August 2023 - ChimeraX-users - RBVI Mailing Lists

Regarding use of attribute assignment files and difference between ChimeraX and ChimeraX daily build
by SUHANI BHATTACHARYYA 23 Aug '23

23 Aug '23

Dear Team Chimera, I am a second-year undergraduate student at IISER, Pune. I have been using ChimeraX for some time. Earlier I have also used some older Chimera versions. They had the kdHydrophobicity under Render by Attribute for residues. However, ChimeraX does not. On reporting a problem, I was told to use attribute assignment files for kdHydrophobicity. I downloaded the file as .txt file with .defattr suffix. Then, following the instructions in the user guide, I tried to use the open command to start using the attribute file. But I was shown an error that no such file existed. I even changed the file location and checked with multiple directories, including where ChimeraX files are stored on my PC to try to open the file, but nothing has worked. Kindly provide clearer instructions on where to save and open the attribute assignment files. Thank you. Regards, Suhani Bhattacharyya

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Fwd: Help with ChimeraX and 3D printing
by Elaine Meng 23 Aug '23

23 Aug '23

Dear Billy, Please use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> mailing list to ask ChimeraX questions (CC'd here so you don't need to re-send) -- I am not sure of the answer, and others on the list have more expertise in this area. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: "Dye, Billy" <Billy.Dye(a)volstate.edu> > Subject: Help with ChimeraX and 3D printing > Date: August 23, 2023 at 8:31:21 AM PDT > To: "meng(a)cgl.ucsf.edu" <meng(a)cgl.ucsf.edu> > > Hello > > I hope you might give some advice on using ChimeraX with dual extrusion 3D printing. > > I have been using ChimeraX to generate STL files for 3D printing models of a variety of protein structures that I use in my biology classes. I recently acquired a dual extrusion printer which should allow me to print models in two different colors. For example, I am currently trying to print a nucleosome from RCSB model 7PFX such that the DNA is printed blue from one extruder and the histones white from the second extruder. I am exporting two different STL files from ChimeraX, one with the DNA and one with the histones, and I am attempting to slice with FlashPrint 5 software for a FlashForge Creator Pro 2 printer. However, when I import the two STL files into the slicing software, they are not aligned. Even if I position both at 0,0,0 coordinates, it is obvious that the DNA and histones are not lining up properly. Is there a way to export the two STL files from ChimeraX such that they have a common reference point or origin and will thus align with one another when both are placed into the slicing software? > > Many thanks for your consideration and advice, > Billy Dye > > > >

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Regarding probeRadius
by Sakiat　Hossain 23 Aug '23

23 Aug '23

Dear Sir/Madam, Greetings. I am a nanomaterial chemist, and I would like to measure solvent accessible surface area (sasa) of my metal nanocluster using its single crystal x-ray diffraction structure. Specifically, I want to calculate H+ accessible surface area. I would appreciate it if you kindly let me know how to change probeRadius for calculating sasa in ChimeraX. I look forward to your kind help. Best, Sakia Hossain Tokyo University of Science, Japan Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Trackpad rotation
by Oliver Clarke 23 Aug '23

23 Aug '23

Hi, The trackpad zoom/rotation settings in ChimeraX seem very different from “old” Chimera. Is there any way to replicate the behavior from Chimera? Specifically, when I pinch to zoom in ChimeraX, I often find the view rotating a lot, unless I am very careful, which does not happen in Chimera. I have tried playing around with the trackpad twist sensitivity, but so far have been unable to find settings similar to the default in Chimera. Cheers Oli

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ChimeraX registration
by Rouzer, Carol A 21 Aug '23

21 Aug '23

To Anyone who can help: I recently downloaded ChimeraX after many years of using Chimera. I keep getting the following warning message: Registration file '/Users/carol/Library/Application Support/ChimeraX/registration' has expired I assume this means I should re-register, but I can’t find any mechanism to do that. Sorry for my stupidity, but I do want to be using the software legitimately. Please instruct. Thanks, Carol Carol A. Rouzer, Ph.D., M.D. Senior Editor/Writer A.B. Hancock Memorial Laboratory for Cancer Research Basic Sciences, School of Medicine Vanderbilt University Nashville, TN 37232-0146 c.rouzer(a)vanderbilt.edu<mailto:c.rouzer@vanderbilt.edu>

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Installation of chimera failing
by Royan, Santana (Manufacturing, Clayton) 20 Aug '23

20 Aug '23

Hi there, I'm having trouble installing chimera on my work windows laptop for the IUCR2023 Phenix workshop. The installation keeps failing due to being unable to create the directory in the C drive (see screenshot). [cid:image003.jpg@01D9D3B7.892B9130] My organisation does restrict administrator rights on this laptop and requires me to apply for it for a limited period of time, but I have enabled these before starting the installation. I note that the installer didn't ask for admin access when installing here on this computer before the License Agreement, but it did on my personal laptop which proceeded with the installation just fine. Am I missing something with the installation package? This is happening for both the daily build executable and the 1.6.1 build. Regards, Santana Santana Royan CERC Fellow in Optimising Biodegradation of Plastics MCM Manufacturing | CSIRO santana.royan(a)csiro.au<mailto:santana.royan@csiro.au> | 03 9662 7107 Building 201 Level 2, Research Way, Clayton VIC 3128 CSIRO acknowledges the Traditional Owners of the land, sea and waters, of the area that we live and work on across Australia. We acknowledge their continuing connection to their culture and we pay our respects to their Elders past and present. CSIRO Australia's National Science Agency | csiro.au<www.csiro.au>

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Difficulty docking proteins
by Weidenbach, Megan 18 Aug '23

18 Aug '23

Hi there, My name is Megan Weidenbach and I am a user of the ChimeraX software. We have been trying to dock built organic molecules to coagulant factor proteins. So far, we have had no luck with the AutoDock Vina feature. This has been tested on the mac and microsoft versions of the software. I was wondering if your team might be able to point us in the direction of some resources that could help dock the proteins and identify their binding sites? Thank you! Megan L. Weidenbach B.A. Biology & Pre-Veterinary Studies meganweidenbach(a)myunt.edu University of North Texas [cid:c8b6bc7f-58c7-4404-8b08-46a6fb60aca9]

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Plugin development questions
by BARRY E DEZONIA 18 Aug '23

18 Aug '23

Hello, I have been developing a plugin in bits and pieces for a while. I am now hoping to build a bundle (or whatever) to make installation pretty seamless. My program is a bit unconventional so I have a few questions on how to proceed. My plugin templating copies one of the examples (maybe the Tool example). My plugin uses a couple of python packages/modules: * mdtraj (https://mdtraj.org/1.9.3/installation.html) * traj2nmr (https://github.com/weberdak/traj2nmr) It also will have some shell scripts I want to include and also a java program. So far we have been getting by installing things like this: * in chimerax using the command prompt entering "pip install mdtraj" or similar * from an OS terminal invoking chimerax's version of python to run traj2nmr's setup.py program so that it goes into chimerax's python's installed packages * including our shell scripts in a Runnable directory under the plugin installation directory (during development) and copying them in a similar directory under the ~/.local/share/....chimerax-path-stuf.../the-plugins-Runnable-dir. Maybe the plugin installation process does this for me already but it is often not showing the latest changes even after plenty of "dev installs" in the chimerax command prompt line. * I am just starting to want to place the java app and the shell script that launches it somewhere. Hopefully in that same Runnable directory. Right now, I am trying to learn what is the best approach to bundle this all together and have a simple installation process. Can someone advise a bit? Thanks.

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Is there a python module to access ChimeraX from outside with Python?
by Jonathan David Karl Krahl 17 Aug '23

17 Aug '23

Good morning, my name is Yona and I am working at the chair of Computational BioEngineering at the Technical University in Dortmund, Germany. I was wondering, if there is a possibility to access ChimeraX from outside with Python; the module "pychimera" provides an API for Python and Chimera, but not ChimeraX, as far as I know. Do you know an alternative or a way to do it? Thanks for your help :) Yona

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info retrieval
by Eduardo Mauricio Martin 17 Aug '23

17 Aug '23

To whom it may concern: According to the documentation sequences infor from a model can be retrieved by the following command: info polymers #1 saveFile "C:\Users\faits\Documents\test8.txt" Though the console keeps throwing the following error attached as image. [cid:image002.png@01D9D083.452CFE10] I just need to retrieve the residue number for each subunit to run a Python script that removes sasa values from hetatm which are not in the protein per se. If there is a work around to acquiere this inforation in a file please let me know. Kind regards, Eduardo M Martin PhD Candidate Information systems Department Autonomous University of Aguascalientes. Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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