November 2023 - ChimeraX-users - RBVI Mailing Lists

Calculating solvent accessible surface area for all residues in a protein?
by Altobelli, Chad 15 Nov '23

15 Nov '23

Hi! Is there a way to calculate the solvent accessible surface area (SASA) for every residue in a protein (5FTL) and output the result to a text file? I am trying to rank order residues by their accessibility. I know I can use the command line to calculate one residue at a time but it's laborious. Is there a way to automate the process or a GUI shortcut? Thanks! Chad

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ChimeraX-1.7.dev202311052311-Ramachandran Plots
by Berkay Ekren 15 Nov '23

15 Nov '23

Hello, FIrst of all, I have been using Chimera for 3-4 years, now, and I would like to thank you for your efforts in the development of Chimera and ChimeraX. Recently, I decided to move to ChimeraX, and stay updated by using the bleeding edge daily version. However, I haven't been able to see the Ramachandran Plots option in either the Model Panel or the Tools section of ChimeraX. Is the Ramachandran Plots function removed from the program? Or is it just that I haven't looked at the correct path. This is a Linux installation in Debian 12 (used Ubuntu 22.04 deb package) It would be great if you could direct me to the right direction. Thank you in advance, I am looking forward to hearing from you at your earliest convenience. --Berkay Y. Ekren PhD candidate in Biostatistics and Bioinformatics

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substitute nonstandard residue
by Dmitry Semchonok 15 Nov '23

15 Nov '23

Dear colleagues, I have a short question - how to substitute nonstandard residue with other ChimeraX. My task is to substitute GTP for GSP. The one may use swapaa, right? Could anyone drop the usage for nonstandard residue? Many thanks. Sincerely, Dmitry

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ChimeraX on Apple M1
by Dennis Dannecker 15 Nov '23

15 Nov '23

Hello, I have a question regarding running ChimeraX on Apple's M1 chip. About two years ago (Nov 2, 2021), there was a post by Tom announcing the development of a version of ChimeraX that would run natively on Apple M1 instead of emulting for the Intel processor. Looking in the download section, I see such a native version is now regularly released. However, I am wondering what is the differen between the "macOS M1 or M2" and "macOS". While the former is only for M1 and M2, the latter on is for M1, M2, and Intel Macs, this one is also quite larger in size. If one is working on a macOS M1 (or M2) machine, is it correct to go for the "macOS M1 or M2"? Would that correspond to natively running ChimeraX and provide the best possible performance, or should one always go for the "macOS" release? I am currently updating my hardware, and since I am working quite a bit with ChimeraX, I would like to also inform my decisions based on the available ChimeraX releases. Thank you very much. Best regards Dennis Dennis Dannecker Master Student of Biochemistry Department of Chemistry Faculty of Mathematics and Natural Sciences University of Cologne Albertus-Magnus-Platz 50923 Cologne, Germany

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Not able to see Glycines in stick form
by Firdous Tarique 14 Nov '23

14 Nov '23

Hi everyone In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any of the structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). My aim is to show the thioester bond between Gly and Cys of two chains which I am able to create in Coot through Molecule Link but not able to see in ChimeraX. The moment I am trying to show Gly in stick form at this position it breaks the cartoon. I realised that this is for all the Glycines in the structure. Showing stick and cartoon together shows all amino acids in the stick except Glycine. (However this is not the case in Pymol and Chimera). Do you know any tricks to fix that in ChimeraX? Best Firdous

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(no subject)
by Enrico Martinez 14 Nov '23

14 Nov '23

Dear Chimera-X users! I am trying to record md trajectory loaded in the chimera as

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Re: [ccpem] Making thioester bond in Chimera/ChimeraX
by Elaine Meng 13 Nov '23

13 Nov '23

Hi Firdous, No trick, it is an option of cartoon (on by default) to prevent showing backbone atoms at the same time. Glycine only has backbone atoms (no sidechain). If you really want to show cartoon and backbone atoms at the same, use cartoon suppress false This is explained in the "cartoon" or "ribbon" command help. Just type command "help cartoon" to see your downloaded copy of the help page, or see the copy on our website here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> The full name of the option is "suppressBackboneDisplay" but you can shorten all options in commands as long as there is no other option that starts with the same letters. Actually Chimera ribbon also hides backbone atoms by default, although you can allow showing both at the same time with the Chimera "ribbackbone" command. The best address to use for ChimeraX questions is the chimerax-users one that I CC'd on this message, unless you are including data that must be kept private. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 13, 2023, at 2:59 PM, Firdous Tarique <kahkashantarique(a)gmail.com> wrote: > > Hi Elaine > > Now I know where the problem is. In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for any structure if you see. By showing a cartoon and stick together, the sticks for all amino acids show up except for Gly where it remains in the cartoon (you can try that). However this is not the case in Pymol and Chimera. Do you know any tricks to fix that in ChimeraX? > > Best > > Firdous > > On Thu, Nov 9, 2023 at 6:11 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hello Firdous, > Probably the problem is that mol A and mol B are two different models. You can't add a bond in Chimera or ChimeraX until after combining them into one model first. > > ChimeraX combine command: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> > > ChimeraX bond command or Build Structure tool, Adjust Bonds section: > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> > <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> > > For the best chance of getting an answer to a question about ChimeraX, please use the chimerax-users(a)cgl.ucsf.edu address: > <https://rbvi.ucsf.edu/chimerax/docs/contact.html> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > From: Collaborative Computational Project in Electron cryo-Microscopy <CCPEM(a)JISCMAIL.AC.UK> on behalf of Firdous Tarique <kahkashantarique(a)GMAIL.COM> > > Date: Thursday, November 9, 2023 at 12:27 PM > > To: CCPEM(a)JISCMAIL.AC.UK <CCPEM(a)JISCMAIL.AC.UK> > > Subject: [ccpem] Making thioester bond in Chimera/ChimeraX > > > > Hi > > > > Does anybody know how to make thioester bonds in Chimera or ChimeraX ? > > > > I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX. > > > > I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so far have been unsuccessful. I don't know if I am missing something. > > > > Any help would be appreciated. > > > > Thanks > > > > Firdous > > > > To unsubscribe from the CCPEM list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 > > >

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projecting full model from monomer
by Dmitry Semchonok 13 Nov '23

13 Nov '23

Dear colleagues, I have a monomer with biomt information that describes the full model. To see the full model, I use the command sym when opening the monomer in Chimera. Could you please prompt the correspondent command in ChimeraX to project the complete model in ChimeraX based on the information stored in the monomer? Thank you Kind regards, Dmitry

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ChimeraX trial license
by Jang,Chang Woon,US-St. Louis 12 Nov '23

12 Nov '23

Dera UCSF ChimeraX Team, My name is Chang Woon Jang working for Nestle Purina. I am interested in ChimeraX for a molecular modeling project. Could I use a trial license for a month before buying the commercial license? Thanks, Chang Woon Jang

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updating ChimeraX for rc/daily build with Isolde
by Dmitry Semchonok 11 Nov '23

11 Nov '23

Dear colleagues, I would like to update ChimeraX to rc version or daily build. Trying to install Isolde / Clipper delivered me the following error (either via the command line within ChimeraX, or via the ChimeraX update button) Clipper toolshed install C:/Users/Dmitry/Downloads/ChimeraX_Clipper-0.22.1-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-clipper) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 ISOLDE toolshed install C:/Users/Dmitry/Downloads/ChimeraX_ISOLDE-1.7.dev0-cp311-cp311-win_amd64.whl ERROR: Could not find a version that satisfies the requirement ChimeraX-Core<1.8,>=1.7.dev202306142048 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core<1.8,>=1.7.dev202306142048 Is it possible to install Isolde/clipper with rc/daily version? If yes, how to fix the error? Thank you. Kind regards, Dmitry

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ChimeraX-users November 2023