- ChimeraX-users - RBVI Mailing Lists

Trajectory smoothing
by Shubham Devesh Ramgoolam 15 May '23

15 May '23

Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 6

REMINDER: ChimeraX website downtime
by Elaine Meng 15 May '23

15 May '23

REMINDER: Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable -- the estimated downtime is from Tuesday May 16 8pm PDT through Wednesday May 17 8pm PDT. Please pardon any inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Re: [chimerax-users] Measuring distance between two atoms in a single protein
by Cheng, Jiaxuan (NIH/VRC) [F] 14 May '23

14 May '23

Hi Elaine, I met a problem when measuring the distance between two atoms. I entered “distance #1.16/B:94 at CA #1.35/B:94 at CA” , but the ChimeraX reports “expected a keyword”. Could you let me know how to solve it? Thanks! Jiaxuan [cid:image001.png@01D98530.82126BB0]

2 2

Scrolling wheel feature request
by vincent Chaptal 12 May '23

12 May '23

Dear ChimeraX team, a very useful feature in Pymol is the use of the scrolling wheel on the mouse to clip the view plane and add depthcue. After centering on one element, it is very convenient to focus on some areas and remove things from the view, for both viewing and article figures. I haven't find a similar feature in ChimeraX, would it be possible to implement it? I've tried to play with the depthcue command, but it I find it much harder to get to what I would like. lighting depthcue true depthCueStart 0.3 depthCueEnd 0.5 If the view with the clipping can be saved with the "view matrix" command, it would be extremely useful. Thank you. Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 1

Re: [chimerax-users] unifold
by Tom Goddard 11 May '23

11 May '23

3 5

coloring a clipped surface cap by property
by Elaine Meng 10 May '23

10 May '23

Hi Noam, Glad you like ChimeraX! (A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#c…> (B) The way to color a clipped surface cap by an atomic or residue attribute is to: 1) color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool) 2) use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model. Example: color zone #1.1.1 near #1 distance 3 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> Since "N" heads are better than one, we generally recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain 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 May 10, 2023, at 7:40 AM, Noam Prywes <noam.prywes(a)gmail.com> wrote: > > Dr. Meng, > > I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. > > Do I need to make a .defattr file that colors by atom instead? > > Thanks for your help and the amazing service that is chimeraX. > > Best wishes, > Noam

3 5

Hiding distance labels during trajectory playback
by Lewandowski, Jozef 10 May '23

10 May '23

Hi, Is there an easy way to hide distance labels during the playback of an MD trajectory? Even if I delete or hide the labels in one frame they get generated when next frame is loaded. I tried to include hiding/deleting the labels command in perframe but they flash on before they are removed. Ultimately, I would like to record a movie where only the pseudobonds are shown but not the labels. Thank you, Józef

3 3

ChimeraX 1.6.1 release
by Eric Pettersen 10 May '23

10 May '23

UCSF ChimeraX version 1.6.1 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html> Updates since version 1.5 (Nov 2022) include: - ESMFold protein structure prediction and residue-residue error plot - Add Charge GUI - Dock Prep GUI to repair side chains, add hydrogens, etc. - Render by Attribute GUI for coloring by atomic or residue values - swapna command to mutate nucleic acid residues - invert chiral center - read SwissDock docking results - Blast Protein query sequence can be pasted in or specified by UniProt ID - browse/fetch medical images from The Cancer Imaging Archive - read medical images in NIfTI (.nii) and NRRD (.nnrd) formats For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> For those of you who downloaded plain 1.6 while it was briefly available, please upgrade to 1.6.1. It has several bug fixes that 1.6 should have had but didn't. --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Clipped surface coloring
by Noam Prywes 10 May '23

10 May '23

Hi all, I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. Do I need to make a .defattr file that colors by atom instead? Best wishes, Noam [image: Screenshot 2023-05-10 at 7.42.14 AM.png]

1 0

Question in using ChimeraX ----mesh parameters
by Wang, Shuhui 09 May '23

09 May '23

Hello developers, I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume? Best, Shuhui

3 3

Re: [chimerax-users] [Chimera-users] Utilizing Chimera in Web-Based Workflows
by Tom Goddard 09 May '23

09 May '23

Hi Rafi, You could have a Google Colab notebook install ChimeraX and then you could run ChimeraX command in nogui mode or python code through the ChimeraX REST facility, and possibly save images of the graphics to show in the notebook. But I don’t grasp the value of it since ChimeraX is all about interactive visualization where you can rotate and inspect structures. One issue you will face is that ChimeraX cannot be installed without agreeing to a license when dowloading - not sure how you might handle that in a notebook. But I suggest figuring out the valuable use case first. Tom > On Apr 21, 2023, at 5:28 AM, Zach Pearson via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Rafi, > > We are working hard to fully deprecate Chimera, and haven’t made its source code accessible for use or extension outside of the desktop application. I would caution against looking for it; the compilation process is complex and depends on resources that may not even be available anymore. Chimera was also written in Python 2.7, a language the computing community is working hard to put to rest — Colab doesn’t support it anymore! > > We do have plans to release a substantial part of ChimeraX on PyPi this year as a public beta, and I’ll make a note to send you an email when that release happens. Then you should be able to use it in Colab like any other PyPi package. Let me know if I can answer any other questions you may have. > > ------------------- > Zach Pearson > Programmer, ChimeraX Team > UCSF RBVI > zjp(a)cgl.ucsf.edu > > > >> On Apr 20, 2023, at 13:44, Rafi Brent via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> To whom it may concern, >> I'm wondering if there's any way to access Chimera without having the GUI downloaded on a local computer. Specifically, I'd like to run chimera as part of a public Google Colab (.ipynb) notebook, which would allow users to access the chimera functionality through either installing a PyPi package or calls to a web-accessible API. Do you know of any tool like this, or have any other ideas for how Chimera could be used in Colab notebook? Thanks so much for any advice you may have. >> >> Sincerely, >> Rafi Brent >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

3 3

request for an example command line
by James Raymond 09 May '23

09 May '23

I am having trouble understanding the manual. I wish to show the side chain for a particular amino acid in my protein. What is the command line to do this? thank you James Raymond

3 12

Failing to complete dimer prediction
by Tal Jeffrey 09 May '23

09 May '23

Dear all, I am trying to use ChimeraX to predict the structure of a dimer as part of my Master’s thesis. I was able to produce a model of the monomeric structure without issue have not been able to do the same for the dimer. I am currently subscribed to Colab Pro so had assumed that the 15.0GB GPU RAM would be sufficient. The structure is 1361 amino acids long but AlphaFold2 is still able to produce the first two models successfully. However, I have not been able to produce any iterations past this stage. Any guidance on how to complete the model would be much appreciated! Alternatively, I would also be glad to extract the output of the first two models (e.g. .pdb files, plDDT plots, PAE plots, MSA heatmaps) but because the prediction does not run to completion I don’t know how to access/extract these. I have really enjoyed using the program and hope to include the structure of the dimer in my thesis before I submit in three weeks’ time. Many thanks, Tal

3 4

Map Comparisons vs Model Comparisons: Which represents differences more accurately?
by Kevin Felt 09 May '23

09 May '23

Dear Chimerax Developers, There is a debate in my lab about the best way to compare two PDBs of the same protein bound to different ligands; the goal is to identify subtle differences in the binding pocket between the ligand-bound conditions. One method of comparison is to fit the two density maps together using the FitMap function, and then fit each PDB into their respective maps which have been aligned. Another way is to simply align the two PDBs (such as the align function in Pymol). Using these two methods results in slightly different alignments of the PDBs and thus give slightly different positional differences of the binding pocket and ligands. The resolution of these density maps range from 2.4 - 3.5 angstroms. Which way would be the more accurate way to look at the differences between two similar models? Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

3 2

pae plot
by John Maximos [Pharma] 09 May '23

09 May '23

Dear Chimerax Team, I have a problem that the pae plot color is not adjusted like the green one. How to solve this problem? I attached here a screenshot from my laptop. Best Regards, John Maximos [cid:image003.png@01D9827F.FEF05100] www.evapharma.com<https://www.evapharma.com/>

2 1

making movie of helical Assembly
by mailman-bounces＠cgl.ucsf.edu 08 May '23

08 May '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: making movie of helical Assembly Date: May 7, 2023 at 11:53:16 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to make a movie where I can show the atomic model of the subunits appearing one after another following the helical pattern forming the filament. How can I do that? Stay safe & Regards Anindito Sen. Ph.D <>

2 1

cannot open chimerax with structureviz (using ChimeraX 1.5 and cytoscape 3.9.1)
by ora.furman-schueler＠mail.huji.ac.il 07 May '23

07 May '23

Dear Support team We are teaching a network course and would like to show an example of analysis of proteins as networks. I have tried to follow the structureviz2 tutorial but I cannot get past the very first step of linking ChimeraX to cytoscape. I did define the Chimera location path /Applications/ChimeraX-1.5.app/Contents/MacOS What am I doing wrong? This is the error message that I get in cytocape. Launching Chimera  Launching Chimera ...  UCSF Chimera could not be launched. Make sure that the correct path to Chimera is set in structureViz -> Settings… thank you for your help! Ora Prof. Ora Schueler-Furman Dept. of Microbiology and Molecular Genetics, IMRIC Jacob Epstein Chair in Bacteriology Hebrew University, Hadassah Medical School POB 12272, Jerusalem 91120 Israel Tel: 972-2-675-7094 FAX: 972-2-675-7308 Furman lab site: www.cs.huji.ac.il/~fora

3 3

Question on Contacts and Distances Tools
by Haleh Shahbazi 05 May '23

05 May '23

Hello, I am using ChimeraX under “version 1.6rc202304182023 (2023-04-18)” and contacting you regarding contacts and distances tools I am working on analyzing biological assembly PDB files including two chains. Simply, I want to identify / calculate distance between residues within each chain and across two chains separately – In the other word, display interchain and intrachain residue distance. To get that done, I’ve already explored “Distances” and “Contacts” tools under “Structure Analysis” but I have difficulty with identifying interchain residue distances and also understanding all those features / options provided. Thanks in advance for your support! Haleh HALEH SHAHBAZI PHD STUDENT @GARTON LAB • she/her • [Personal/Lab LinkedIn] <https://www.linkedin.com/in/haleh-shahbazi> IBME, University of Toronto haleh.shahbazi(a)mail.utoronto.ca<mailto:haleh.shahbazi@mail.utoronto.ca> www.gartonlab.org<http://www.gartonlab.org/> • bme.utoronto.ca<https://bme.utoronto.ca> • [LinkedIn] <https://www.linkedin.com/school/bme-uoft> [Twitter] <https://twitter.com/bme_uoft> [Instagram] <https://www.instagram.com/bme_uoft/> [signature_283494549]<https://bme.utoronto.ca/>

2 1

Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. Please pardon any inconvenience, --Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Re: [chimerax-users] Merging and covalently joining two pdb's together in chimeraX
by Elaine Meng 04 May '23

04 May '23

Hi Rayees, For the best chance at getting a good answer, we recommend sending ChimeraX questions to the chimerax-users list (CC'd here) unless you are including private data. If the two models are already positioned appropriately to form the bond, you could first combine them into a single model and then add a bond (e.g. "bond" command or Build Structure tool, Adjust Bonds section). <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> However, if you didn't necessarily put the models in the right place to form the bond, you can use "build join" which will include all of the following: moving one model to the appropriate position to form the bond, combining the models into one, and forming the bond. You cannot use "build join" if the models are already combined or if you don't want the models to move relative to each other. There is also a graphical interface to "build join," which is the Build Structure tool, Join Models section. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#join> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> You can open the Build Structure from the menu under Tools... Structure Editing. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> I don't know much about refinement, but sounds like you should take a look at the ISOLDE plugin for ChimeraX. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> <https://isolde.cimr.cam.ac.uk/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 4, 2023, at 11:24 AM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Elaine, > I am trying to merge two models (say #1 and #2) and join the two models with a covalent bond at amino acid residue number say 240 (#1)and 241 (#2). I first combined the two models (#1 and #2) using combine command. However, when I use build join command it does not seem to work. Is there a better way to covalently join two models in chimeraX? > > Also, is there a way to refine models in chimeraX like Real Space refine in Coot? > > Thanks > > Rayees

1 0

Info on ChimeraX
by Fabrizio Fierro 04 May '23

04 May '23

Hi, I work for a startup called Protai and I am interested in ChimeraX. 1) Are all the functions available in Chimera implemented also in ChimeraX? 2) Specifically, with Chimera it was easy to load, visualize and work with cryoEM maps. Does ChimeraX work in the same way? 3) Would it be possible to get a free trial period for ChimeraX? Thanks, Fabrizio Fierro.

2 2

Installing other python packages in chimeraX
by Shubham Devesh Ramgoolam 03 May '23

03 May '23

Dear ChimeraX team, I have some python scripts for performing computation using chimeraX in the nogui mode. Those scripts rely on packages not available in the python environment of chimeraX and I installed them using: ChimeraX-console.exe -m pip install add_package --user I intend to distribute my scripts to other users and they will also need to install these packages. As such, I have written another python script to automate the installation of these packages (the path to ChimeraX-console.exe (if Windows) or ChimeraX.exe (if Mac) must be supplied in a text file for this to work). The heart of the automation script is as follows: for item in list_packages: subprocess.call([path_chimeraX, '-m', 'pip', 'install', item, '--user']) Is this approach of installing python modules in chimeraX valid, considering that different users may have a different environment for their chimeraX? (I am worried that pip install might not work on some setups.) Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

3 2

Question about viewing chain pdb in ChimeraX
by Thu Nguyen 02 May '23

02 May '23

Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you. Best regards, Thu

2 2

Virtual Crash Course - Understanding PDBx/mmCIF | Tomorrow, May 3rd | REGISTER NOW!
by Brian Hudson 02 May '23

02 May '23

Virtual Crash Course The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT 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. The program: https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras… Free registration: https://go.rutgers.edu/u3vpwjet If you have questions, please contact Michelle Sanghera: msanghera(a)iqb.rutgers.edu

1 0

Plugin development: how to install python packages
by BARRY E DEZONIA 01 May '23

01 May '23

Hello, I am developing a chimerax plugin. My code will have some interaction with mdtraj. I need mdtraj to be installed in the python that ships with chimerax. I tried "chimerax -m pip install mdtraj" but I get all kinds of error dialogs popping up in the chimerax instance that gets launched during the installation. I terminate all the error dialogs and then exit chimerax (as the python install seems frozen) and then it indeed says installation has failed and gives unusual error messages (like setuptools was less than version 48.0.0 while chimerax reports it to be 65.x.y and even 66.x.y after upgrading). Can someone tell me the correct syntax to use to install mdtraj in chimerax's python? Thank you.

3 6