July 2022 - ChimeraX-users - RBVI Mailing Lists

ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Export list of contacts
by Asmahan Alghamdi 12 Sep '22

12 Sep '22

Dear Chimerax team, Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online. Your help would be much appreciated in this respect. Thanks in advance Asmahan Alghamdi The university of Nottingham Get Outlook for iOS<https://aka.ms/o0ukef> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

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Superposing protein structures
by Alicia Gardiol 01 Aug '22

01 Aug '22

We have experimental protein structures in PDB, and Alpha Fold predicted structures. Which is the best software to superpose these structures using a MAC computer. - Two different predicted proteins (predicted 1 to predicted 2) and - Same protein predicted and experimental (predicted 1 to experimental 1) Thank you and best wishes. Alicia Gardiol, PhD

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Reduce figure size for export for publication
by Fossati, Andrea 01 Aug '22

01 Aug '22

Hi, How to best export figure at high-ish resolution to then add it to an already made illustrator panel? After some googling seems vector-based export is not possible so what is the recommended format and which resolution is best for 3x3 inch illustrator panel? At the moment I am exporting as TIFF with transparent background and size 5000 and supersampled 4 times to keep high res but the file has like 15Mb per structure which is not feasible/handy to modify. What is the suggested solution for paper figures? Best, Andrea Fossati, Ph.D Krogan Lab

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How to estimate 2dlabels fading?
by Edoardo D Imprima 01 Aug '22

01 Aug '22

Hi, Could you please explain more how the frames option works when changing 2dlabels? Let’s say I have 100 frames and I wish to have an arrow to appear at frame 10 for 5 frames? 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

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Side view in command line
by HONG ZHAN 31 Jul '22

31 Jul '22

Hi all, I would like to setup a movie sequence using cxc file. It is very useful to setup in the UI window, however, any tricks could I use to set the clip plane in the command line to generate a view as in the attached picture? So that I can run my cxc file together with other actions? Many thanks! Hong [cid:12317B70-9FE5-4C25-933C-E56EF2888E9D]

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ChimeraX on Mac
by Lisa Käshammer 30 Jul '22

30 Jul '22

Dear developers, I have problems to get chimeraX to work on my computer. It had a previous version installed (1.1) which did not work anymore. So I removed that version and installed the newest version, however, it does not open. There is no error message so I am a bit lost at what I can do to resolve this issue. The macOS is 10.15.7. Thank you very much in advance. Best, Lisa

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command inquary
by Kwangjun Lee 29 Jul '22

29 Jul '22

Hello, Do you have any command that displays a selected region only? For example, I have a protein structure AA1 to AA300. I only want to display AA100 to AA200. Thanks!

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Re-scaling maps
by Nebojsa Bogdanovic 29 Jul '22

29 Jul '22

Hello, I have two maps. One from cryosparc @ 1.06 A/pix and another EM-gan sharpened map @ 1.0 A/pix. They are different in size upon visual inspection in chimeraX so I tried relion_image_handler --i cryosparc.mrc --angpix 1.0 --rescale_angpix 1.06 --o cryosparc-rescaled.mrc however, the resulting map is still smaller than the original input. I also tried to rescale in this way to several different angpix values but maps are still not the same. Is there any command in chimeraX or chimera to play with pix sizes to find the right one? Thank You and regards, Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Application to enter the chimeraX user's group
by Xiaofeng CHU 28 Jul '22

28 Jul '22

Dear chimeraX team Sorry for the interruption. My name's Xiaofeng Chu, the phd candidate in Misha Kudryashev's group working on cryoET and structural biology. Could you please help me to enter the group of chimeraX users? So I can raise some questions about how to use it. Thank you very much in advance! And have a nice day. Best regards Xiaofeng -- Xiaofeng Chu (he/him) Ph.D. candidate in M. Kudryashev's research group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association 13125 Berlin, Germany

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ChimeraX-users July 2022