- ChimeraX-users - RBVI Mailing Lists

Structure editing
by Niklas Laenger 06 Sep '22

06 Sep '22

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

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AlphaFold prediction template structures
by Tom Goddard 06 Sep '22

06 Sep '22

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

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

06 Sep '22

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

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

06 Sep '22

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

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Assistance
by Priyanka Abeyrathne 06 Sep '22

06 Sep '22

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

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ChimeraX docked panels
by Tom Goddard 06 Sep '22

06 Sep '22

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

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

06 Sep '22

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

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protonation of small molecule
by Enrico Martinez 05 Sep '22

05 Sep '22

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

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AlphaFold
by Hernando J Sosa 02 Sep '22

02 Sep '22

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

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

01 Sep '22

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

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