September 2022 - ChimeraX-users - RBVI Mailing Lists

2D plots and graphs for protein-ligand interactions
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5734306/ Many thanks in advance! Cheers Enrico

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Create Complete Oligomers
by Samuel Kyobe 09 Sep '22

09 Sep '22

Dear ChimeraX We have a protein NLRX1 which functions as a trimer, however only the terminal component of this trimer has been experimentally resolved (3UN9) and in alpha fold the complete monomer of NLRX1 has been predicted (Q86UT6). Is it possible to build a complete trimer of NLRX1 starting with the partial X-ray resolved structure as a reference using ChimeraX and the alphafold model. We would like to use the complete structure for MD studies. Thank you Samuel

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Visualization of the carbon - Cl bond in a small molecule
by Enrico Martinez 09 Sep '22

09 Sep '22

Dear ChimeraX users! I have an issue with the visualization of the small molecule obtained from the tleap module of the amber tools. First of all in vmd and pymol everything looks OK. In the ChimeraX there is no bond between atom CL of the ligand and the aromatic C atom. I've tried to change atom type for the CL: setattr :lig@CL1 atoms idatm_type CL show :lig@* but the bond is still absent. Would it be possible to rebuild it manually? Cheers, Enrico

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How to update the bonding status in a molecular trajectory?
by 洪冉 08 Sep '22

08 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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image
by 洪冉 08 Sep '22

08 Sep '22

Dear ChimeraX developers and users, I tried to use ChimeraX to visualize my MD trajectory and I found some bonds were stretched very long and weird, see below In VMD, I could fix this phenomenon using updatebond features, could anybody tell me how to enable this feature in ChimeraX? Many thanks in advance. Ran hong hongran(a)ahpu.edu.cn Anhui polytechnic university Wuhu, China, 241000

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Moving one map in a session while keeping the other/s inactive
by mailman-bounces＠cgl.ucsf.edu 08 Sep '22

08 Sep '22

Dear All, This question might have been answered before but could you let me know how to move 1 map from one position to another without disturbing the other map/s (as we inactivate the maps in Chimera). Stay safe & Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 <http://microscopy.tamu.edu/>Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu <http://microscopy.tamu.edu/>

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Re: [chimerax-users] [Chimera-users] How to caluculate buried surface area
by Elaine Meng 07 Sep '22

07 Sep '22

Hi Kenji, You are using ChimeraX? I CC'd the ChimeraX address chimerax-users(a)cgl.ucsf.edu (different than chimera-users(a)cgl.ucsf.edu) The "measure buriedArea" command does not require picking any blobs. You just specify the parts that you want in the command line. <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> So, maybe something like command: measure buriedarea protein with ligand ...but maybe "ligand" doesn't get your ligand. You would have to use whatever kind of specification works for your ligand, e.g. if residue name is UNK, something like this instead: measure buriedarea protein with :UNK You sent a Pymol session... I don't use Pymol so I can't open that file, sorry. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 5, 2022, at 9:45 PM, Kenji MATSUI via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera > > I am sorry to interrupt your busy schedule. > > My name is Matsui, and I am a second-year master's student at a Japanese university. > Thank you for taking time out of your busy schedule to respond to my question the other day. > > We are investigating the buried surface area to see the magnitude of the interaction between protein and ligand. > > For this purpose, I calculated the solvent accessible area of the ligand. However, the value is 9955, which shows the entire surface area of the protein. > > What should I do? I am not in a hurry for answers , so I would appreciate a reply when you have the time. > > In this case, the ligand was in the binding pocket of the protein, so I would like to calculate the ligand's solvent contact area = buried surface area. > > I tried to check and tried , but it did not work. > > 1.See https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-January/003521.html > > 2.Try to use measure blob using chimera X. > Reference: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea > > However, I didn't know how to solve this command. > Command ;ui mousemode right "pick blobs > > Reference; https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html > --------------------------------------------------------------------------- > Kenji Matsui > Graduate School of Tokyo University of Agriculture and Technology　M2 > 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan > > <Buried_surface_area_LXRα_1UHL_24,25-epoxy_cholesterol (remove LXRβ_1P8D).pse>_______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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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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