- ChimeraX-users - RBVI Mailing Lists

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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