- ChimeraX-users - RBVI Mailing Lists

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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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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Re: [chimerax-users] unsubscribe to ChimeraX-users Digest, Vol 43, Issue 15
by Hua tiger 14 Jul '20

14 Jul '20

On Tue, Jul 14, 2020 at 11:31 AM <chimerax-users-request(a)cgl.ucsf.edu> wrote: > Send ChimeraX-users mailing list submissions to > chimerax-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > or, via email, send a message with subject or body 'help' to > chimerax-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimerax-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of ChimeraX-users digest..." > > > Today's Topics: > > 1. Re: re-assignment of mousemode (Elaine Meng) > 2. Re: re-assignment of mousemode (piskacek(a)post.cz) > 3. Re: re-assignment of mousemode (Elaine Meng) > 4. Fwd: [Chimera-users] re-assignment of mousemode (Elaine Meng) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Jul 2020 13:45:33 -0700 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > To: "<piskacek(a)post.cz>" <piskacek(a)post.cz> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] re-assignment of mousemode > Message-ID: <3BB2DAA6-5B94-4965-B973-F72CFA5E2CFC(a)cgl.ucsf.edu> > Content-Type: text/plain; charset=us-ascii > > Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that > you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse > with a right button, or can you use trackpad + Alt as the right button? If > you click any other icons in the Right Mouse tab of the Toolbar, can you > successfully assign any of those other functions to the right mouse button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght > Mouse icon, except that there will be a light green box around that icon. > Clicking the icon only reassigns the function of the right mouse button, > but does not perform any action at that time. However, if you reassign to > pivot by clicking the Right Mouse pivot icon, for example, then later > clicking with the right mouse button (if you have one) on an atom will make > that atom the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" > command (instead of icons) to assign the function to a different mouse > button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> > wrote: > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o > improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> > > > > > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu > > Manage subscription: > > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Jul 2020 23:48:44 +0200 (CEST) > From: <piskacek(a)post.cz> > To: "ChimeraX Users Help" <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] re-assignment of mousemode > Message-ID: <KC.3Mchj.NQenTdcZLM.1V3DQy(a)seznam.cz> > Content-Type: text/plain; charset="utf-8" > > exactly? all as you described all this is not working > > > > I assigned what my wright? mouse should execute,? > > but if I try to apply this function on amino acid from my protein it is > not > working > > > > Should I need to activate my mousemode somehow? > > I? suppose, that ChimeraX? is not working properly on windows in my case > I need some correction of some script to solve some hidden conflict in > windows > > thank you very much for you help > -- > Martin Piskacek > Laboratory of Cancer Biology and Genetics? > www.piskacek.org > Department of Pathological Physiology > Faculty of Medicine > Masaryk University Brno > Kamenice 5 > 625 00 Brno > Czech Republic > > > ---------- P?vodn? e-mail ---------- > Od: Elaine Meng <meng(a)cgl.ucsf.edu> > Komu: <piskacek(a)post.cz> <piskacek(a)post.cz> > Datum: 13. 7. 2020 22:45:47 > P?edm?t: Re: [chimerax-users] re-assignment of mousemode > "Another way to set pivot (without changing mouse-button functions) is by: > > (1) selecting an atom (Ctrl-click on the atom in the graphics window) that > you want as the center of rotation > (2) using menu: Actions... Set Pivot > > Elaine > > > On Jul 13, 2020, at 1:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > > > Hi Martin, > > It is not clear what you mean by "no response." Do you have a mouse with > a > right button, or can you use trackpad + Alt as the right button? If you > click any other icons in the Right Mouse tab of the Toolbar, can you > successfully assign any of those other functions to the right mouse > button? > > > > Maybe it is a misunderstanding of how the icons work: > > If it is working correctly, nothing will happen when you click a RIght > Mouse icon, except that there will be a light green box around that icon. > Clicking the icon only reassigns the function of the right mouse button, > but > does not perform any action at that time. However, if you reassign to > pivot > by clicking the Right Mouse pivot icon, for example, then later clicking > with the right mouse button (if you have one) on an atom will make that > atom > the pivot point. > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > > > If you do not have a right mouse button, you can use the "mousemode" > command (instead of icons) to assign the function to a different mouse > button. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > >> On Jul 13, 2020, at 9:02 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> > wrote: > > >> > >> Dear Authors of ChimeraX, > >> > >> I load and start to use your very useful program ChimeraX on Windows 10 > >> (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), > >> > >> I could do the same and more as in PyMol, but > >> I have trouble with re-assignment of mousemode in window "Right Mouse" > >> as result is no response for re-assignment into Pivot or Rotate model > >> > >> I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o > improvement > >> > >> Please, could you help me > >> Thank you very much for support > >> > > > > > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu > > Manage subscription: > > https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users > > " >

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Fwd: [Chimera-users] re-assignment of mousemode
by Elaine Meng 14 Jul '20

14 Jul '20

sending to chimerax-users instead of chimera-users (I'd accidentally set the "reply-to" to the wrong list, sorry -- Elaine ) > Begin forwarded message: > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] [chimerax-users] re-assignment of mousemode > Date: July 14, 2020 at 8:25:20 AM PDT > To: "<piskacek(a)post.cz>" <piskacek(a)post.cz> > Cc: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > Reply-To: "chimera-users(a)cgl.ucsf.edu BB" <chimera-users(a)cgl.ucsf.edu> > > Hi Martin, > The "Pivot" function sets the center of rotation for the whole view, for when you rotate everything with the mouse. It does not rotate the bond. If you want to rotate the bond, instead use the "Bond rotation" mouse mode, the icon much further right on the same toolbar as shown in your image. > > The Right Mouse icons and what they mean are listed here: > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > Best, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > >> On Jul 14, 2020, at 5:16 AM, <piskacek(a)post.cz> <piskacek(a)post.cz> wrote: >> >> Dear Elaine, >> thank you very much for your assistance, but >> I do everything correctly, but it just did not work = see figure >> I would like to rotate tryptofan in my figure, so as first I need to set pivot on the C-atom (designated here as CB) and than rotate with right mouse the tryptofan >> >> <Mail Attachment.png> > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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re-assignment of mousemode
by piskacek＠post.cz 13 Jul '20

13 Jul '20

Dear Authors of ChimeraX, I load and start to use your very useful program ChimeraX on Windows 10 (Alienware 17 x64, I7-4900MQ 2.8GHz, RAM 32GB, GeForce GTX 780M), I could do the same and more as in PyMol, but I have trouble with re-assignment of mousemode in window "Right Mouse" as result is no response for re-assignment into Pivot or Rotate model I tried ChimeraX versions 0,93, 1.0 and 1.1 (daily version) w/o improvement Please, could you help me Thank you very much for support -- Martin Piskacek Laboratory of Cancer Biology and Genetics www.piskacek.org Department of Pathological Physiology Faculty of Medicine Masaryk University Brno Kamenice 5 625 00 Brno Czech Republic

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ChimeraZ: show surface under another surface
by Anastasiya Oguienko 13 Jul '20

13 Jul '20

Dear ChimeraX developers, Hello! Thanks for this amazing tool, I enjoy every second of using it! I have a question about surface imaging: I have several subunits in the protein, and I would like to show surfaces of particular regions of different subunits. However, when one surface is above another, the lower one is not displayed no matter what the transparency value is. Is there a way to display both of the overlapping surfaces? Thanks in advance! -- With Best Regards, Anastasiya Oguienko

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Which color/palette was used
by Maria Maldonado 10 Jul '20

10 Jul '20

Hello, I was wondering if there’s a command that reports the color/palette of a chain/model. I saved a session with the palette I wanted, but didn’t make a note of what the palette was, and I would now like to use the same palette on a different session. Thank you for your help! Maria

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[chimeraX-users] to display cylinder and helical ribbon of one chain
by Yingyi Zhang 10 Jul '20

10 Jul '20

Dear ChimeraX Team, I have one model (pdb format), which contains multiple chains. Each chain (chain A for instance) consists of several helices. Is it possible to display ChainA in this manner - first two helices as cylinders but the others as ribbons? I tried to specify the residues, but it always changed the entire presence of the model, including the un-selected ones. Could you help me with this? I am still not very familiar with chimeraX. Thank you very much. Best regards, Yingyi

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Subscript in 2Dlabels
by Derek Harris 08 Jul '20

08 Jul '20

Is there a way, or code, to do sub/superscripts in a 2Dlabel? Derek Harris Postdoctoral Fellow Seefeldt Lab Department of Chemistry and Biochemistry Utah State University

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Re: [chimerax-users] label_seq_id in mmcif files for Chimera
by Greg Couch 08 Jul '20

08 Jul '20

On 7/7/2020 3:50 PM, Marcin Wojdyr wrote: > On Tue, 7 Jul 2020 at 22:38, Greg Couch <gregc(a)cgl.ucsf.edu> wrote: >> As you know, the entity_poly_seq table says which polymeric residues are >> adjacent to each other (entity_poly_seq.num values are the >> atom_site.label_seq_id values). > Yes, it's an enhanced equivalent of the SEQRES record in the PDB > format. Files from the wwPDB always have it, but files from other > sources will often miss it. I think currently almost all the mmCIF > files in circulation originate from the wwPDB. But this is slowly > changing and people are starting to use mmCIF as a working format. The sequence information is extremely useful for eliminating ambiguities in the atom_site data. And it is frequently known by the user, even when it is missing from the mmCIF file. >> Without that information, ChimeraX >> still needs the atom_site.label_seq_id to imply the polymeric ordering. > Ok. It would be useful, though, if ChimeraX could infer the ordering > and connectivity in the same way as it does for PDB files. > > Thanks, > Marcin Adding a atom_site.label_seq_id isn't different from supplying a residue number in PDB file. When there are adjacent residues of the same type, does the PDB reader see a duplicate atom and generate a new residue? merge the residues? generate an error? I haven't tested the PDB reader, but a residue number helps it too. Learning to use mmCIF effectively will take time. Programmers should use the PDB's mmCIF Dictionary Suite to validate the mmCIF their programs output -- it won't validate completely (because it's for mmCIF files served by the PDB), but it will show where the mmCIF output can be improved. For more information about ChimeraX reading mmCIF, see https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guide…. ChimeraX's mmCIF reader tries really hard to show you the data exactly as it is specified. So if there's badly specified data, you'll be able to see it. Over time, we will improve ChimeraX's ability to handle underspecified data as developers start generating mmCIF files. But we don't plan to modify the mmCIF reader if we can help it. Adding code, to infer information that should be explicitly given in the mmCIF file, slows down the mmCIF reader for everyone. This is especially true for large structures with over a million atoms. -- Greg

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Re: [chimerax-users] [Chimera-users] Chimera X - Windows 7 home premium
by Greg Couch 08 Jul '20

08 Jul '20

(This is a ChimeraX question, so sending the reply to the chimerax-users mailing too.) Looking at the image, the three gray boxes are icons for previously opened data files. To get an interactive 3D image, you would need to open an appropriate data file. If you type in the command "open 3rec" and press Enter/Return afterwards to open PDB model 3rec, does an interactive 3D image show up? If you can't get an interactive 3D image, then you probably need a newer graphics driver. I'd recommend going to the Lenovo support web site and installing a newer graphics driver. If the driver from Lenovo doesn't fix the problem, then you'll need to get one directly from Intel at https://downloadcenter.intel.com/. From the DxDiag.txt output, you have a 2nd generation i7 with HD Graphics 3000 driver version 8.15.10.2656. Lenovo has version 8.15.10.2274 from 6/9/2011 for your computer. On the Intel site, I see that version 15.28.24.4229 from 6/5/2015 is available. And you should know that we don't test ChimeraX on Windows 7, so technically you are on an unsupported platform. That said, we are unaware of anything that would prevent ChimeraX from running on Windows 7. However, with the age of your laptop, you should consider switching from Windows to Ubuntu (Linux). Intel is still supporting the Linux graphics driver for older systems. HTH, Greg On 7/8/2020 7:29 AM, MONICA MESA CADAVID wrote: > I would like to use the new Chimera X. > I installed and open the program easily. > But the images did not appear. > I attach the information of my computer because I would like to know > if I can fix the problem. > Thank you > * > * > image.png > *Monica Mesa Cadavid* > Profesor Titular > Instituto de Quimica > Facultad de Ciencias Exactas y Naturales > monica.mesa(a)udea.edu.co <http://udea.edu.co/> > Grupo Ciencia de los Materiales > Sede de Investigacion Universitaria, SIU -Torre 1, laboratorio 310 > Cra 53 # 61 - 30 > Tel. 574 - 219 6546 > > http://www.udea.edu.co/ <http://www.udea.edu.co/> > > > > *Universidad de Antioquia* > www.udea.edu.co <http://www.udea.edu.co/> > Sede Principal: Cll 67 # 53 - 108 > Medellín, Colombia > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > > > "La información aquí contenida es para uso exclusivo de la persona o > entidad de destino. Está estrictamente prohibida su utilización, > copia, descarga, distribución, modificación y/o reproducción total o > parcial, sin el permiso expreso de Universidad de Antioquia, pues su > contenido puede ser de carácter confidencial y/o contener material > privilegiado. Si usted recibió esta información por error, por favor > contacte en forma inmediata a quien la envió y borre este material de > su computador. Universidad de Antioquia no es responsable por la > información contenida en esta comunicación, el directo responsable es > quien la firma o el autor de la misma." > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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ChimeraX bug report submission
by Nicco 08 Jul '20

08 Jul '20

The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC) Description Hi, I'm trying to record a movie and the movie generated stops before executing all final steps. It's like the last frames are not recorded even when I see a very high limit. I feel like movie encode starts processing before it is called. For example these commands below are not present in the movie but the movie encode is called afterwards. # Select last interaction area select /F:370,375 /E:270,309,314 show sel atoms hbonds sel select clear # Final show turn x 15 60 rock 130 turn -y 15 60 rock 130 I'm a bit puzzled of why this is happening and I don't really now how to fix it. I attach the .cxc file with the set of instructions that I use to create the movie. Please consider that my experience level is beginner so there could be something that I'm doing wrong. Thank you! Nicco Log: UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open "/Users/niar/Dropbox (CRG > ADV)/Nicco/projects/06_Chimera/src/movies/6NQ3_Suz12_AS_event.cxc" > open 6NQ3 6nq3 title: Crystal Structure of a SUZ12-RBBP4-PHF19-JARID2 Heterotetrameric Complex [more info...] Chain information for 6nq3 #1 --- Chain | Description A E | Histone-binding protein RBBP4 B F | Polycomb protein SUZ12 C G | PHD finger protein 19 D H | Protein Jumonji Non-standard residues in 6nq3 #1 --- ZN — zinc ion 6nq3 mmCIF Assemblies --- 1| software_defined_assembly 2| software_defined_assembly > select all 11928 atoms, 12213 bonds, 30 pseudobonds, 3 models selected > show sel cartoons > style sel stick Changed 11928 atom styles > hide sel atoms > select /A,B,C,G,D,H 6565 atoms, 6720 bonds, 15 pseudobonds, 3 models selected > hide sel cartoons > select /E 3045 atoms, 3128 bonds, 2 pseudobonds, 2 models selected > color (#!1 & sel) purple > select /F 2318 atoms, 2365 bonds, 13 pseudobonds, 3 models selected > color (#!1 & sel) cyan > select clear > set bgColor white > lighting soft > graphics silhouettes true > view > view name start > movie record supersample 1 size 720,720 limit 5000 directory > /Users/niar/Desktop/tmp_chimera pattern Frame_n* > turn z -70 > turn x 24 > turn y -40 > view name hole > wait 5 > select sequence > EEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLP 1138 atoms, 1174 bonds, 1 model selected > color sel orange > select clear > wait 10 > select sequence NHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYT 540 atoms, 552 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHQKEGYGLSWNPNLSGHLLSASDDHTICLWD 500 atoms, 516 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAVVEDVSWHLLHESLFGSVADDQKLMIWD 512 atoms, 526 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence AHTAEVNCLSFNPYSEFILATGSADKTVALWD 488 atoms, 500 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence SHKDEIFQVQWSPHNETILASSGTDRRLNVWD 532 atoms, 546 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence GHTAKISDFSWNPNEPWVICSVSEDNIMQVWQ 522 atoms, 540 bonds, 1 model selected > color sel spring green > select clear > wait 10 > select sequence RKTFKVDDMLSKVEKMKGEQESH 299 atoms, 299 bonds, 1 model selected > color sel red > select clear > wait 10 > turn x 20 120 rock 120 > wait > turn y 35 150 rock 150 > wait > turn y 4 90 > wait > turn y 1 50 > wait > turn x 1 35 > wait > zoom 1.5 80 > wait > move x 0.75 15 > move y -0.75 15 > wait > view name side > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > show sel atoms > hbonds sel 51 hydrogen bonds found > select clear > wait 20 > turn x 15 60 rock 60 > wait > turn y 15 60 rock 60 > wait > ~hbonds > select /E:9-28 /E:32-39 239 atoms, 242 bonds, 1 model selected > hide sel atoms > select clear > wait 5 > move y 0.75 15 > move x -0.75 15 > wait > zoom 0.5 80 > wait > turn -x 1 35 > wait > turn -y 1 50 > wait > view hole > move x 0.75 25 > move y -0.5 25 > wait 25 > turn x 0.5 25 > zoom 3 80 > wait 80 > turn x 0.75 25 > move y 0.5 25 > wait 25 > view name zoom1 > select /F:129 /E:409 /E:346 31 atoms, 29 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 12 hydrogen bonds found > select clear > wait 15 > turn -y 15 120 rock 120 > wait > turn x 15 60 rock 130 > wait > wait 15 > view name zoom2 > turn y -1.5 25 > move x -0.5 25 > wait 25 > turn x -1 25 > turn z 1 25 > move x 0.4 25 > wait 25 > select /F:135 /E:285,304,330 34 atoms, 30 bonds, 1 model selected > show sel atoms > color (#!1 & sel) byelement > hbonds sel 11 hydrogen bonds found > select clear > turn y -10 120 rock 180 > wait > turn x 15 120 rock 120 > wait > wait 20 > view name zoom3 > zoom 0.5 50 > turn -y 1 150 > wait > move x 0.75 15 > wait > turn x 1 20 > wait > zoom 1.5 50 > select /F:370,375 /E:270,309,314 42 atoms, 37 bonds, 1 model selected > show sel atoms > hbonds sel 8 hydrogen bonds found > select clear > turn x 15 60 rock 130 > turn -y 15 60 rock 130 > movie status \-----Movie status------------------------------ Recording 1785 frames (in 'PPM' format) saved to directory '/Users/niar/Desktop/tmp_chimera' using pattern 'Frame_n*' . Est. movie length is 74.375s. \------------------------------------------------ > movie encode /Users/niar/Desktop/Suz12_test1.mp4 format h264 quality low > wait true verbose false Movie saved to /Users/niar/Desktop/Suz12_test1.mp4 executed 6NQ3_Suz12_AS_event.cxc OpenGL version: 4.1 INTEL-14.4.23 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro12,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 2,7 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 3 MB Hyper-Threading Technology: Enabled Memory: 8 GB Boot ROM Version: 189.0.0.0.0 SMC Version (system): 2.28f7 Software: System Software Overview: System Version: macOS 10.15.3 (19D76) Kernel Version: Darwin 19.3.0 Time since boot: 1 day 20:31 Graphics/Displays: Intel Iris Graphics 6100: Chipset Model: Intel Iris Graphics 6100 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x162b Revision ID: 0x0009 Metal: Supported, feature set macOS GPUFamily1 v4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal HP LP2065: Resolution: 1600 x 1200 (UXGA - Ultra eXtended Graphics Array) UI Looks like: 1600 x 1200 @ 60 Hz Framebuffer Depth: 24-Bit Color (ARGB8888) Display Serial Number: CNG70302V3 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: 6NQ3_Suz12_AS_event.cxc

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Re: [chimerax-users] [Chimera-users] Difference in alignment of cofactor between Chimera and ChimeraX
by Elaine Meng 07 Jul '20

07 Jul '20

Hello Derek, You're welcome! Thought I should also mention that in matchmaker you can specify more than one pair of chains, i.e. use multiple pairs of chains for the fit. Which way is better depends on what you are trying to achieve: overall superposition of whole complex, or best fit of a single pair of chains. This multichain fit can be done in either Chimera or ChimeraX with a matchmaker command option. I'll use ChimeraX commands to illustrate: open 3u7q open 5n6y hide ribbon The ChimeraX log shows that 3u7q has four chains, two alpha (A,C) and two beta (B,D) whereas 5n6y has 6 chains, two alpha (A,D), two beta (B,E) and two delta (C,F). So perhaps you want to use all of the alpha and beta chains from the structures for the fit instead of only A with A. Now the trick is to figure out which alpha goes with which alpha and which beta with which beta. I might be lazy and first just try ABCD in 3u7q as pairing with ABDE in 5n6y and see if that looks right. I might also use coloring by polymer (figures out a color based on chain sequence) to make it clearer what's what. color bypolymer mm #2/A,B,D,E to #1/A,B,C,D pair ss <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> .... which actually looks right. The alphas and betas are colored the same within a given PDB structure but different between the structures, probably because of small sequence differences (something like one structure has a couple more residues on one end or the other; I didn't investigate, but it's expected). The Log reports: RMSD between 1026 pruned atom pairs is 1.314 angstroms; (across all 1783 pairs: 3.281) ...now to check the placement of cofactors: show ligand ~ribbon You can see a more symmetrical fit, with similar displacements on both sides. I hope this helps, Elaine > On Jul 7, 2020, at 9:39 AM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > Hello Elaine, > > Thank you very much for the rapid response. Following your commands, and seeing all the ligands, I now see what's happening. Just as you said; the proteins are each composed of two identical catalytic halves. In one half there is a nice alignment of the cofactors, but in the other half there is not. I was isolating, and only viewing, the chain where there isn't good alignment. > > Thanks again! > > Derek Harris > Postdoctoral Fellow > Seefeldt Lab > Department of Chemistry and Biochemistry > Utah State University > > > On Tue, Jul 7, 2020 at 9:35 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Derek, > It does not make sense for the cofactor alignment to be different if the protein alignment is the same, because the cofactors are just moved rigidly along with their proteins. Also the results should be identical between Chimera and ChimeraX, assuming you are using the same options. > > I get exactly the same alignment between these two proteins in the Chimera vs. ChimeraX. > > Chimera commands (including display ligand only): > open 3u7q > open 5n6y > mm #0 #1 > ~ribbon > show ligand > > ChimeraX commands: > open 3u7q > open 5n6y > mm #2 to #1 > ~ribbon > hide > show ligand > > In both programs, I get the same RMSD message to the Log: > > RMSD between 375 pruned atom pairs is 0.968 angstroms; (across all 450 pairs: 2.998) > > In both programs, matchmaker ends up choosing to align chain A to chain A. Thus the cofactors in chains A are better superimposed than the ones in the other chains. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Jul 6, 2020, at 6:47 PM, Derek Harris <derek.harris(a)aggiemail.usu.edu> wrote: > > > > Hello, > > > > I am trying to reproduce an alignment I had previously done in Chimera in ChimeraX with matchmaker command. > > > > The protein alignment between the two programs is the same, but in ChimeraX the active-site cofactor of the matchstruct isn't aligning appropriately to the refstruct cofactor and is unreasonably placed in relation to even its own protein. In Chimera the two cofactors align nicely. > > > > The two structures I am trying to align are 3U7Q and 5N6Y. > > > > Thanks in advance for any assistance you can offer! > > > > Derek Harris > > Postdoctoral Fellow > > Seefeldt Lab > > Department of Chemistry and Biochemistry > > Utah State University > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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how to turn molecule centering a specific atom in ChimeraX
by Shin Inchul 07 Jul '20

07 Jul '20

Hi, I was trying to turn molecule around specific atom. Since I am a beginner of ChimeraX, I would like to have some working examples in the command line. Without it, I have difficulties in applying the usage as appeared in the user guide. In PyMOL, mouse middle button click on a atom sets the centering on the atom then use rotate command. I appreciate all the supports provided. Thank you. Inchul

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Re: [chimerax-users] session file sizes
by Tom Goddard 07 Jul '20

07 Jul '20

To close molecular surfaces surface close #1 or just surf close If instead you do ~surface that hides the surface. I discourage use of these obscure "~" commands that Chimera used. Use "surface hide #1" or "surface close #1". If you just hide the surfaces they are still in the session file. You can also see the surface models in Model Panel by clicking the little triangle and the left of the model name to show submodel of your molecule. And you can choose those surface models and close them. Tom > On Jul 7, 2020, at 2:48 PM, Melissa Jurica <mjurica(a)ucsc.edu> wrote: > > That was my first guess, so I turned off the surface view. However, no change in file size. I don’t see how to delete the surface that I calculated- still trying to get the hang of ChimeraX after switching from Chimera. > > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > Melissa S. Jurica, Ph.D. > Professor, Molecular, Cell & Developmental Biology > Center for Molecular Biology of RNA > University of California, Santa Cruz > 1156 High Street > Santa Cruz, CA 95064 > > Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs > Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 > http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > >> On Jul 7, 2020, at 2:41 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> Hi Melissa, >> >> Molecular surfaces make session files very large because they save all the surface triangles. Did you have a molecular surface in that large session? I have considered not saving the molecular surfaces and just recomputing them although that will make restoring the session slower as it tries to recompute the surface. >> >> Tom >> >> >>> On Jul 7, 2020, at 2:28 PM, Melissa Jurica <mjurica(a)ucsc.edu <mailto:mjurica@ucsc.edu>> wrote: >>> >>> What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? >>> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> Melissa S. Jurica, Ph.D. >>> Professor, Molecular, Cell & Developmental Biology >>> Center for Molecular Biology of RNA >>> University of California, Santa Cruz >>> 1156 High Street >>> Santa Cruz, CA 95064 >>> >>> Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs >>> Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 >>> http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> >>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >> >

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session file sizes
by Melissa Jurica 07 Jul '20

07 Jul '20

What deterimines the file size of saved ChimeraX sessions (.csx files)? I saved a session of one structure (6Y5q) at 4 MB, and another structure (6y50) at 2.6 MB. However, when I saved a session with both structures open, it was a whopping 120.6 MB. Is there a way to reduce that file size? ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Melissa S. Jurica, Ph.D. Professor, Molecular, Cell & Developmental Biology Center for Molecular Biology of RNA University of California, Santa Cruz 1156 High Street Santa Cruz, CA 95064 Office: 450 Sinsheimer Labs Lab: 434 Sinsheimer Labs Office phone (831) 459-4427 Lab phone (831) 459-2463 Fax (831) 459-3139 http://www.mcd.ucsc.edu/faculty/jurica.html <http://www.mcd.ucsc.edu/faculty/jurica.html> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

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