April 2021 - ChimeraX-users - RBVI Mailing Lists

Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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ChimeraX Cheat Sheet/List
by André Graça 30 Apr '21

30 Apr '21

Hi everyone, There is no doubt that we have a very good documentation on the different functions of ChimeraX as well as for Chimera. Nevertheless, sometimes it is easy to have a summarized sheet with the most used functions and options. I plan to start doing a cheat sheet for me, and it would be great to make it open source. However I might not be aware of the existence of one already. Does anyone know/have one and would be willing to share with the community, or point me to one available online? Or has the ChimeraX team any plans to do one in the near future? Thank you, André

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Re: [chimerax-users] ChimeraX-Deeplearning plugin
by Yongcheng MU 29 Apr '21

29 Apr '21

Hello Tom, Hope you are doing well. I am creating a GUI, and I have some problems. At the right bottom DL Struct window, I want to click the browse button and select a file, but it holds this error. I wonder if you know what's the problem? (My goal is let users find or input the path of a file, and use this path to submit jobs) Best regards, Yongcheng [image: Screen Shot 2021-04-29 at 1.24.02 PM.png] On Fri, Apr 23, 2021 at 7:20 PM Yongcheng MU <ymu004(a)odu.edu> wrote: > Hello Tom, > > Thank you for the information. I will check these documents you have > provided. > > Best regards, > Yongcheng > > On Fri, Apr 23, 2021 at 7:01 PM Tom Goddard <goddard(a)sonic.net> wrote: > >> Hi Jing, Yongcheng, >> >> ChimeraX requires all different code from Chimera so I suggest not >> looking at a Chimera example, that will only confuse you as none of it is >> right for ChimeraX. There are simple examples of Python scripts for >> ChimeraX at the ChimeraX recipes site >> >> https://rbvi.github.io/chimerax-recipes/ >> >> For packaging up a plugin there are examples in the ChimeraX programming >> manual >> >> https://www.rbvi.ucsf.edu/chimerax/docs/devel/index.html >> >> And it can also the packaging for plugins using a bundle_info.xml is used >> by each of the tools in ChimeraX and you can look at any of those as >> examples at the ChimeraX GitHub code repository >> >> https://github.com/RBVI/ChimeraX/tree/develop/src/bundles >> >> Let me know if you run into trouble. >> >> Tom >> >> >> >> >> On Apr 23, 2021, at 2:53 PM, He, Jing <jhe(a)cs.odu.edu> wrote: >> >> Hi Tom, >> >> Yongcheng has been setting up the bundle of a PyTorch-based deep learning >> method to detect secondary structures from medium-resolution density maps. >> He is able to install the bundle on Mac and PC and it looks like working. >> He started to create a GUI. I passed him our previous code for a Chimera >> plugin. Below he shows a few snapshots for that code. We are wondering if >> ChimeraX has similar functions to be called. Previously our code uses >> Chimera's functions to do input, output, and any display of some calculated >> results. How do we do this in ChimeraX? >> >> Jing >> >> ------------------------------ >> *From:* Yongcheng MU <ymu004(a)odu.edu> >> *Sent:* Friday, April 23, 2021 2:04 PM >> *To:* He, Jing <jhe(a)cs.odu.edu> >> *Subject:* ChimeraX-Deeplearning plugin >> >> Dear Dr. He, >> >> I am trying to create a GUI for the bundle. When I check the previous >> work, I find some codes were called such as chimera.extension. I wonder if >> ChimeraX needs this kind of code or package as well, and where I can search >> and find this useful information. >> >> Best regards, >> Yongcheng >> >> [image: Screen Shot 2021-04-23 at 1.55.24 PM.png] >> [image: Screen Shot 2021-04-23 at 1.55.40 PM.png] >> [image: Screen Shot 2021-04-23 at 1.56.01 PM.png] >> >> >>

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Display chain annotations w/o having to reopen files
by Alexander Julian 28 Apr '21

28 Apr '21

Good afternoon, I was wondering if there was any built-in functionality to show the chain annotations that are shown when the file is first open? When I save a session (.cxs) and reopen it later, this information is missing. Best, Alexander -- *Alexander T. Julian* PhD Student, Department of Biology, Microbiology Bachelor of Science, Biomedical Engineering, Cell and Tissue Specialization 2021 Master of Advanced Study, Chemical Engineering 2021 Illinois Institute of Technology Chicago, IL 60616 *Phone (727)-735-7104*

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Hide dashed lines (chain breaks)
by Gabriele Cerutti 28 Apr '21

28 Apr '21

Hello, I am displaying a protein molecule in cartoon representation and chimeraX automatically shows dashed lines for chain breaks (see attached). Is there a way to hide these dashed lines? Best, Gabriele [image: Screen Shot 2021-04-28 at 9.50.54 AM.png]

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Scale bar in ChimeraX
by Sen, Anindito 27 Apr '21

27 Apr '21

Dear All, How to put a scale bar in a ChimeraX session depicting a density map ( as in Chimera Tools - High-Order structure -Scale Bar). 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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Adding amino acids to end of chain
by Tom Goddard 26 Apr '21

26 Apr '21

Alexis Rohou asked on Twitter In @UCSFChimeraX <https://twitter.com/UCSFChimeraX> 1.1.1 and #Isolde <https://twitter.com/hashtag/Isolde?src=hashtag_click> by @CrollTristan <https://twitter.com/CrollTristan> is there an easy way to add aa residues to the end of a chain? https://twitter.com/AlexisRohou/status/1386171500604977152 <https://twitter.com/AlexisRohou/status/1386171500604977152> Elaine says: There isn't an "add amino acid" yet in ChimeraX, only Chimera.... unless ISOLDE can do it (I don't know). So maybe it's an ISOLDE question. ChimeraX itself has building peptides from scratch but not sticking them on to the end of an existing peptide. Build Structure, Start Structure: peptide <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#start>> or command "build start peptide" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start <https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start>> Elaine

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Re: [chimerax-users] Cannot install
by Tom Goddard 26 Apr '21

26 Apr '21

Volodymyr says it is necessary to choose "save" when downloading the Linux ChimeraX, not "open". > On Apr 25, 2021, at 5:30 AM, Volodymyr Dvornyk wrote: > > Dear Tom, <> > > Fixed. That was my error: I selected “open” when downloading instead of “save”. > > Best, > > Volodymyr >

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z-slice movie making
by Stapleton kevin2017/4/3 26 Apr '21

26 Apr '21

Greeting everyone in the ChiX community. Long time listener first time caller :-) I was wondering if anyone could help me with making a movie that is essentially slicing (clipping) through a given volume. I am pretty comfortable with the movie making movie parameters and I have read through the sections 1) help:user/movies.html 2) help:user/commands/clip.html However the command parameters explanation is juuuuust a smidgen beyond my limits (almost there...damn!) and cant seems to get this into a working movie (if possible at all). So, using the emdb entry: 22910 for example case, how can I make a movie that is 10 seconds long and extends through the clipping plane of a given volume, moving front to back (from the "view orient" perspective; the clipping plane will extend forward through the volume, and back again) Thanks for all your help in this specific case, and for all of the efforts put into to this mailing list. It has been a well spring of fun learning for me over the years. SO many cool tips and tricks to make macro-molecular structures look top notch and cool. THANKS CHIMERA TEAM!! All the best and well wishes from Japan, Kako PS. apologies if this was covered in a previous thread. I must have missed it.

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ChimeraX-users April 2021