July 2020 - ChimeraX-users - RBVI Mailing Lists

Can I get atomic coordinates from an electron density map in xplor format via ChimeraX software?
by 王超 28 Jul '20

28 Jul '20

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Interfaces
by Reza Khayat 28 Jul '20

28 Jul '20

?Hi, Is it possible to save the image generated with residue plot from command interfaces? I can use screen capture to do this, but an internal save would keep the images a constant size. Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Clip surface but not atoms
by Pufall, Miles A 27 Jul '20

27 Jul '20

Hi! I’ve used Chimera for years (though not recently) and am switching to ChimeraX. I’m looking to display the ligand binding pocket with the ligand, and the tutorial you have is great. I generated this picture, which is really close to what I want. It shows the ligand, and the pocket, and I’m able to slice it with the interactive side view tool to get to this point. However, the left side of the ligand is slightly clipped. I’ve played with rotation and with moving the slice plane, but can’t find an orientation that shows the pocket so nicely (without any surface in the foreground) and not ligand clipping. My question is: is there a way to tell ChimeraX to clip the surface but not the ligand? Thanks! Miles [cid:9F2E9E3C-2209-4033-98F8-C1726F0DFD85@dynamic.uiowa.edu] ________________________________ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only for the use of the individual or entity to which it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify the sender immediately and delete or destroy all copies of the original message and attachments thereto. Email sent to or from UI Health Care may be retained as required by law or regulation. Thank you. ________________________________

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Alternate locations
by Jeschke Gunnar 27 Jul '20

27 Jul '20

Hi ChimeraX team, very nice program and remote control scheme! Clear thinking, cool implementation. My question/suggestion is about alternate atom locations. ChimeraX knows about them. I load 1lcd info atoms /A:8@NE2 attribute alt_locs correctly responds: atom id /A:8@NE2 alt_locs A,B When I show /A:8@NE2 or I show /A:8 as sticks, only location A is displayed. When I retrieve atom coordinates, only location A is returned. Could you implement full handling of alternate locations (or am I doing something wrong here? I really tried a lot to find location B). Kind regards Gunnar --- Der Schlaf der Vernunft gebiert Ungeheuer - Francisco Goya Prof. Dr. Gunnar Jeschke ETH Zurich Department of Chemistry and Applied Biosciences Vladimir-Prelog-Weg 2 CH-8093 Zurich Switzerland www.epr.ethz.ch

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surface colouring by selected residues
by Oleksiy Kovtun 27 Jul '20

27 Jul '20

Dear ChimeraX community, I need to colour the surface by selected side chains to highlight an intermolecular contact. The command sequence: #select atoms on the buried surface. The selection works correctly: measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true #make a surface. A new surface #10.1 is generated: surface #10/C resolution 7 #color surface yellow at selected residues. color #10 & sel yellow target s The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution. Where is a mistake in the colouring approach? I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04. Thank you and best regards. Oleksiy Dr Oleksiy Kovtun Research Fellow Briggs group MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Tel: + 44 1223 267551 Email: okovtun(a)mrc-lmb.cam.ac.uk

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Cleanest Way to Install Daily Build
by Anderson, Jacob 24 Jul '20

24 Jul '20

Just wanted to reach out to see if there is a clean way to replace one's current ChimeraX with the daily-build (specifically Ubuntu). Is it best to uninstall/the prior and just install the desired version? Thank you for any thoughts! ~jacob

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CryoET map problems
by Andrea Dallapè 21 Jul '20

21 Jul '20

Hi, I have an EM map -from a cryoET experiment- and I would like to use ChimeraX in order to fit the protein -the ribosome, in this case- in such EM map. I don't understand why the PDB of the ribosome I open in ChimeraX is far bigger than the EM map I have, and I don't really know how to resize them in order to have a fittable model. Could you suggest me a solution? Thank you for your help and attention, Andrea

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How to set RGB color for user selected atoms?
by Donovan Chin 17 Jul '20

17 Jul '20

Hi How do i set RGB colors for user-selected atoms? Or for custom atom selections? Cmd line? Regards -D Donovan Chin | Director of Computational Drug Discovery | +1 617 899 5333 | dchin(a)arrakistx.com<mailto:dchin@arrakistx.com> Disclaimer The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful. This email has been scanned for viruses and malware.

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Bond between two sequential residues
by Derek Harris 17 Jul '20

17 Jul '20

Hello, When I hide the backbone and choose to show side chain and base any sequential residues shown have a small line between the CA's. I can select them, but not delete them or hide them as an atom or bond, only hide sel, but when the selection they are a part of is hidden and reshown they reappear. I can also assign them as a selector and hide/show them, but also as soon as I hide and reshow the selection they are a part of they reappear and the designated selector for them is gone from the list. I want to retain the side chain and base appearance but lose these lines permanently. Any help would be appreciated. Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

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About "color by RMSD "
by Dr.Jason 17 Jul '20

17 Jul '20

Dear Chiemra X team: Briefly, I want to ask you how to color a protein structure by RMSD in chimera X, after done matchmaker of two structures ? I know chimera can do this job, but I did’t find the equivalent function in chimera X. Allen Wu Allenwu1991(a)163.com Chengdu. China

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