March 2021 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Map Coloring in ChimeraX
by Tom Goddard 05 Mar '21

05 Mar '21

Hi Jagannath, Here's a video showing how to use the ChimeraX color zone tool to color a cryoEM so each protein has a different color. https://youtu.be/zU3Xb6LRFco <https://youtu.be/zU3Xb6LRFco> Tom > On Mar 5, 2021, at 11:09 AM, Jagannath Maharana <jmbhu7(a)gmail.com> wrote: > > Dear Tom, > Greetings of the Day. I'm Jagannath, a PhD student, IIT Kanpur, India. I'm truly a fan of your program and it's amazing potential in creating beautiful illustrations. Specially the CryoEm maps. I had a query regarding that. I wanted to colour different domains differently in a single map. I've been trying hard for this but unable to figure it out. I'd really appreciate if you could extend your help regarding this. For your reference I've provided a picture. > > Looking forward to hearing from you > Best Regards > Jags. > PhD Student > GPCR biology lab > IIT kanpur, India > > > <Screenshot_2021-03-06-00-37-33-325_com.android.chrome.jpg>

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Re: [chimerax-users] trouble with importing chimerax module
by Tom Goddard 05 Mar '21

05 Mar '21

Hi Greg, ChimeraX like Chimera includes Python within the application. So the normal way to run a ChimeraX Python script is to just open it in ChimeraX for example with the open command "open myscript.py" or you can run ChimeraX from a shell without a graphical user interface and have it run the script chimerax --nogui myscript.py With Chimera there is a pychimera PyPi module (https://pypi.org/project/pychimera/ <https://pypi.org/project/pychimera/>) created by Jaime Rodriguez-Guerra outside our lab to use Chimera with your own Python 2 installation. There currently is not a PyPi module to use ChimeraX in your own Python 3. I made a ChimeraX PyPi module (a "wheel") a few months ago as a test but it only partly works and we have not released it. Various initializations in the ChimeraX code need to be fixed to work outside the ChimeraX application. We proposed doing that work in a grant application to Chan-Zuckerberg Initiative last month, their Visual Proteomics call for proposals (https://chanzuckerberg.com/rfa/visual-proteomics/ <https://chanzuckerberg.com/rfa/visual-proteomics/>). We will not know whether we get funding to pursue that until at least May 2021. Is it essential to your use of ChimeraX that you run Python scripts in your own Python? If so we could try to get something rigged up that would work for you. If the main issue is you need other PyPi packages that are not in ChimeraX for your Python scripts, you can install those packages easily into ChimeraX using chimerax -m pip install <NameOfPyPiPackage> Tom > >> On Mar 5, 2021, at 12:49 PM, Gregory Babbitt <gabsbi(a)rit.edu> wrote: >> >> Hi Dr. Meng >> >> Some of us at RIT are having trouble importing chimerax.core.commands to python3 so we can write a script to run things in chimerax. >> >> Does debian have it? I also noticed my pip list does not show the older chimera module even though we call it alot in python. Does it have a different name like midas or pychimera? >> >> What is chimeraX equivalent...how do we install it via pip/pip3? >> >> thx >> >> Greg B >> >> Dr. Gregory A Babbitt >> Associate Professor >> T.H. Gosnell School of Life Sciences >> Rochester Institute of Technology >> Rochester NY USA >> website: http://people.rit.edu/gabsbi >> >> > >

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chimera X troubles
by Dorian Armando Acevedo Castro 05 Mar '21

05 Mar '21

Good morning, I tried to install chimera X for Ubuntu 16 but I have the following problem. (base) da.acevedo10@colab14:~$ sudo apt-get install /home/UANDES/da.acevedo10/chimerax-daily.deb Reading package lists... Done Building dependency tree Reading state information... Done Note, selecting 'ucsf-chimerax-daily' instead of '/home/UANDES/da.acevedo10/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily : Depends: ffmpeg but it is not installable E: Unable to correct problems, you have held broken packages. I really appreciate if you can tell me why I can't install chimera x Cordialmente, Dorian Armando Acevedo Castro COBO - Computational Bio- Organic Chemistry Bogotá cobo.uniandes.edu.co<http://cobo.uniandes.edu.co/> Estudiante Doctorado Ciencias-Química. M. Sc. Química, U. de los Andes. Químico, U. Nacional. <mailto:daacevedoc@bt.unal.edu.co> <mailto:dorian.acevedo@gmail.com>

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An urgent question about Chimera (need help)
by 陆萌 05 Mar '21

05 Mar '21

Dear developers: I have always failed to minimize my structure in Chimera, even if I reinstalled my Chimera or tried another version of Chimera. I can not fix this bug by myself, so I have to ask for help to you. I'll appreciate very much if you can help me solve the problem. Thank you very much! Sincerely! Meng Lu 2021.3.5

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Attribute files in ChimeraX
by David Leeming 04 Mar '21

04 Mar '21

Dear ChimeraX users, I'm trying to write a script that will export an attribute file in ChimeraX, (specifically the attribute sasa) I'm looking for a similar output to that of the attribute calculator function in Chimera (see image below) [cid:9fd01eec-1765-4ec9-8172-dec4315fa1d6] I'm currently trying to run the command below to export the attribute file: [cid:6e286ca4-a133-49bc-a34e-1a2f39bb7243] However, when I run this script, it produces the error: "No known data format for file suffix '.defattr'" Any advice on how I can better go about producing this file or how I can modify my script to prevent this error would be greatly appreciated. Thank you for your time. Kind regards, David

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Re: [chimerax-users] How to expand the RAN in ChimeraX?
by Tom Goddard 03 Mar '21

03 Mar '21

Hi Andrea, The volume command dataCacheSize option will do this. For example for 32 Gbytes of memory cache for volume data use command volume dataCacheSize 32000 The default is to set it to half the physical memory of the computer. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#sampling> I would not suggest changing it because surface and image rendering typically use an amount memory for the graphics similar to the data size. The cache is only for the volume data, so with graphics, the current setting can utilize all your memory. Increasing it can cause data to be paged out to disk with horrible performance. The above setting is not saved. If you did want to change it for every ChimeraX session you would use Preferences / Startup / Execute these commands at startup. Tom > On Mar 3, 2021, at 9:04 AM, Andrea Fera <andrea.fera(a)revealgc.com> wrote: > > Dear Mr. Goddard, > > This is Andrea. I am not sure that you remember me, but we met in 2013 or so in S. Francisco and Berkeley. > > I am a strenuous fan of your software! Especially for volume rendering of cryo-type tomograms. > I do have a tomogram pf a few Gb that I would like to render with your software. I use a Lynux server with LOTS of RAM. How can I increase the RAM allocated by ChimeraX? > > Thank you and all best… > Andrea Fera > > -- > Andrea Fera, PhD > Senior Data Scientist > <image003.jpg>

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Accessing shapes created through a .BLD script
by Tanmoy Sanyal 03 Mar '21

03 Mar '21

Hi, I have a bunch of shapes (spheres and cylinders) created through a .bld script. I'd like to load this script once, and then be able to change the colors of said shapes in successive operations. It is possible to set the colors directly in the .bld script, but I need to make an animation out of this. E.g: if my .bld script contains lines that draws shapes like so: .sphere 0 0 -1 5.0 .cylinder 0 0 0 1 1 1 1.0 I want to be able to later have a bunch of scripts called 1.cxc, 2.cxc, 3.cxc, .... each of which change the color of the sphere and cylinder. This way, I can load these scripts in the per-frame mode, to create an animation out of the color changes. Alternatively, I tried doing this with just the shape command and without a .bld script, but I have over ~10000 shapes; the shape command interprets each as a different model, and my computer hangs. ----- Thanks, Tanmoy Tanmoy Sanyal Postdoctoral scholar, Sali lab <https://salilab.org/>, Department of Bioengineering and Therapeutic Sciences <https://bts.ucsf.edu/>, University of California San Francisco Phone:- (+1) 805-637-0375

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Help with surfaces
by Eoin Winston 02 Mar '21

02 Mar '21

Hello, I create molecular animations and use ChimeraX to import PDB files and convert them to surfaces which I then export for use in Autodesk 3dsmax. I have a very limited understanding of this fantastic software however I am wondering if there is a quick way to solve my problem. I have a PDB file I was sent containing a trimer. When I use a command such as: *molmap #13,1 20 *(I found this on a YouTube video BTW) It creates a surface model of the entire PDB file. How do I create separate surface models for each of the trimers? So the PDB exports with three meshes as opposed to a single mesh. Hope that makes sense. Best regards, Eoin *Eoin Winston, *Head of Design *Phone:* +353 877991603 | Email <eoin(a)nexucreative.com> | Web <http://www.nexucreative.com/> | Instagram <https://www.instagram.com/NEXU.creative/> | Twitter <https://twitter.com/NEXU_Science> Raptech Ltd. t/a *NEXU* Science Communication is registered in Ireland as a private company limited by shares. Registration No. 610585. Registered business address: 3 Mruigtuaithe, Ratoath, County Meath, Ireland. A85 Y883

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ChimeraX-users March 2021