- ChimeraX-users - RBVI Mailing Lists

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.*

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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

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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 >>>>>> >>>>> >>>>> >>>> >>> >>> >> >

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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

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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

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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

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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

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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]

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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

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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

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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

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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

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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

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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.

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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

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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

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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

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