- ChimeraX-users - RBVI Mailing Lists

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

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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

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The ChimeraX Toolshed is temporarily down
by Greg Couch 17 Jun '22

17 Jun '22

Due to database corruption. Hope to have it back up soon. -- Greg

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ChimeraX: chashes in no-gui execution
by Enrico Martinez 17 Jun '22

17 Jun '22

Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script. Here is an example of my script that calculates hbonds and contacts between protein and ligand open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico

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Centos7 version of ChimeraX version 1.4 possible?
by Martin Moche 16 Jun '22

16 Jun '22

Dear ChimeraX developers, Thanks for an outstanding piece of software! Is it possible to have a CentOS7 variant of version 1.4 of ChimeraX? Best regards, Martin Head of Macromolecular X-ray Crystallography<https://ki.se/en/mbb/psf-mx> | Protein Science Facility<https://ki.se/en/mbb/protein-science-facility> Medical Biochemistry and Biophysics<https://ki.se/en/mbb/department-of-medical-biochemistry-and-biophysics> 171 65 Solna | Solnavägen 9 +46 8 524 868 43 | +46 73 322 93 27 martin.moche(a)ki.se<mailto:martin.moche@ki.se> | ki.se<https://ki.se/> ______________________________________ Karolinska Institutet - a medical university När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy>. Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI's processing of personal data here<https://ki.se/en/staff/data-protection-policy>.

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ChimeraX 1.4
by Eric Pettersen 10 Jun '22

10 Jun '22

UCSF ChimeraX version 1.4 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/ This will be the last release to support macOS 10.14 (Mojave). Also, ChimeraX 1.4 is not available for CentOS 7, Ubuntu 16.04 and 18.04 because the Qt 6 window toolkit does not support those older Linux distributions. Updates since version 1.3 (Dec 2021) include: - search/retrieve from EBI AlphaFold DB 3rd release, ~1 million structures - display AlphaFold predicted aligned error (PAE) plots - can BLAST UniRef100,90,50 (+ previous choices AlphaFold, PDB, NR) - AlphaFold prediction of multimers (of limited size) on Google Colab - independent centers of rotation available as mouse mode - join models with Build Structure tool or command - define axes for display and/or use in measurements - increase/decrease VDW radii relative to their current values - switch PDB residue numbering scheme (author/canonical/uniprot) - align sequences with Clustal Omega or MUSCLE - calculate % identity in sequence alignments - window toolkit updated to Qt 6.2.3 from 5.15.2 For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Saving PDB file as a string
by Sophie Liu 08 Jun '22

08 Jun '22

Hi, My organization has some extra information at the end of a PDB file that I would like to be printed onto the Log Console of ChimeraX. I am currently writing a bundle to do so by adding a command (however if this is best implemented by overriding the open command for PDB files then I would switch to that). I am wondering how I can have the bundle work like so: 1. the user types a command call it, "showdata" 2. the bundle would read all Models (that are pdb files) that are being displayed 3. for each model it would read the PDB text file, and say go to indices 200-251 of the string and display that in the Log console I hope this makes sense. I am mainly struggling on how to access the original PDB text of the model. Best, Sophie

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Licensed software source
by Jeya Priya Senthilkumaran 07 Jun '22

07 Jun '22

Hi Community, To use ChimeraX licensed software. I have few queries Do we have a separate source {tar file} to be downloaded or the same source from https://www.cgl.ucsf.edu/chimerax/download.html should be used? While purchasing the license, will we be provided with separate source to download the software? We have bought license, now we need to upgrade to newer version of ChimeraX ,do we have instructions to upgrade to the newer version? In case, we have installed open source of the software, how should we upload the license to the ChimeraX? Kind Regards, Jeya Priya Scientific Cloud Computing [cid:image001.png@01D874F0.89D1F100]<https://www.zifornd.com/> [cid:image002.png@01D874F0.89D1F100] M +91 8098223555 [cid:image003.png@01D874F0.89D1F100] www.zifornd.com<http://www.zifornd.com/> [cid:image004.png@01D874F0.89D1F100] IST (Time Zone) [cid:image005.png@01D874F0.89D1F100] Follow us on [cid:image006.png@01D874F0.89D1F100]<https://www.linkedin.com/company/zifo-technologies/> ******************* CAUTION ******************* This e-mail is intended exclusively for the individual(s) to whom it is addressed and may contain information that is PRIVILEGED and CONFIDENTIAL. If you are not the intended recipient, please notify the sender and delete the original message. Further, you are not to copy, disclose or disseminate this e-mail or the information contained to any other person and any such actions are unlawful. Zifo Technologies has taken every reasonable precaution to ensure that this e-mail and attachment(s) has been swept for viruses, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment(s). Zifo Technologies is neither liable for the proper and complete transmission of the information contained in this e-mail nor for any delay in its receipt. *************************************************

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Save the map after surface dust
by Dai, Xin 07 Jun '22

07 Jun '22

Dear ChimeraX developers, I'm trying to save a density map following the command "surface dust". However, the map saved remains to be the original one. Is there any command to save the cleaned map? I found this old post http://www.cgl.ucsf.edu/pipermail/chimera-dev/2015/001263.html asking the same question using Chimera. But unfortunately, it's not working for me. Thank you, Xin

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Analog of Chimera "addcharges" command in ChimeraX
by Rafi Brent 06 Jun '22

06 Jun '22

To whom it may concern, I have about 20,000 pdb files to which I'd like to add Hydrogens, add partial charges, and convert to the mol2 format using either Chimera or ChimeraX. I have not had much success with Chimera, as the process slows down quite drastically over time when run through the GUI, and when I run Chimera from the terminal (using chimera --nogui python_script.py), I run into errors with ANTECHAMBER that do not occur when my script is run through the GUI. I'll write to the Chimera support email with more details, and I'd appreciate any advice if you have any, but based on these errors I'm thinking that there is likely a better way to perform this task using ChimeraX. I noticed that the "addcharges" command no longer exists in ChimeraX, and the "write" command which I was using to convert to mol2 files in Chimera appears to have been replaced as well. Because of this, any recommendations about how to run my operation using the closest analogs to the original Chimera methods would be greatly appreciated. Thanks so much for any advice you may have. Sincerely, Rafi Brent

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