the "rmsd" command to calculate RMSDs over any sets of atoms that you choose (with or without sidechains) without changing the current positions of the structures. The more tricky part is that you have to specify in the command which atoms to pair with which atoms, since it is not calculated automatically like it is in Matchmaker. The syntax is a little different than in Chimera: there is a "to" between the two sets of atomspecs, and in ChimeraX the slash symbol "/" is used to indicate chains. "rmsd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> ChimeraX atomspec including many examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2024, at 8:09 AM, Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> wrote: > > Dear Dr Elaine Meng, > > We wrote to you a few years ago regarding Chimera RMSD and you were kind enough to send the information below. We now have a few Q's regarding Chimera X Matchmaker, which displays RMSD values, e.g., when all beta-strands are selected in the Sequence Viewer window. > > • We would like to know what the RMSD values correspond to after aligning two protein sequences using Matchmaker Iwhich uses only only one point per residue for fitting) and selecting all b-strands in the Sequence Viewer window. Is a single RMSD value calculated for each residue to obtain the average RMSD for the "pruned" or all atom pairs and, if so, is the RMSD value between the single point per residue that was used for fitting? > > • Is there some way to obtain the C-alpha RMSD values but not the side chain values, after aligning two protein chains in Matchmaker in Chimera X? > > • What does "pruned" atom pairs mean in this context? > > T > hank you in advance for your help - > > Sincerely, > > Sharyn A. Endow, PhD > Professor of Cell Biology, DUMC > DUS, Cell Biology > PO Box 3709 / 245/247 Sands Bldg / 303 Research Drive > Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2021 at 4:26:34 PM EST > To: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Chimera RMSD > Reply-To: Chimera <chimera-users(a)cgl.ucsf.edu> > > > From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn > > Hi Sharyn, > You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > > > In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like > > rmsd #0:12.A,57-63.A #1:14.A,59-65.A > > ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: > > rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca > rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o > > Of course the numbers could be the same in the two models, I just was trying to give a more general example. > 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. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

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isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 25 Mar '24

25 Mar '24

Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha

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ISOLDE query - non crystallographic symmetry?
by Oliver Clarke 25 Mar '24

25 Mar '24

Hi Tristan, I've been using the latest version of ISOLDE with ChimeraX 1.7.1 and it is working beautifully - very smooth simulation and very helpful for fixing up problem areas! One query - is there any support for non crystallographic symmetry in ISOLDE, or if not is this on the roadmap? Thinking both in terms of NCS restraints, but also in terms of propagating edits from one subunit of an oligomer to all the others - this would be very helpful to have for a lot of folks I think, as so many proteins are oligomeric. Thanks for the wonderful piece of software! Cheers Oli

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Difficulty unsubscribing
by BARRY E DEZONIA 24 Mar '24

24 Mar '24

I am trying to leave this email list and currently am unable to. I send email to: chimerax-users-leave(a)cgl.ucsf.edu And it processes and says my email barry.dezonia(a)wisc.edu is not a list member. That is because I signed up with bdezonia(a)wisc.edu.. My mail service treats them as equivalent but it only sends out on the incorrect email address. Can someone unsubscribe ndezonia(a)wisc.edu? I can't figure out how to get my email client to use my other email address as the sending address.

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Adding lipid bilayers to chimerax movie
by Kevin Felt 24 Mar '24

24 Mar '24

Hello ChimeraX Users, I'm trying to make a movie in chimerax involving a membrane protein, and I would like to have some representation of where the inner and outer lipid bilayer leaflets are relative to the protein transmembrane region, ideally represented as phospholipids. Is it possible to do this within Chimerax? I've thought about encoding the movie to mp4 and then figuring out how to simply overlay a bilayer image onto the mp4 where I want with some other software , but I foresee resolution and scaling issues when doing that. Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

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Color a surface by seq_conservation of neighboring residues
by Esser, Lothar (NIH/NCI) [E] 22 Mar '24

22 Mar '24

Hi, my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor. Thanks for any advice. Lothar NIH

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Visualisation of distances
by Enrico Martinez 21 Mar '24

21 Mar '24

Dear ChimeraX users ! I need to draw several distance vectors on the 3D structure. Could you provide me with an example of the commands that could automatically draw the distances between two selected atoms with some basic labels on it ? Many thanks in advance Enrico

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Re: Trying to join two structures unsuccessfully
by Maja Divjak 17 Mar '24

17 Mar '24

Alternatively, I guess I could just cut this disordered domain into fragments, move them around and the rejoin them.... -----Original Message----- From: Maja Divjak Sent: Tuesday, 5 March 2024 11:44 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: RE: [chimerax-users] Trying to join two structures unsuccessfully Dear Elaine, No worries at all, I have received multiple replies, so it is working! Thank you for your response below. Basically, it seems what I'd like to do can't really be done in this way. In another conversation, someone mentioned the tug command. Could this yield what I'm hoping for please? The two ends I'm trying to join are indeed in separate models, so I tried the following command: tug #16/a:345-355 toAtoms #18/A:345-355 which gave the following error: For 0 tugged atoms expected 0 destination atoms, got 84 Would this be the correct approach (I've clearly got the syntax wrong) or is there really no way to do this in Chimera X? Thanks so much and best wishes, Maja PS. How do I join the member's list please? -----Original Message----- From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 11:33 AM To: Maja Divjak <Maja.Divjak(a)petermac.org> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Trying to join two structures unsuccessfully ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport(a)petermac.org Dear Maja, Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list! So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam! Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> You can see what model(s) you have by looking in the Model Panel: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first. You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected: info atoms sel atom id #1/A:29@C idatm_type Cac atom id #2/A:1@N idatm_type N3+ However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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How to change transparency of ladder mode of nucleic acids
by Yan ZHANG 张艳 15 Mar '24

15 Mar '24

Dear ChimeraX Team, I hope this email finds you well. My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task? Thank you for your attention to this matter. Best regards, Zhang Yan

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Is the site down ?
by Marie PREVOST 14 Mar '24

14 Mar '24

Hello, I would like to install ChimeraX on my new laptop but the site seems to be down… Do you know if there are other option to download the installer ? Thank you for your help Best wishes ------- Marie Prevost, PhD Pierre-Jean Corringer’s lab ( site<https://research.pasteur.fr/en/member/marie-prevost/> ) Channel-Receptors Unit Institut Pasteur 25 rue du Dr Roux 75015 PARIS France +33 (0)1 53 55 15 06 (via Teams)

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Question about interpreting variable ipTM scores
by David S. Fay 14 Mar '24

14 Mar '24

Hi, This question isn’t specifically about chimerax, but I hope it’s in the ball park. For most of the protein pairs I’ve tested using multimer, the ipTM scores for the 5-10 models are relatively consistent. For example all 0.2–0.3, or 0.75–0.85, or 0.4–0.6. But occasionally I’ll get one or two very high scores (>0.7) with the rest being low or somewhat randomly scattered. My instinct, of course, is to put more faith in scores when the models converge. At the same time, I don’t want ignore a potentially real interaction. So, I’m wondering how people interpret ipTMs when the numbers are variable between models. What is the reason that some protein pairs show this pattern? Is the good score(s) indicative or something real or a false positive. Are the bad scores indicative of true or false negative? Any thoughts, insights, and possible follow up approaches would be greatly appreciated! David

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Downloading chimera
by Pincus, Seth 14 Mar '24

14 Mar '24

When I try to download Chimera (or connect to any Chimera site), I get the attached error message saying that “www.cgl.ucsf.edu has refused the connection”. I am running Chrome version 122 on a Mac Powerbook running OS12.7.1. My computer is owned by Montana State University and may have some additional security is installed. But I could find nothing in Chrome’s settings that would allow me to connect. Please respond bydirect e-mail, since I cannot get to the site to join the mailing list. Thank you, Seth Pincus, M.D. Professor Department of Chemistry and Biochemistry WWAMI Medical Program Montana State University Bozeman, MT 59717

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only make selection highlighted
by 张楠 13 Mar '24

13 Mar '24

Dear developers, How does chimerax make the stick I selected highlighted and the carton in other areas blurred? I tried to click on view selected, but that only makes the back of the structure blur, not the front. May I ask how to operate to achieve the effect in the picture, only highlight stick？ Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan(a)nankai.edu.cn

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Isolde can't be installed inside ChimeraX 1.5
by Jun Zhang 13 Mar '24

13 Mar '24

Hi ChimeraX, I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible? Many thanks in advance and have a nice day! Best regards, Jun Zhang

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a bug with saving Chimera-X session
by Enrico Martinez 13 Mar '24

13 Mar '24

Dear Chimera-X users! I got the following error on my iMAC equipped with Intel CPU after an attempt to save a Chimera-x (ver 1.71) session containing a loaded netcdf trajectory with 7500 frames (with the same system containing only 5000 frames, ain't no problems !!). Yours with thanks Enrico Traceback (most recent call last): File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62, in display run(session, cmd) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641, in save fserialize(stream, data) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) ^^^^^^^^^^^^^^^^ File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "stringsource", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File "src/_serialize.pyx", line 253, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "stringsource", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File "src/_serialize.pyx", line 226, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack *See log for complete Python traceback.*

2 4

Problem Installing ChimeraX
by Stephen P. Molnar 11 Mar '24

11 Mar '24

I am running Debian-12.6.0 and have encountered a problem installing ChimeraX.flatpak: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found The installation was necessitated due to a system crash. Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

4 5

Re: Difficulty with Z-translation - bug?
by Elaine Meng 11 Mar '24

11 Mar '24

I don't know if that is really true.... it's just that it is what I experienced this morning, and I am extremely uncoordinated... I have to turn off the multitouch actions, for example, because I just can't deal with them personally. Tom G would have to confirm if that's actually in the code before I would want to immortalize it in writing! The current documentation is what was explained to me, although it's possible I misunderstood. Elaine > On Mar 11, 2024, at 9:58 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Ah I see - the modifier absolutely has to be added after starting an ongoing XY-translation... that is a bit of a pain if you just want to translate something in Z (e.g when moving something with respect to a density map). > > It might be worth making both limitations (initiating from an ongoing XY translation and vertical mouse movement only) a bit more explicit in the help page - it states that the order of the keys is important, but it doesn't really say that you need to start translating in XY before trying it in Z (or at least that wasn't my read of it). Thanks Elaine I think I get it now, very helpful! > > Cheers > Oli >> On Mar 11, 2024, at 12:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Oli, >> Sorry I meant include this info in your bug report, not necessarily to the email list (athough that's fine too)! I won't be the one looking at the bug report, and it might not be addressed right away, so it's good to put the information there. >> >> If by "move models" button you mean the icon for mousmode "translation": >> >> I got a selection box at first and then after I did an XY-translation, being very careful about adding the Ctrl to an ongoing drag, I got Z-translation. >> >> Elaine >> >>> On Mar 11, 2024, at 9:46 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> I'm on a MBP with M2-Max chip and running Sonoma (14.1). >>> >>> If I activate move models for right-mouse using the GUI "move models" button, then adding a ctrl modifier does not translate in Z, I just get a selection box even with Ctrl-right-drag - same is true if I activate translation from the GUI. >>> >>> Cheers >>> Oli >>> >>>> On Mar 11, 2024, at 12:41 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> I'm on a Macbook Pro with M1 chip running Monterey 12.7.3. I guess we would also be interested whether the Z-translation works with the regular "translation" mode in your situation, as it did for me in my tests this morning. You would also need to use the ChimeraX 1.7 release or newer, of course, since Z-translation wasn't added until last September, according to the Change Log: >>>> >>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog >>>> >>>> Elaine >>>> >>>>> On Mar 11, 2024, at 9:18 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>>>> >>>>> Hi Elaine, >>>>> >>>>> Thanks for the explanation! Yes I am on a mac using a trackpad. I did explicitly assign it (mousemode alt left "translate selected models"). It still doesn't work reproducibly for me (in either daily or stable build), even with vertical motion and after translating in X-Y first... I will report it as a bug, thanks! >>>>> >>>>> Cheers >>>>> Oli >>>>>> On Mar 11, 2024, at 12:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hi Oli, >>>>>> Short answer is that (at least in my hands) the horizontal motions don't elicit much Z-translation -- try moving the cursor vertically. In all my tests below that worked with translation assignment +Ctrl to give Z-translation. >>>>>> >>>>>> Long answer with several rounds of testing: >>>>>> >>>>>> I don't know if this applies to you, but since I work on a Mac with a trackpad most of the time, I avoid explicitly assigning anything to alt-left or command-left because these emulate the middle and right mouse buttons. >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#touchpad> >>>>>> >>>>>> I don't know whether you actually assigned alt-left to translate, but the factory default assignment for middle mouse ( = alt-left if you call trackpad click-drag "left") is translation, so it's effectively the same as what you said. >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> >>>>>> >>>>>> Using the factory defaults (translation nominally assigned to middle mouse), the Z-translation with alt-left-drag-Ctrl is working for me on a Mac with trackpad and UCSF ChimeraX version 1.7.1 (2024-01-23) as well as recent daily build 1.8.dev202403072314 (2024-03-07). >>>>>> >>>>>> Next I tried it with two models open, one selected, and the "translate selected models" assigned to right mouse button (= Mac trackpad command-left) and it works fine to XY- and Z-translate (with added Ctrl) the selected model only. >>>>>> >>>>>> If I actually assign >>>>>> >>>>>> mousemode alt left "translated selected models" >>>>>> >>>>>> That also works alt-left to XY translate and Z-translate (with added Ctrl) the selected model only. >>>>>> >>>>>> However, I usually have to try a little XY-translation first before attempting Z-translation because it is a little persnickety and/or I am not coordinated enough to use these multiple keys at the same time. And again, I don't know what exactly is going on in the video you sent, but, horizontal cursor motion doesn't seem to do much Z-translation for rme, only vertical. >>>>>> >>>>>> If you can't get it to work, please use Help.. Report a Bug so we will know your exact version and platform details. >>>>>> >>>>>> I hope this helps, >>>>>> Elaine >>>>>> ----- >>>>>> Elaine C. Meng, Ph.D. >>>>>> UCSF Chimera(X) team >>>>>> Resource for Biocomputing, Visualization, and Informatics >>>>>> Department of Pharmaceutical Chemistry >>>>>> University of California, San Francisco >>>>>> >>>>>>> On Mar 11, 2024, at 7:33 AM, Oliver Clarke via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. >>>>>>> >>>>>>> Watch the selected yellow marker in the side view here on the right hand side: >>>>>>> >>>>>>> https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… >>>>>>> >>>>>>> 1. Initially I translate in x-y using Alt-drag - works fine. >>>>>>> 2. I try to translate in z using alt-ctrl-drag - nothing happens >>>>>>> 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. >>>>>>> >>>>>>> Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? >>>>>>> >>>>>>> Cheers >>>>>>> Oli >>>>>> >>>>> >>>>> >>>> >>> >>> >> >

1 1

Enclose volume within radius?
by Oliver Clarke 10 Mar '24

10 Mar '24

Hi ChimeraX-ers, Finding an equivalent contour level for 3D classes in cryoEM can be challenging, particularly if the density histograms are sufficiently different that setting a single level does not suffice (and particularly when comparing many classes from a large classification). The options "enclosevolume" and "fastenclosevolume" for the "volume" command are very useful for this (e.g. "volume #* fastenclosevolume 200000"), but fail in the presence of compositional heterogeneity (if there is more ordered stuff in one class and the volume is fixed, the contours will no longer be equivalent). To address this, would it be possible to add a "within_radius" modifier for the "volume fastenclosevolume" command? This would mean one could then set a fixed volume to be enclosed by the contour within a set radius of either the center of rotation, or of an atom selection, making the contour levels at least locally equivalent (which is often what one wants for the purposes of comparison). Cheers Oli

3 4

Notepad or info dialog in ChimeraX?
by Oliver Clarke 08 Mar '24

08 Mar '24

Hi, Is there a command in ChimeraX to launch a notepad? Or to display some text? I would like to make a button that will launch a little window with some info about shortcuts and the like. In Chimera, there was a notepad (the contents of which could be saved with a session) - does something similar, or some kind of custom info dialog, exist in ChimeraX? Cheers Oli

3 3

Question about accreditation
by Enrico Martinez 08 Mar '24

08 Mar '24

Dear ChimeraX users ! I am wondering if I am obligated to mention the name of the ChimeraX software if I use it to creat a cool image and post it to any social media like Facebook or Instagram ?? Or alternatively on the personal web page ? Obviously it could be obligatory for a scientific publication but what s about usage in fully artistic context ?? Many thanks in advance ! Yours sincerely Enrico

2 4

Loading multi-frame pdb using open command
by Enrico Martinez 08 Mar '24

08 Mar '24

Dear Chimera-X users! I have a question regarding the handling of a trajectory saved in multiple-pdb format. Loading such ensemble using dedicated open command typically load all frames at once: open ./my_trajectory.pdb coordset true Would it be possible to specify the range of the loaded frames to reduce the time for data loading e.g. i) to load first 3000 frames or ii) to load from 50 to 5000 frames? Many thanks in advance ! Best wishes, Enrico

3 6

Trying to join two structures unsuccessfully
by Maja Divjak 07 Mar '24

07 Mar '24

Hi there, Hope you're well. I am trying to join the two structures as shown in the image attached. I would like to join the disordered chain shown in green to the purple chain and the residues I would like to join are highlighted. I would like the green disordered chain to be dragged over to join the purple structure without moving any of the ordered domains that are linked to it (orange). I have tried selecting individual atoms ie N and C atoms from these residues (as shown) and using the command tools > structure editing > build structure > join models from the drop down menu. I adjusted C-N length to 1.6 and set to 'move atoms in larger model', thinking this would move the green chain. Hitting apply gives me the error dialogue 'No atoms selected'. I also tried Adjust Bonds > with options for Delete selected bonds > and add reasonable. There are no error messages, but the log says that no bonds were created. Not sure what I'm doing wrong or what the correct process is for joining models in this way please? Is this even possible? Clearly I'm not selecting the atoms appropriately. I am using Chimera X version 1.6.1 Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60]

2 5

ISOLDE: unable to work with map after selecting another model
by Alexis Rohou 06 Mar '24

06 Mar '24

Hi Tristan, ISOLDE users, Sometimes it's useful to create a new model (e.g. by merging the model of the protein you've been working on with an initial model of the ligand) and then continue working with this new model in ISOLDE. For me, this leads to trouble. Specifically, here's what I do: - start ChimeraX - open a PDB and a map - start ISOLDE - select the PDB model in the "Working on" dropdown - select the map in the "From loaded volume" dropdown - do some simulations until I'm happy with the protein - open a PDB of the ligand - combine the ligand model with the protein model - select the combination model in the "Working on" dropdown - press "start simulation"... get warning "about to start simulation with no map" - press Cancel - check the "From loaded volume" dropdown - it's not possible to select the already-loaded map, which is in the initial "Data manager" Is this intended behavior? I was hoping to be able to continue working against the same map. Cheers, Alexis

2 2

Silhouettes only on selected models
by Pedro Bule 06 Mar '24

06 Mar '24

Hi, I'm writing to know if there is a way to turn on the silhouette graphical option only on selected models in ChimeraX, or is it just a global option? I have a model of an enzyme with its ligand and another model with the electron density loaded from a .map file. I want to display the electron density around the ligand as a slightly transparent mesh without silhouettes (see below) while still having silhouettes on the enzyme and ligand. Is there a way to do this? The silhouettes on the mesh make it too dark and dense (see image 2). Thank you very much Pedro Bule [image: image.png] [image: image.png] -- *Pedro Bule* *Assistant Professor* GLYCOBIOLOGY AND STRUCTURAL ENZYMOLOGY LAB *P:* (+351) 21 365 28 84 // 431379 | pedrobule(a)fmv.ulisboa.pt <email(a)fmv.ulisboa.pt> *Centro de Investigação Interdisciplinar em Sanidade Animal* Faculdade de Medicina Veterinária Av. Universidade Técnica | 1300-477 Lisboa | PORTUGAL

3 2

Connection to GPU
by Minu Chaudhuri 06 Mar '24

06 Mar '24

Hello, I am trying to build a multimeric structure using AlphaFold collab, but it is not connecting to the GPU. How can I get a connection? Is there a fee for this? How to pay for this? Thanks for your help. Minu Chaudhuri, Ph.D. Meharry Medical College Nashville TN 37208 USA

3 2

need Section 508 compliance statement
by Weiss, Carol 06 Mar '24

06 Mar '24

Hello, I would like to use ChimeraX, but the FDA IT administrators will not download the Chimera X software without a statement about its Section 508 compliance for users. Would you please send me available Section 508 compliance information for this software? Thank you, Carol Weiss

2 2

Improvement suggestion: single letter code for swap
by Vorländer,Matthias Kopano 05 Mar '24

05 Mar '24

Dear ChimeraX team, A small feature request: It would be helpful if the swapaa command could accept the single letter code for amino acids as well as the three letter code. This makes it easy to quickly fix a sequence, i.e based on a sequence that is open in the sequence viewer. Many thanks, Matthias

2 2

Mainchain and sideonly atom names
by Sabrina Moffit 05 Mar '24

05 Mar '24

Dear ChimeraX team, So far I've found that these are the atom names classified as mainchain atoms by ChimeraX: ['H3', 'HA2', 'H2', 'CA', 'H', 'H1', 'HA', 'C', 'O', 'HA3', 'OXT', 'N'], by using such command: sel #1 & mainchain; info atoms sel. I'm not sure if there are more atom names classified as mainchain atoms by ChimeraX. Could you please provide me with a comprehensive list of all the atom names of the mainchain atoms (and sideonly atoms as well, if possible) of all types of amino acids? Thank you.

2 1

Conctac map in ChimeraX?
by PABLO HERRERA NIETO 05 Mar '24

05 Mar '24

Hi everyone, I started using chimera after some years. In the new ChimeraX I could not find an option to calculate contact/distances heatmaps for proteins or protein complexes. Is that old funcionality gone for good? However, to check AlphaFold's pLLDT there is a really nice intereactive chart. Is there any option/hack to use that to visualize contacts/distances for any structure? Thanks Pablo -- Pablo Herrera Nieto Dpto. de Estructura de Macromoléculas, lab 15 Centro Nacional de Biotecnología - CSIC

2 1

movie record / encode
by Enrico Martinez 05 Mar '24

05 Mar '24

Dear ChimeraX users! I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments. Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results: movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000 how could I modify / add something more with the aim to obtain the best molecular animations ?? Yours sincerely Enrico

3 19

Question
by 张楠 04 Mar '24

04 Mar '24

Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX? Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan(a)nankai.edu.cn

2 2

Inquiry - UCSF ChimeraX
by Fumi JINUSHI 04 Mar '24

04 Mar '24

Dear Sirs, We are a sales agent and a custom made computer manufacture in Japan. We focus on R&D sector as a key business area and help researchers and engineers in universities, research institutes and large companies, and provide them with a good selection of industrial products. I wonder if we can sell UCSF ChimeraX and provide our customers with the software installed on our custom made computers. We look forward to your reply. Thank you ! Kind regards, Fumi +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Fumi JINUSHI web_delivery(a)tegara.com Tegara Corporation 211-17, Higashimikata-cho, Chuo-ku Hamamatsu-shi, Shizuoka, 433-8104 Japan T +81-53-543-6691 F +81-53-543-6689 UNIPOS https://en.tegara.com/service/unipos/ TEGSYS https://en.tegara.com/service/tegsys/ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

2 1

right-mouse clipping
by Daniel Larsson 01 Mar '24

01 Mar '24

Hi all, I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching). For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels. Some questions 1. How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)? 2. If so, is it possible to set a default thickness of that slab? 3. Is it possible to change the radius of the Zone clipping tool? 4. Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool? 5. Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)? 6. I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 2

Isolde add nucleotide?
by Vorländer,Matthias Kopano 01 Mar '24

01 Mar '24

Dear all, Is it possible to add nucleotides to existing chains, similar to Isolde add aa? Many thanks, Matthias

3 3

Re: Seeking Assistance with PyCharm Debugging Configuration
by Zachary Pearson 28 Feb '24

28 Feb '24

Hi Himal, I'm confused by a couple of things. First, your system packages should list all of ChimeraX's packages, like the screenshot attached to this email. Did you build ChimeraX (make build-from-scratch) and subsequently use ChimeraX's internal Python, not your system Python, to make your virtual environment? Second, the path to your interpreter looks like it's a path to a virtual environment inside ChimeraX itself. In /the base directory of the git repository:/ ./ChimeraX.app/bin/python.exe -m venv .venv --system-site-packages Then in PyCharm -> Settings -> Project: ChimeraX -> Python Interpreter Add a new interpreter path/to/ChimeraX/.venv/Scripts/python.exe Use that as the interpreter for your run or debug configuration. -- Zach On 2/27/2024 1:36 PM, Eric Pettersen wrote: > Nudge, nudge... :-) > >> Begin forwarded message: >> >> *From: *Himal Godage <himalgodage2759(a)gmail.com> >> *Subject: **Re: [chimerax-users] Seeking Assistance with PyCharm >> Debugging Configuration* >> *Date: *February 20, 2024 at 11:34:54 PM PST >> *To: *pett(a)cgl.ucsf.edu >> *Cc: *chimerax-users(a)cgl.ucsf.edu >> >> Hi Eric, >> Thank you for the reply and I appreciate your assistance. >> >> I've been using the internal Python to create a virtual environment >> in my project’s folder, and I've set the Python interpreter path as >> outlined in the documentation. The first attached screenshot is my >> interpreter configuration. >> >> However, my current challenge lies in the debugging section. I've >> created a new Run/Debug Configuration(third attachment) following the >> instructions , as shown in the second attached screenshot. >> Regrettably, when attempting to run the configuration, I encountered >> an error in the console: "No module named chimerax.core" (refer to >> the fourth attached screenshot). >> >> I believe that the issue is regarding a module named chimerax.core >> which I couldn’t find on the project. >> Thank you in advance for your help. >> >> Himal >> >> On Wed, Feb 21, 2024 at 12:39 AM Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> >> Hi Himal, >> The person on our team that uses PyCharm and that wrote >> that documentation is on a trip to NIH this week and may not be >> able to respond promptly. Reading that page myself, it seems >> that the Debugging section assumes that you set up a virtual >> environment as outlined in the preceding "IDEs" section. Did you >> do that? >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> > On Feb 19, 2024, at 9:40 PM, himalgodage2759--- via >> ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> > >> > Dear ChimeraX Dev Team, >> > >> > I'm Himal Godage, and I am currently in the process of >> developing a bundle for ChimeraX software. I have been thoroughly >> following the provided documentation, successfully completing the >> steps related to setting up a ChimeraX development environment, >> obtaining the code, and compiling ChimeraX. However, I have >> encountered a challenge in the IDEs, Debugging, and Profiling >> section, specifically within PyCharm. Following the provided >> steps, I am instructed to: >> > 1. Create a new Run/Debug Configuration. >> > 2. Set the script path field to point at a module. >> > 3. Set the module to “chimerax.core”. >> > 4. Set the Python interpreter to ChimeraX’s internal Python. >> > 5. Uncheck “Add content roots to PYTHONPATH”. >> > 6. Uncheck “Add source roots to PYTHONPATH”. >> > While attempting to follow these instructions, I encountered >> difficulty in locating the "chimerax.core" module. Unfortunately, >> the provided directory structure or module seems to be difficult >> to find in my current project. However there is a module named >> core in the following path. ChimeraX > src > bundles > core >> > >> > I am reaching out to seek your guidance on resolving this >> issue. Could you please provide insights on how I can locate or >> create the necessary "chimerax.core" module or suggest an >> alternative approach to address this problem? >> > >> > Thank you in advance for your time and support. >> > Best regards, >> > >> > Himal Godage >> > himalgodage2759(a)gmail.com >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> > Archives: >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> > >> >

1 0

Commands not working
by Heinen, Cobey J 28 Feb '24

28 Feb '24

Hello, I am new to this program and am learning the commands. However, when I type the commands from the tutorial, they don't work. For instance, when I do "start<https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/start.html> Side View" it registers it as an unknown command. Also, when I do the command "color hot pink :lys", it says it does not know what the residue is. Am I missing anything? Thank you for your time. Best, Cobey Heinen

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Fwd: protein-molecule contact log issue
by Eric Pettersen 27 Feb '24

27 Feb '24

> Begin forwarded message: > > From: Mario Rodriguez Monteverde <mrodriguez.81(a)alumni.unav.es> > Subject: protein-molecule contact log issue > Date: February 26, 2024 at 2:52:17 PM PST > To: "ChimeraX-bugs(a)cgl.ucsf.edu" <ChimeraX-bugs(a)cgl.ucsf.edu> > > Good afternoon. > > To whom it may concern. > > I am attempting to identify the residues with which a compound (A) is interacting with a target protein (B). I opened both pdb files in ChimeraX, I selected the compound and did as follows: Tools > Structure Analysis > Contacts (selected output info to log). > The results which I get are the contacts inside the same protein (prot(B) with prot(B)), instead of compound(A) with protein(B). > I have tried selecting only the target protein, selecting both, creating a new pdb file with the comp and the compound together, but nothing works, I still can not get to know which residues from the compound are contacting my target prot. > > How could I solve this? > > Thank you > > Best, > Mario

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Re: right-mouse clipping
by Daniel Larsson 27 Feb '24

27 Feb '24

Ok, by trial-and-error I figured out the answer to question 3. One right-clicks and hold while dragging the mouse up/down to change the radius. I would much prefer to be able to set the contour-level by right clicking-and-hold and drag, since that is something one needs to change much more frequenly than the Zone radius. Also, I realize that Zone does not hide atoms outside of the sphere, so one has to hide atoms first and then zone will show the atoms inside of the sphere. From: Daniel Larsson via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> Reply to: Daniel Larsson <daniel.larsson(a)icm.uu.se> Date: Tuesday, 27 February 2024 at 09:42 To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> Subject: [chimerax-users] right-mouse clipping Hi all, I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching). For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels. Some questions 1. How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)? 2. If so, is it possible to set a default thickness of that slab? 3. Is it possible to change the radius of the Zone clipping tool? 4. Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool? 5. Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)? 6. I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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Seeking help
by 林萌萌 27 Feb '24

27 Feb '24

What's the command for “colored by atoms by rmsd” ？

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Help saving a modified protein for 3d print
by Jana Villemain 23 Feb '24

23 Feb '24

Greetings, I have downloaded the attached .pdb. Also attached is a screenshot of same model, but sliced specifically at histidine 65. I need to export the edited file, sliced, as an .stl so that I can print it. However, try as I might, every time I save, or export the file, it is unedited - and includes the entire model. Any help you could provide would be great! [cid:image001.png@01DA667E.93B731E0] Thank you, Jana Jana Villemain, Ph.D. Associate Professor of Chemistry Dept. of Chemistry, Biochemistry, Physics and Engineering Indiana University of Pennsylvania Weyandt Hall 239D jvillema(a)iup.edu 724-357-2180

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ChimeraX Core module Issue
by Himal Godage 23 Feb '24

23 Feb '24

Dear ChimeraX Dev Team, I am currently in the process of developing a bundle for ChimeraX. I have clone the code from the git repository and made the necessary installations according to the documentation. But I have an issue with the location of the ChimeraX core module. I found that it's in the *ChimeraX > src > bundles > core > src* . But in most of the bundle codes it's located as a *chimerax.core * which gives me errors (screenshot is attached). Do I have to change the path to the above mentioned path or is there any other way I can locate the core module? Thank you Best regards Himal Godage

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Question regarding licensing
by Brandon Benson 22 Feb '24

22 Feb '24

Hello, I'm Brandon Benson and work in IT supporting the colleges of Engineering and Science. We would like to use your software on campus. To do so, we have to fill out some information and have the licensing agreement approved by our legal team and info sec teams. Who would be a point of contact that I can use for this? Thanks, Brandon B -- Brandon Benson Client Support Analyst Engineering and Science Computing University of Notre Dame

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