June 2023 - ChimeraX-users - RBVI Mailing Lists

clashes & contacts
by Dmitry Semchonok 06 Jun '23

06 Jun '23

Dear colleagues, Probably very simple question, non the less - how to calculate&show the contacts/clashes in the model? We have heptamer and we would like to find out what are the contacts & clashes with 6 surrounding units. I know that chimera can do that. Also, I heard that there is also software called DIMPLOT. Does ChimeraX do the same? Thank you in advance. Sincerely, Dmitry

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Daily builds
by BARRY E DEZONIA 05 Jun '23

05 Jun '23

Hello, I am looking for the daily build for Ubuntu. I go to this page: https://www.rbvi.ucsf.edu/chimerax/download.html No daily build releases are shown for Ubuntu. Are you having trouble with the website?

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The AlphaFold predicted model is always saved as best_model.pdb. It would be nice if you could specify a different name when you start the prediction run but that is not available. I made a ChimeraX feature request for that https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9128 You can request new features directly with ChimeraX menu entry Help / Report a Bug.... This can be used for both bugs and new feature suggestions. Tom > On Jun 5, 2023, at 11:51 AM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thank you. I am slowly learning how to use ChimeraX. > One other question that I haven't solved yet: when I paste a sequence into the box for structure prediction, is there a way to name it right at the beginning? > All my previous jobs are given the same name "best_model".I know I can rename them later, but it would be easier if I could name them at the start. > Jim > > > On Mon, Jun 5, 2023 at 11:30 AM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. >> >> Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command >> >> ui dockable false "AlphaFold Run" >> >> Tom >> >> >>> On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu <mailto:james.raymond@unlv.edu>> wrote: >>> >>> Thanks, Tom, >>> I sent another email to say that I think I solved the problem but you didn't see that one. >>> >> >>> >>> >>> Here's a cool protein structure I made today with ChimeraX. >>> I used Yasara to view it. >>> This is so great! >>> Jim >>> >>> >>> >>> On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>> Hi Jim, >>>> >>>> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >>>> >>>> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >>>> >>>> Tom >>>> >>>> >>>> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> > >>>> > Dear ChimeraX, >>>> > I keep losing this window, whenever I click on it or move it. >>>> > How do I get it back again? >>>> > thank you >>>> > Jim >>>> > >>>> > >>>> > <image.png> >>>> > _______________________________________________ >>>> > 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> >>>> > Manage subscription: >>>> >> >>

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ChimeraX - windows 10 installation/running issue
by Dmitry A. Semchonok 05 Jun '23

05 Jun '23

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Re: how to view Alphafold Run window
by Tom Goddard 05 Jun '23

05 Jun '23

Hi Jim, The ChimeraX panels are can be dragged and dropped on the main ChimeraX window to allow stacking them. In your case you dragged the AlphaFold Run panel on top of the Log panel. Then it shows the two tabs (AlphaFold Run, Log) at the bottom and you can click on those to switch between them. You can make the AlphaFold Run window free-floating again by showing its tab then dragging the title-bar of the panel out of the main ChimeraX window. All the ChimeraX panels work this way -- they can be made free-floating windows or "docked" in the main window. Sometimes it is annoying when you drag a ChimeraX window and it tries to drop it on top of another panel. You can tell ChimeraX to not allow dropping the AlphaFold Run window on another panel using the command ui dockable false "AlphaFold Run" Tom > On Jun 2, 2023, at 6:36 PM, James Raymond <james.raymond(a)unlv.edu> wrote: > > Thanks, Tom, > I sent another email to say that I think I solved the problem but you didn't see that one. > > > Here's a cool protein structure I made today with ChimeraX. > I used Yasara to view it. > This is so great! > Jim > > > > On Fri, Jun 2, 2023 at 4:34 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Jim, >> >> You kind of shoot yourself in the foot if you close the AlphaFold Run. But Google Colab does not immediately kill your AlphaFold job. So you could reconnect to Google Colab in whatever web browser you normally use (search for Google Colab). When it asks if you want to load some previous notebook say Cancel. Then use Google Colab menu Runtime / Manage Sessions and click on your AlphaFold session that you started from ChimeraX. Then you should see your job still running. When it completes it will ask to download the results. The original ChimeraX window you closed would have downloaded the prediction and opened it in ChimeraX. But now you have Colab in a normal web browser so it will simply download to your ~/Downloads folder (not where ChimeraX usually puts it in ~/Downloads/ChimeraX/AlphaFold/prediction_N) so you would have to open the results.zip and load the predicted structure yourself. >> >> In short don't close the AlphaFold Run window. It isn't quite as bad as opening a terminal, starting a computation, then closing the terminal before it finishes. Since it is running on Google's servers and Google kindly doesn't immediately shut it down, you can rescue it. But it is not intended to work that way. >> >> Tom >> >> >> > On Jun 2, 2023, at 4:04 PM, James Raymond via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Dear ChimeraX, >> > I keep losing this window, whenever I click on it or move it. >> > How do I get it back again? >> > thank you >> > Jim >> > >> > >> > <image.png> >> > _______________________________________________ >> > 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> >> > Manage subscription: >>

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AlphaFold2 coloring is not according to the database
by Julia Varga 05 Jun '23

05 Jun '23

Hi, I was preparing a figure and we opened the same AF2 structure both in chimerax and pymol, and colored according to pLDDT. We expected something quite similar, but some of the residues were not colored the same (left chimerax, middle official AF2 coloring, right pymol) [image: image.png][image: image.png][image: image.png] These are the corresponding CA atoms from the file, there are several that are above 70. ATOM 2 CA MET B 1 26.541 -48.983 -34.346 1.00 49.18 C ATOM 10 CA ALA B 2 23.562 -47.870 -36.454 1.00 60.35 C ATOM 15 CA ASP B 3 25.250 -49.497 -39.528 1.00 68.46 C ATOM 23 CA ALA B 4 25.752 -52.804 -37.641 1.00 69.86 C ATOM 28 CA TRP B 5 22.024 -53.025 -36.747 1.00 68.46 C ATOM 42 CA GLU B 6 21.036 -52.590 -40.351 1.00 71.02 C ATOM 51 CA GLU B 7 23.249 -55.575 -41.294 1.00 76.21 C ATOM 60 CA ILE B 8 21.578 -57.739 -38.645 1.00 74.81 C ATOM 68 CA ARG B 9 18.177 -56.653 -39.803 1.00 70.07 C ATOM 79 CA ARG B 10 19.226 -57.507 -43.334 1.00 74.00 C ATOM 90 CA LEU B 11 20.598 -60.932 -42.264 1.00 74.36 C ATOM 98 CA ALA B 12 17.459 -61.553 -40.194 1.00 69.47 C ATOM 103 CA ALA B 13 15.384 -60.625 -43.205 1.00 69.30 C ATOM 108 CA ASP B 14 17.563 -62.981 -45.430 1.00 70.53 C ATOM 116 CA PHE B 15 17.273 -65.769 -42.888 1.00 71.78 C ATOM 127 CA GLN B 16 13.568 -65.190 -42.812 1.00 64.74 C ATOM 136 CA ARG B 17 13.352 -65.300 -46.586 1.00 65.36 C ATOM 147 CA ALA B 18 15.491 -68.455 -46.645 1.00 64.05 C ATOM 152 CA GLN B 19 13.261 -70.000 -44.028 1.00 60.46 C ATOM 161 CA PHE B 20 10.117 -69.389 -46.168 1.00 62.26 C ATOM 172 CA ALA B 21 11.642 -70.083 -49.654 1.00 56.65 C ATOM 177 CA GLU B 22 11.244 -73.693 -49.767 1.00 53.68 C ATOM 186 CA ALA B 23 7.622 -74.493 -50.250 1.00 56.47 C After looking at again the docs, I understood that chimerax has a different coloring [image: image.png] AFDB [image: image.png] Can you maybe change this? Most people are probably used to the database's coloring, and could interpret it wrong (like me... It drove me crazy when showing somebody else, why the plddt-s do not match to what I have shown before, just in a figure by chimerax). I understand that in the documentation the colorbar is according to the coloring that chimerax does, but it would be better if it was according to the standard. Thank you so much! Kind regards, Julia Varga

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smooth object surface
by Jesse Hansen 05 Jun '23

05 Jun '23

dear all, I have an object imported from segmentation in dragonfly that is quite jagged and rough looking. Is there a way to smooth the surface? When I try "surface smooth" that doesn't work because I guess it's looking for atoms/surface render. Is there a way to smooth .stl or .obj files? Thanks Jesse

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makind disulfide bonds in Chimera x
by Vladimir Saudek 03 Jun '23

03 Jun '23

Hello, Is it possible to make a disulfide bond between two Cys in spacial proximity and write it to the PDB file? Thank you Vladimir

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how to view Alphafold Run window
by James Raymond 02 Jun '23

02 Jun '23

Dear ChimeraX, I keep losing this window, whenever I click on it or move it. How do I get it back again? thank you Jim [image: image.png]

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Blast protein results
by postmaster＠cgl.ucsf.edu 02 Jun '23

02 Jun '23

From: Lynne Howell <howell(a)sickkids.ca <mailto:howell@sickkids.ca>> Subject: Blast protein results Date: June 2, 2023 at 2:18:42 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> HI I’m a novice ChimeraX user and wondered whether there is a way of saving to an excel file the blastprotein results against the Alphafold database that appear in the session window? Was looking to capture all the information for cross reference to another file. Thanks in advance Lynne This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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