July 2020 - ChimeraX-users - RBVI Mailing Lists

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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Re: [chimerax-users] Using Vive controllers with webcam function in ChimeraX
by Tom Goddard 15 Jul '20

15 Jul '20

Hi Józef, The Vive controllers only work in VR mode. You could enable VR mode and just not put on the headset. The "vr roomCamera" command would allow showing the molecular graphics in the desktop window from a specific position which you would want to match your webcam's physical position in the VR space. And you will want to match the vr roomCamera field of view to the field of view of the webcam. Then you will have several problems. First, the hand controller cones won't line up perfectly with the video of the hand controllers -- there will be unpleasant lag. And without the VR headset on it will be very challenging to point at things. But you might as well put on the VR headset to solve that. Then it should work -- you can use the VR with webcam AR. This is just what I did with VR plus a depth sensing camera except that the depth camera also can blend the depth correctly. Tom > On Jul 15, 2020, at 12:22 PM, Lewandowski, Jozef <J.R.Lewandowski(a)warwick.ac.uk <mailto:J.R.Lewandowski@warwick.ac.uk>> wrote: > > Hi Tom, > > Would it be possible to use Vive controllers without going into the vr mode but rather during the webcam session? > > Thanks, > Józef > > ------------------------------------------------------------------------------------------------------ > Józef R. Lewandowski > Professor | Department of Chemistry | University of Warwick <http://www2.warwick.ac.uk/> > j.r.lewandowski(a)warwick.ac.uk <mailto:j.r.lewandowski@warwick.ac.uk> | External: +44 (0) 24 76151355 | Internal: 51355 > Millburn House: F07 | Coventry CV4 7AL | Find us on the interactive map <http://www2.warwick.ac.uk/about/visiting/maps/interactive/> > Lewandowski group website <https://www2.warwick.ac.uk/fac/sci/chemistry/research/lewandowski/lewandows…> | Warwick solid-state NMR group website <http://www2.warwick.ac.uk/fac/sci/physics/research/condensedmatt/nmr/>

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Non existent attributes default to all objects
by Daniel Esteban Palma Igor 15 Jul '20

15 Jul '20

Hi, if in a command you use an attribute that does not exist, ChimeraX (1.0) uses all the objects, for example: show @@asdf Is this intended? Regards, Daniel Palma Igor

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Color electrostatic ValueError
by Maria Maldonado 14 Jul '20

14 Jul '20

Hello ChimeraX team, I was hoping you could help me with a python error I get when trying to use the color electrostatic command. I have my protein surface and my electrostatic map from Delphi in cube format. When I run “color electrostatic #1 map #2 palette -10,red:0,white:10,blue”, I get long error ending in “ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() File "/programs/i386-mac/chimerax/0.91/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/map/data/gaussian/gaussian_format.py", line 120, in matrix if self.matrices == None: See log for complete Python traceback.” (I can send you the full error if useful.) I don’t get the error if I use a Delphi .phi file. However, the .phi files from this Delphi version have a bug that distorts the map, so the Delphi developers recommended using the .cube format instead. (The newer version of Delphi does not seem available for Mac at the moment.) Is the ValueError to do with ChimeraX or is it something to do with the .cube files? Do you have any suggestions as to how to solve this? Thank you very much for all your help, Maria

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ChimeraX-users July 2020