June 2022 - ChimeraX-users - RBVI Mailing Lists

Pymol view
by Rechiche, Othman 24 Jun '22

24 Jun '22

Hi everyone, Is there a way to import/open “views” set with PyMol and open them in Chimera or ChimeraX? Best Regards, Othman

3 7

How to gradually crop a volume with perframe command
by Edoardo D Imprima 24 Jun '22

24 Jun '22

Hi all, I would like to make a movie showing a volume gradually cropped along one axis .e.g. volume #1 region 0,0,0,410,375,336 (start) volume #3 region 0,0,0,410,375,31 (end). Could you please tell me how to provide the range in “perframe” command to perform this operation? Ie as trying something like this perframe "volume #1 region $1" 0,0,0,410,375,200 0,0,0,410,375,336 frames 10 without success though. Many thanks in advance, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

2 1

user inputs for python scripts
by Pranav Shah 24 Jun '22

24 Jun '22

Hi Team, Is there a way to provide user input to python script files? I tried using sys.argv but I keep getting an out of list error message when I call the script from the ipython shell (accessed from within the chimeraX window) Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 2

Version 1.4 for CentOS 7?
by Ricardo Righetto 24 Jun '22

24 Jun '22

Hi, First, apologies if this has already been announced elsewhere. I see on the download webpage that there is no production release for CentOS 7 and the latest daily release for this platform was built on 2022-05-06. Any chance we could get a production release of 1.4 and/or a newer daily build for CentOS 7? Thank you very much! Best wishes, -- Ricardo Diogo Righetto

5 8

How to show fib-sem tomography data as solid volume
by Edoardo D Imprima 23 Jun '22

23 Jun '22

Hello, Could you please tell me how to display fib-sem tomography data as a compact volume that can be navigated by sliding planes? The data consists of a series of frames that I can convert as .mrc volume or .mrcs stack. I attach a snapshot taken from a review that illustrates (middle panel) the visualisation I would like to obtain. The medical-image panel in ChimeraX is very handy however, the “full” option shows the volume while I need to display the planes of each side to slice through them. Looking forward to your feedback, Best wishes, Edoardo ------------------------------------------------------ Dr. Edoardo D'Imprima Postdoctoral fellow Structural and Computational Biology Unit EMBL Heidelberg - Mahamid Group Meyerhofstraße 1 69117 Heidelberg Germany Phone: +49 6221 387-8531

4 7

where can I find the mesh option in chimeraX?
by 王超 23 Jun '22

23 Jun '22

Dear All,I want to setting the mesh option in ChimeraX like "Chimera way".Like "open Volume Viewer of a map, and click features-data display option".but I cannot find toolbar of Volume Viewer, I am puzzle where to find it?

2 4

Chimera question
by Daniel VillanuevaAvalos 23 Jun '22

23 Jun '22

Hello, I am trying to create a spirosome, and I am entering *sym #1 h,56.5,164.4,12* but the radius of the helix is wrong. How can I change it? What I am trying to do is move my obj closer to origin but I cannot find a way to do that. I can only move the pivot to center with *cofr 0,0,0*. Thank you, Daniel.

2 4

quality of life imporovement suggestion for view matrix output
by Pranav Shah 22 Jun '22

22 Jun '22

Hi Team, I use the view matrix command regularly to save orientation of the maps/models in a command file. As it currently stands, the output needs to be formatted appropriately so that the command can be run. As a one off, it is trivial to format the output from the log window into an appropriate format but, when it has to be done repeatedly as is my case it becomes quite annoying. Therefore, I was wondering if you would agree to format the output so that it can be directly copy pasted in a ready to use format? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 3

alphafold in Google colab
by Roberto Marabini 20 Jun '22

20 Jun '22

Hi, Starting today, when I try to execute AlphaFold calculations using Google Colab, I get the message: ====== ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. kapre 0.3.7 requires tensorflow>=2.0.0, which is not installed. xarray-einstats 0.2.2 requires numpy>=1.21, but you have numpy 1.19.5 which is incompatible. datascience 0.10.6 requires folium==0.2.1, but you have folium 0.8.3 which is incompatible. albumentations 0.1.12 requires imgaug<0.2.7,>=0.2.5, but you have imgaug 0.2.9 which is incompatible. Successfully installed absl-py-0.13.0 biopython-1.79 chex-0.0.7 dm-haiku-0.0.4 dm-tree-0.1.6 docker-5.0.0 flatbuffers-1.12 gast-0.4.0 grpcio-1.34.1 immutabledict-2.0.0 jax-0.2.14 keras-nightly-2.5.0.dev2021032900 ml-collections-0.1.0 numpy-1.19.5 pandas-1.3.4 scipy-1.7.0 tensorflow-cpu-2.5.0 tensorflow-estimator-2.5.0 typing-extensions-3.7.4.3 websocket-client-1.3.3 wrapt-1.12.1 + pip3 install --upgrade jaxlib==0.3.2+cuda11.cudnn82 -f https://storage.googleapis.com/jax-releases/jax_releases.html Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/ Looking in links: https://storage.googleapis.com/jax-releases/jax_releases.html ERROR: Could not find a version that satisfies the requirement jaxlib==0.3.2+cuda11.cudnn82 (from versions: 0.1.23, 0.1.29, 0.1.32, 0.1.40, 0.1.41, 0.1.42, 0.1.43, 0.1.44, 0.1.46, 0.1.50, 0.1.51, 0.1.52, 0.1.55, 0.1.56, 0.1.57, 0.1.58, 0.1.59, 0.1.60, 0.1.61, 0.1.62, 0.1.63, 0.1.64, 0.1.65, 0.1.66, 0.1.67, 0.1.68, 0.1.69, 0.1.70, 0.1.71, 0.1.72, 0.1.73, 0.1.74, 0.1.75, 0.1.76, 0.3.0, 0.3.2, 0.3.5, 0.3.7, 0.3.8, 0.3.10) ERROR: No matching distribution found for jaxlib==0.3.2+cuda11.cudnn82 ======= The error seems to be obvious but, can someone point me towards a solution? Thanks Roberto

3 2

Research associate / Group leader position at the University of Luebeck (Northern Germany)
by Guido Hansen 20 Jun '22

20 Jun '22

The Institute of Biochemistry (Director: Univ.-Prof. Dr. Thomas Krey) at the University of Luebeck has an opening for a position as a *Research associate / Group leader (m/w/d)* in full-time (currently 38.7 hours per week) for an initial period of 4 years. Within the position, the opportunity for further qualification (habilitation) is given. *Main areas of activity:* * Own research (incl. acquisition of third-party funding) on topics in structural infectiology * Supervision of technical assistants, bachelor, master and doctoral theses * Co-responsibility for the cryo-electron microscope planned at the site * Organisation and implementation of teaching (in English) in biochemistry for the Molecular Life Sciences programme (lectures, practicals, seminars, performance review and booking, preparation of certificates) * Participation in teaching (in German) in biochemistry for medical students (lectures, practicals, seminars and their performance review and booking) *Requirements:* * Completed university degree in a natural science or medical programme, e.g. biochemistry, molecular life sciences, chemistry or biology. * Completed or nearly completed PhD thesis in natural sciences (defense in 2022), preferably in the field of structural infectiology * Proven research focus in the field of structural infectiology * Experience in the field of cryo-electron microscopy * Experience in teaching natural sciences and/or human medicine (in German and English) More information can be found here https://www.biochem.uni-luebeck.de/fileadmin/files/pdf/Ausschreibung1043-22… Please contact Prof. Dr. Thomas Krey (krey(a)biochemie.uni-luebeck.de) for any further questions, and send your written application with the usual documents (cover letter with research interests, curriculum vitae, references) summarised in a single PDF document by July 4^th , 2022 (*date of receipt*) at the latest to*bewerbung(a)uni-luebeck.de*, quoting the reference number*1043/22*. Best wishes Thomas *Prof. Dr. Thomas Krey* University of Luebeck *University of Lübeck Institute of Biochemistry* phone: +49-451-3101-3100 fax: +49-451-3101-3104 e-mail: krey(a)biochem.uni-luebeck.de <mailto:krey@biochem.uni-luebeck.de> www.biochem.uni-luebeck.de <http://www.biochem.uni-luebeck.de> Ratzeburger Allee 160 23562 Lübeck Germany -- Re: email signature

1 0

ChimeraX-users June 2022