- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] Selecting planes using command line
by Elaine Meng 14 Mar '23

14 Mar '23

Hi Prathvi, I believe you would have to use ChimeraX to do this, not Chimera. So this answer is for ChimeraX only: You can select the plane models with Ctrl-click in the graphics window, or you can use the selection checkboxes in the Axes/Planes/Centroids tool (ChimeraX) or in the Model Panel, where you may need to use the disclosure triangles to see the submodels and their numbers. Or you can just look in the Model Panel to find out the number to specify that model directly in commands without using selection. You can move them separately from other models in the same was as any other models in ChimeraX. I.e. with "models" keyword of move/turn commands, or with mouse modes that move only the selected and/or clicked models. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2023-February/004945.html> Of course, if you do this with the planes defined from the membrane "atoms" from the OPM database, you are no longer using their predicted membrane locations. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 13, 2023, at 5:24 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I see that after defining a plane, it gets listed in the "Axes/Planes/Ellipsoids" section with each plane having a unique ID. However, I am unable to use these IDs to select planes individually via command line. Moreover, when I hover my mouse over a plane, it displays: #0:? > > How to select the planes using the command line? And, can I move these planes independent of the protein model? > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > 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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Possible to read a trajectory "lazily" or in the background?
by Ben Webb 13 Mar '23

13 Mar '23

Am I right in thinking that when reading a trajectory (e.g. .dcd file), all requested frames from that trajectory are first read in, after which the "coordset" command can be used to work with the trajectory? I am reading frames from an RMF file (using the RMF plugin, the "rmf readtraj" command) which is quite slow, perhaps a second per frame - because RMF stores local coordinates which must be transformed to make the global coordinates ChimeraX is using. So if the user asks to read 100 frames, ChimeraX becomes unresponsive for ~100s, which is not a great user experience. One possible solution would be to read the 100 frames "lazily", e.g. just create 100 copies of the active coordset, then when the user writes "coordset #1 N" for the first time or scrolls to frame N with "coordset slider", read in frame N from the RMF file and overwrite coordset N. That way there would be a 1s delay only the first time that frame is shown. Is this possible? I see there is an "active coordset changed" trigger - perhaps I could attach to that? Alternatively, is there an API for tools to run long-running processes in the background so that the user can work on other things in the meantime, or cancel it if it takes too long? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Interface residue plot.
by Amber Smith 11 Mar '23

11 Mar '23

I want to save the 2D image of the residue plot (the gray circles with the interacting residues outlined and numbered by residue number). When I left click I can see the menu but save plot as is not an option. Is there a way for me to save that window as an image? -- ammariesmith(a)gmail.com Amber.Smith(a)ucsf.edu Amber M. Smith, Ph.D Department of Biochemistry and Biophysics Yifan Cheng Lab, Genentech Hall University of California, San Francisco 600 16th Street, San Francisco CA 94158-2517 Lab: 415.514.9708

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Showing atoms of select residues while also showing the remainder of the model
by McClean, Phillip 10 Mar '23

10 Mar '23

Hi Everyone, I would like to show the atoms for just a few of the amino acid residues in a protein model will displaying the remainder of the model using the default format. Here is what I did: 1. Opened the model from my working directory 2. Selected a subset of residues using the select command: sel /A:102,105,106 3. Then used this command: show target a This command gives me the atoms for all of the residues. Is there a way to just show the atoms for the selected residues while also leaving the remainder of the model in the standard format. Thanks for any advice. Phil McClean

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circular balls instead of residue
by Revan Katte 09 Mar '23

09 Mar '23

Hello sir/Madam, I'm labeling (or marking) the residues of my protein structure with Chimerax. So I want to use circular balls instead of residue, but he doesn't have that option. Could you please assist me with this? Thank you! Revan -- Revan Katte, Ph.D. Postdoctoral Research Associate, Prof. Maolin Lu Laboratory, Department of Cellular and Molecular Biology, The University of Texas Health Science Center, Tyler, Texas 75708, USA. E-mail: *Revansiddha.Katte(a)uthct.edu <Revansiddha.Katte(a)uthct.edu>* Professional Website: Google Scholar <https://scholar.google.com.tw/citations?user=phuOXjgAAAAJ&hl=en> LinkedIn <https://www.linkedin.com/in/dr-revan-katte-3b53a788/>

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Virtual Crash Course - Understanding PDBx/mmCIF | May 3rd | REGISTER NOW!
by Brian Hudson 09 Mar '23

09 Mar '23

Use PDB data to their full extent: Understanding PDBx/mmCIF Wednesday, May 3rd 2023 | 1:00 PM EDT Registration: go.rutgers.edu/u3vpwjet <https://go.rutgers.edu/u3vpwjet> * This RCSB Protein Data Bank (PDB) virtual course will be broadcast on Zoom. Please fill out the registration form to receive the Zoom link. Registration will be available online from March 1, 2023 to May 3, 2023. LEARNING OBJECTIVES Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. Main topics: * PDBx/mmCIF format description and examples * PDBx/mmCIF data model * Software tools for generating, editing, and visualizing PDBx/mmCIF files * PDBx/mmCIF dictionary extensions, including ModelCIF for computed structure models (CSM) from AI/ML * Parsing data from PDBx/mmCIF files for your research WHO SHOULD ATTEND Professionals and graduate students interested in learning about strategies to take full advantage of PDB data in the fields of: * Structural biology * Cheminformatics and computational chemistry * Bioinformatics and computational biology PROGRAM | Download Printable Program <https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras…> 1:00–1:10 PM Welcome Stephen K. Burley, M.D., D.Phil. Director, RCSB PDB and Founding Director, Institute for Quantitative Biomedicine, Rutgers University 1:10–1:25 PM Introduction and course objectives Gregg Crichlow, Ph.D., RCSB PDB, Rutgers University 1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB format Ezra Peisach, Ph.D., RCSB PDB, Rutgers University 1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the black box Brian Hudson, Ph.D., RCSB PDB, Rutgers University 2:05–2:50 PM Programmatic data access and analysis using PDBx/mmCIF files Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., RCSB PDB, Rutgers University 2:50–3:00 PM Closing remarks and acknowledgements Stephen K. Burley, M.D., D.Phil. Development and management of the PDBx/mmCIF data dictionary is a collaborative effort involving RCSB PDB, Worldwide Protein Data Bank (wwPDB, wwPDB.org <http://www.wwpdb.org/>) partners, and members of the wwPDB PDBx/mmCIF Working Group (wwpdb.org/task/mmcif <https://www.wwpdb.org/task/mmcif>). CO-ORGANIZERS RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova, Monica Sekharan, Chenghua Shao, Jasmine Young (Rutgers, The State University of New Jersey). QUESTIONS Contact Michelle Sanghera msanghera(a)iqb.rutgers.edu CO-SPONSORS RCSB Protein Data Bank rcsb.org <https://www.rcsb.org/> RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. RCSB PDB is supported by grants from the NSF (DBI-1832184), the US DoE (DE-SC0019749), and the NIH (R01GM133198). RCSB PDB is a founding member of the wwPDB. Institute for Quantitative Biomedicine iqb.rutgers.edu <https://iqb.rutgers.edu/>

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Mutated several residues (amino acids or nucleotides) at the same time
by Vorländer,Matthias Kopano 08 Mar '23

08 Mar '23

Hi there, I wondered if it would be possible to change several residues at the same time using the “swapna” and “swapaa” commands in order to change the model file so that it matches a target sequence. This would be extremely helpful for model building purposes. Many thanks, Matthias

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Re: [chimerax-users] Some beginner's questions
by Elaine Meng 07 Mar '23

07 Mar '23

Hi Boaz, Glad you're getting acquainted with ChimeraX! Now I find it easier to use than Chimera. (1) no, it is not necessary to name the selection. The "save" command for PDB has an option to include selected atoms only, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> (2) do you mean the Side View tool? (ChimeraX does not have a per-model clipping gui currently). There is an icon in the Graphics tab of the toolbar across the top to show the Side View, or you can open it from the menu: Tools... General... Side View (3) if the surfaces are different, yes, that would be the reason for different min/max values found at surface vertices (4) Chimera's ~longbond command just hides the "missing segments" pseudobond group. In ChimeraX, you can look in the Model Panel (may need to use disclosure triangle on the model that contains it) to find the "missing structure" model. In that tool, you can just un-check the display box in the column under the eye icon to hide the whole model, or see what the model number is to use in a hide command, e.g. open 1www hide #1.1 (5) I would need more information: Are you trying to show isopotential surfaces, or to color the molecular surface by the potential value? If the latter, are you coloring the molecular surface of the protein or of the ligand? Do you have your own dx file already or do you just want to calculate Coulombic ESP and color by that? Coloring the protein surface by Coulombic ESP is as simple as clicking the icon in the Molecule Display tab of the toolbar. It is also covered in several tutorials, e.g. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#e…> <https://www.rbvi.ucsf.edu/chimerax/data/mole-channel/mole-channel.html#esp> <https://www.youtube.com/watch?v=FEIJ0lmybXo> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 7, 2023, at 9:12 AM, Boaz Shaanan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > Hi, > > I checked the commands-user guide but couldn't find answers: > • To write out a selection of atoms to a PDB, do I need to name the selection first? > • I couldn't find the clipping tool (after setting a pivot I see only small part of the model). > • The min/max values of a potential from APBS (.dx) seem to be different in Chimerax than they are in Chimera. I'm working on a tetramer and while in Chimera the whole tetramer surface is covered by the potential, in Chimerax it' shown for each monomer. Is that the source of the difference? > • What's the Chimerax equivalent of ~longbonds of Chimera? > • Just wondering, is there a demo for electrostatic potential surface around a ligand? I seem to be making progress on that but a demo would be most helpful. > Thanks, > > Boaz

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Build Structure - peptide
by Jeffrey D. Hartgerink 07 Mar '23

07 Mar '23

Hello, I’m trying to build a series of related peptides with ChimeraX’s Build Structure - peptide tool. The way it currently works is simple and easy to use. However it is cumbersome to input phi/psi angles repeatedly, especially if the peptide sequences is anything more than very short. I am wondering if there is a way for this tool to take in either a text file list containing (Amino Acid, Phi, Psi), to paste in the same data into the input window, or any other related way to more efficiently generate peptide structures for starting points. This would greatly reduce the time needed to compare a variety of related sequences and conformations. Thank you very much for your time and consideration! -Jeff ---------------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University jdh(a)rice.edu / 713-348-4142 https://hartgerink.rice.edu

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Fwd: Request for Help with Chimerax and Protein Visualization
by Eric Pettersen 02 Mar '23

02 Mar '23

> Begin forwarded message: > > From: Ratchanont Viriyakitkosol <ratchanont.vir(a)gmail.com> > Subject: Request for Help with Chimerax and Protein Visualization > Date: March 2, 2023 at 12:26:42 AM PST > To: pett(a)cgl.ucsf.edu > > Dear Eric Pettersen, > > I hope this email finds you well. I am a medical school undergraduate student, and I have been using Chimerax to visualize protein structures that I predicted using AlphaFold. I am reaching out to you as I have encountered some difficulties with visualizing chemical bonding interactions in Chimerax, and I was hoping you could provide some guidance. > > Firstly, I have been using the "contacts" command in Chimerax to visualize chemical bonding interactions that interact with a single amino acid. However, I am not sure if this is the correct command to use. The visualization only shows blue dashlines, which I assume are hydrogen bonds. However, I am not sure if it is showing all direct interactions, including polar and nonpolar, favorable and unfavorable (including clashes). I want to know what is meant by "favorable and unfavorable" interactions in this context. > > Secondly, I have been unable to find a command to show disulfide bonds within a protein in Chimerax. I know that Pymol can show disulfide bonds in the same model, but I find Chimerax easier to use. Could you please let me know how to visualize disulfide bonds in Chimerax? > > As an undergraduate student with limited knowledge of structural analysis, I want to ensure that the bonding I use in my manuscript is shown correctly. I would greatly appreciate any advice or guidance you could provide. > > Thank you for taking the time to read my email, and I look forward to your reply. > > > > Best regards, > > James >

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