- ChimeraX-users - RBVI Mailing Lists

VR movie
by Matthias Wolf 13 Mar '20

13 Mar '20

Hi Tom, I really liked your CoV movie https://www.youtube.com/watch?v=dKNbRRRFhqY&feature=youtu.be It’s a new way of storytelling. Although we have used chimeraX in the lab with a Vive and Vive pro for about 2 years, it’s usually one person at a time, with a dark background. But your way opens up interactive VR to a larger audience (even if they don’t get to enjoy the stereoscopic 3D). And it’s cool. I have some questions: 1. How did you overlay the chimera viewport sync’d with the life camera feed showing yourself? Did you use a frame grabber on a different PC to capture the full-screen chimeraX VR viewport while simultaneously recording the camera video stream, e.g. using Adobe Premiere? 2. How did you control flipping out the outer spike domain with your hand controller? I guess you assigned control of a torsional angle in the atomic model to a mouse mode? 3. Did you enable the headset cameras to orient yourself in the room? Thanks for keeping improving chimeraX and VR! Matthias

3 4

Making movies and fitting structures into cryoEM
by Tom Goddard 13 Mar '20

13 Mar '20

> Begin forwarded message: > > From: "Tirumalai, Madhan R" > Subject: ChimeraX > Date: March 11, 2020 at 1:10:41 PM PDT > To: "goddard(a)cgl.ucsf.edu" <goddard(a)cgl.ucsf.edu> > > Dear Dr. Goddard > > Warm Greetings! > > We have been using ChimeraX to look at mrc files. > > While I am able to use the "Spin movie" option, am not able to use the make movie option, which I could with the Chimera version. > > I would much appreciate if you could kindly let me know how: > > I can use the movie making option to make movies using different images with increasing/ decreasing thresholds (Volume Viewer)? > > Since am not familiar with docking programs, I would like to know how can one a related crystal structure into a new Cryo-EM structure to show the differences between the crystal structure and the Cryo-Em? > > Thanks > Madhan > > > Madhan R Tirumalai, Ph.D., > Houston Science Center, #421 > Dept Biology & Biochemistry, University of Houston, 3455, Cullen Blvd, Houston, TX,77204-5001, USA. > Contact nos: 713-632-5463 (Cell); 713-743-8365 (office); 713-743-8351 (Fax) > > email: mrtirum2(a)central.uh.edu <mailto:mrtirum2@central.uh.edu>, madhanrt(a)gmail.com <mailto:madhanrt@gmail.com> > > ORCID link: http://orcid.org/0000-0002-5999-333X <http://orcid.org/0000-0002-5999-333X>

3 3

Re: [chimerax-users] HP Reverb headset
by Tom Goddard 12 Mar '20

12 Mar '20

Hi Shingo, I think Oculus Rift S is the best choice for ChimeraX VR. Unfortunately all the good VR headsets are sold out apparently because of production delays in China the last few months. So you will have to be patient. I think it is worth waiting instead of getting a headset that will not function well. Tom > On Mar 12, 2020, at 5:47 PM, 永野真吾 <snagano(a)tottori-u.ac.jp> wrote: > > Tom, > > Thank you for the very quick response and useful information. I will get Oculus Rift S. > > All the best, > > Shingo > > > > 2020年3月13日(金) 4:01 Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>>: > Hi Shingo, > > I have not used the HP Reverb VR headset but I have used another Windows Mixed Reality headset, the Samsung Odyssey, which worked fine in ChimeraX. ChimeraX just uses the Windows Mixed Reality runtime through SteamVR so I expect any Windows Mixed Reality headset will work. That said, the reviews on the HP Reverb are poorer than other headsets > > https://www.amazon.com/HP-Reverb-Virtual-Reality-Headset/dp/B07R768KJP <https://www.amazon.com/HP-Reverb-Virtual-Reality-Headset/dp/B07R768KJP> > > I would recommend Oculus Rift S which I have used extensively with ChimeraX. I also have used Vive Pro, Vive, Oculus Rift, and all those work well. > > Tom > > > On Mar 12, 2020, at 3:25 AM, 永野真吾 <snagano(a)tottori-u.ac.jp <mailto:snagano@tottori-u.ac.jp>> wrote: > > > > Hi all, > > > > Has anyone used HP Reverb headset for virtual reality on ChimeraX? > > That headset works fine? > > > > Any comments are welcome. > > > > Best, > > > > Shingo Nagano > > _______________________________________________ > > ChimeraX-users mailing list > > ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> > > Manage subscription: > > http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> > > >

1 0

flatten a cryoEM map
by Hongtao Zhu 12 Mar '20

12 Mar '20

Hi there, Could you show me how to flatten a cryoEM map in chimera just like the attachment? My map has several subunits but with C1 symmetry. Thanks, Hongtao

3 3

ChimeraX does not start after installation
by Lewandowski, Jozef 12 Mar '20

12 Mar '20

Hi, I am trying to get ChimeraX on a Windows 10 installation on a workstation with 4 GPUs (RTX 2080Ti). The program installs just fine but when I start it, it shows the splash screen up to Loading main interface and then quits. I have tried both with the 0.92 release and the daily_build. Any chance you could help with with getting it to work? Browsing archives I learned that this may be down to some incompatibilities with drivers. The onboard graphics is ASPEED Graphics Family with driver version 9.0.10.102 The four Nvidia GeForce RTX2080Ti have driver 26.21.14.4219 installed (I updated to the latest drivers hoping it fixes it - it doesn't). Any ideas or suggestions? Thanks, Józef

2 1

HP Reverb headset
by 永野真吾 12 Mar '20

12 Mar '20

Hi all, Has anyone used HP Reverb headset for virtual reality on ChimeraX? That headset works fine? Any comments are welcome. Best, Shingo Nagano

2 1

Error opening sequence viewer
by Y. Mutum 12 Mar '20

12 Mar '20

Hi I am working with ISOLDE to build my model using ChimeraX interface. There I had added an deleted a few sequences in chain a. This was done while the sequence viewer was closed. Now, when I try to view the sequence by ' sequence chain #1/a', I am getting this error (attached as screenshot) Could you please help? I hope I don't have to start from the begining. Thanks Yaikhomba

3 2

How to save the ChimeraX startup settings?
by Steve Chou 11 Mar '20

11 Mar '20

Dear ChimeraX team, It seems that if the startup window size settings ( display window size, log window width) are different, I get different views after I run the same script, which has a lot of operations, like “move”, “turn”. How to save the startup settings and load them back or is there a startup settings file saved somewhere? Many thanks, Steve Chou -- Steve Chou

2 1

Re: [chimerax-users] pseudobond between atom and center of a ring
by Elaine Meng 10 Mar '20

10 Mar '20

Hi Alexis, I can reproduce the problem with reading the pb file transparency using a color specification of the form: /a:1@c3' /a:1@n3 rgba(20,90,90,70) However, if I use these alternative forms of transparent color specification, it works, i.e. the pseudobond is transparent: /a:1@c3' /a:1@n3 20,90,90,70 - OR - /a:1@c3' /a:1@n3 #00ced155 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> Those atoms are in PDB 1bna, for example. Tested in current daily build I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 6, 2020, at 10:33 AM, Alexis Rohou <a.rohou(a)gmail.com> wrote: > > Thanks Elaine! > > Great - so now I'm using "measure center" to create markers with 0.0000001 radius at the center of my rings with specified modelId's. Then I have a .pb file that specifies the pseudobonds to draw between markers and atoms. That all seems to work pretty well, thanks! > > Only little snag right now is I can't seem to get transparency working when the color-spec in the .pb file is in the format rgba(). Setting the transparency after opening the pb file using "transparency" works fine though, so I'm not stuck. > > Thanks again for the help. > > Cheers, > Alexis > > On Fri, Mar 6, 2020 at 9:36 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Here is the more detailed description of pseudobond file format: > > <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html#pbfiles>

3 7

sessions vs. logging
by Eric Pettersen 09 Mar '20

09 Mar '20

Hi all, As of tomorrow’s daily build, restoring a session will by default clear the log and restore the contents of the log from the session, hidden under a dated disclosure triangle. There is a preference in the “Log” preferences category to not clear the log (but still add the old log under a disclosure triangle). If you are a big fan of the current behavior and don’t want the old log to be added at all, I can add an option for that. If you are, feel free to speak up (but maybe try out the new behavior first?). These dated disclosure triangles “nest”, in that if you do some work and save a session, then later restore that session and do more work and save a second session, when you restore that second session you will see one disclosure triangle that shows the second set of work you did — but at the top of that second set of work will be a disclosure triangle that can be opened to show the first set of work you did. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Re: [chimerax-users] not showing non-traced amino acids in sequence view after splitting a molecule
by Tom Goddard 06 Mar '20

06 Mar '20

Hi Marta, Thanks for the explanation of why you use split. Suppose Model Panel showed each chain, and you deleted all the unwanted chains. Would that work as well as split? Definitely split should preserve the sequence information for missing structure, so we appreciate you bringing that to our attention. Tom > On Mar 6, 2020, at 3:04 AM, Marta Perez Illana <marta.perez(a)cnb.csic.es> wrote: > > > Thanks a lot for the ideas and opening the topic, that was absolutely great and appreciated. I just wanted to make sure that I was not messing around myself with the splitting+sequence thing. > > Ideally I wouldn't use the split as you both suggested... However, I frequently use the match maker with several homology proteins coming from big viruses with lots of proteins... and having less proteins in the session really helps me not to get confused and focus and switching on and of every protein at each time... So I am afraid that I really adore the split command. > > Having the full sequence on the other side helps me out to compare the homology proteins and see which areas are traced in one protein but not in the other (or parts of the protein that are subjected to protease fragmentation and not visualized in the structure) , as well as to get full alignments based on structure... > > I am really grateful for all the help and sorry for being a bit picky on the split+sequence... > > Marta > > > >> On 05.03.20 20:56, Tom Goddard wrote: >> Hi Marta, >> >> The sequence for the missing structure should be preserved by the split command but it currently is not being preserved. We have opened a request for that >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2913 >> >> I agree with Elaine, that you should rarely need to use the split command. >> >> Tom >> >> >>> On Mar 2, 2020, at 9:15 AM, Marta Perez Illana wrote: >>> >>> Hi Elaine >>> >>> Thanks a lot for the quick reply! I though that maybe there was a way to keep that info of the non-traced amino acids after doing splitting. >>> >>> I use split because we work with huge molecules, and therefore is really convenient for focusing on a particular chain. And as well for fitting as you mention... I will try the alternatives you proposed! now knowing that making/saving new models implies for sure kind of "loosing that info"... >>> >>> Regards >>> >>> Marta >>> >>> >>>> On 02/03/2020 18:05, Elaine Meng wrote: >>>> Hi Marta, >>>> When you open a structure from PDB or mmCIF format, there is a special part of the file that gives the full sequence of the structure used in the experiment, even if parts of that structure are not visible in the density (and therefore do not have atomic coordinates). This is part of the model information. >>>> >>>> However, “split” makes new models, and it currently loses various kinds of information. I believe this is the case in both Chimera and ChimeraX. After splitting, it must only look at the coordinates to get the sequence. >>>> >>>> My personal opinion is to avoid using “split” unless it is really necessary. >>>> >>>> In Chimera it sometimes helped with molecular surface calculation, but in ChimeraX there is less reason to do it. You can specify chains individually without splitting. The main reason one might split is for separately fitting the chains. However, if having the full sequence is important, you can instead open multiple copies of the original model and just delete the parts of each that you don’t need. >>>> >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>>> On Mar 2, 2020, at 8:30 AM, Marta Perez Illana wrote: >>>>> >>>>> Hi all >>>>> When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure). >>>>> >>>>> Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please? >>>>> >>>>> P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed... >>>>> >>>>> Thank you!!! >>>>> Marta >>> >>> -- >>> Marta Pérez Illana, Ph. D. student >>> Dept. of Macromolecular Structures Lab 15 >>> Centro Nacional de Biotecnología (CNB-CSIC) >>> Darwin, 3 >>> 28049-Madrid (SPAIN) >>> http://wwwuser.cnb.csic.es/~sanmartinlab >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > -- > Marta Pérez Illana, Ph. D. student > Dept. of Macromolecular Structures Lab 15 > Centro Nacional de Biotecnología (CNB-CSIC) > Darwin, 3 > 28049-Madrid (SPAIN) > Email: marta.perez(a)cnb.csic.es > Phone: (0034) 91 585 4508 > http://wwwuser.cnb.csic.es/~sanmartinlab

1 0

pseudobond between atom and center of a ring
by Alexis Rohou 06 Mar '20

06 Mar '20

Hi all, Looking for ideas on how to achieve the following, if possible: I'd like to draw lines to represent favorable ring-ring stacking interactions (lines between the center of two arene rings), ring-ring edge-to-face interactions (between one atom of one ring and the center of the other ring), and between a regular atom (not part of a ring) and the center of an arene ring. So I'm guess what I'm looking for is a way to: 1. compute the center coordinates of a ring 2. place an invisible atom there 3. create a pseudobond between this virtual atom and other atoms/virtual atoms Any suggestions as to how I could achieve this? Cheers, Alexis

3 6

Depth cueing and silhouette
by Aritz Roa Eguiara 05 Mar '20

05 Mar '20

Dear ChimeraX team, I write you to ask about the depth cueing option. I have a structure with the silhouette true option and now I want to change the depth cueing to obtain a slice of the structure but with some of the fog coming from the background. The cartoon color disappear gradually as expected, however the black line of the silhouette is 100% or nothing, is there anything I am doing wrong or is it what I should expect? Is there anyway to obtain also that smooth disappearing of the silhouette? Thank you for your help. All the best, Aritz

4 6

not showing non-traced amino acids in sequence view after splitting a molecule
by Marta Perez Illana 05 Mar '20

05 Mar '20

Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure). Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please? P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed... Thank you!!! Marta

3 4

Secondary structure display - pdb and cif
by Tetter Stephan 04 Mar '20

04 Mar '20

Dear ChimeraX users and developers, I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue? The attachments show the lines from the two file types concerning secondary structure definitions. Kind regards, Stephan

3 3

"zone" near MULTIPLE residues in ChimeraX
by Steve Chou 03 Mar '20

03 Mar '20

Dear ChimeraX team, I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve -- Steve Chou

3 3

Bug: selection of atoms by attribute = color
by Pavol Bardy 393791 27 Feb '20

27 Feb '20

Hello, since version 0.91 I am experiencing problems with selecting atoms by color attribute "@@color=color". I am getting an error message "Expected an objects specifier or a keyword". In version 0.90 everything works fine. Other attributes like "bfactor" or "idatm_type" seems to work normally. Kind regards, -- Pavol Bárdy Laboratory of Microbial Molecular Diagnostics Department of Experimental Biology, Masaryk University Kamenice 5 / A25 Brno, 625 00, Czech Republic

2 1

change residues to helix
by Meinan Lyu 24 Feb '20

24 Feb '20

Dear cgl.ucsf.edu, In chimerax, Helix is disrupted for some reason, could I change the intermediate residues into helix? There are two ways I tried, 1: use 'dssp' command, 2: use 'setattr :467-469/A res ss_type 1'. But both didn't not work. Could you tell me how to change this? Best regards, Meinan [image: image.png]

2 2

Default mrc/ccp4 file opening by ChimeraX
by Kim, Doo Nam 20 Feb '20

20 Feb '20

I use mac (10.14.6). But when I double-click mrc/ccp4 file, chimera automatically opens it. I want to open it with ChimeraX (which is faster). However, even when I right-click on ccp4 file -> open with -> always open with -> ChimeraX_Daily, only that specific file is opened with chimera automatically. Does anyone know how to set up so that all (including future) .mrc and .ccp4 files are opened with ChimeraX? Thank you Best, Doonam

2 2

Error in reopening session
by Maximiliane Wieland 20 Feb '20

20 Feb '20

Hi, When I try reopening a session I have been using for two weeks now (so many saved view :( )and I get the following error: Unable to restore session, resetting. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 653, in restore obj = sm.restore_snapshot(self, data) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot cmd.name_frozen(session, name, Objects(**value)) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/cmd.py", line 54, in name_frozen raise UserError("nothing is selected by specifier") chimerax.core.errors.UserError: nothing is selected by specifier This is the error from the daily build, in the production release one I get the same error, only difference is in "cmd.py", line 52, in name_frozen When trying to open an older version (that I saved but did not open, since I kept using the same session and saved it to the latest version) I am asked to replace missing files, which are in fact not missing but still in the very same directory and with the very same name, so it feels like the real error lies elsewhere? Can I make it reopen the session without reopening the volume? The last version of the session I can open without a problem is close to two weeks old, I named some selections in the meantime, could that cause such an error? I use ChimeraX on MacOS X 10.12.6 I will also submit the bug but since it is kind of urgent I thought I would try submitting here, too, in hopes of a quick response. Best, Maxi

1 0

Set view
by Aritz Roa Eguiara 19 Feb '20

19 Feb '20

Dear ChimeraX, I am trying to produce a script .cxc to open on ChimeraX and I want to set a specific camera position coordinates that can be opened by anyone. I do obtain the position by just using the command camera, but then I do not know how to obtain that position without saving the view. How should this be written on the command line so that anyone can open it and get that view? For example, I know that PyMol allows the get view command to obtain all the information that later only need to be pasted on the script, is there anything similar? Thank you in advance for your help. Best regards, Aritz

2 2

undo/redo move?
by Oliver Clarke 18 Feb '20

18 Feb '20

Hi, I like the expanded undo/redo capabilities in Chimerax - particularly having the capacity to undo selection/deselection and color commands is very helpful. However it seems like there is no undo/redo move functionality. I find myself using this a lot in Chimera, is there any possibility of incorporating this into Undo/Redo in ChimeraX? Basically adding the possibility to Undo/Redo translation, rotation and scaling? Cheers Oli

4 5

workflow suggestions
by Joel Meyerson 17 Feb '20

17 Feb '20

Hi, I'm a reasonably experienced Chimera user making the shift to ChimeraX. So far I'm really enjoying it. I'm writing because the biggest challenge I'm having so far is that there doesn’t seem to be anything quite like the "activate" features in the original Chimera Model Panel. Are the "activate" features available in ChimeraX, or are there plans to implement them? If not, can you suggest a way to achieve a similar degree of agility for manipulating objects in ChimeraX? So far I have been clicking between Right Mouse modes which does not feel so fluid yet. Perhaps there are keyboard shortcuts or other workflow tricks that you could suggest to improve the feel of navigation. Thanks, Joel

2 1

Re: [chimerax-users] [Chimera-users] Default storage folder, ChimeraX
by Elaine Meng 14 Feb '20

14 Feb '20

Hi Martín, Currently there is no way in the user interface to change the ChimeraX downloads location, described here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> You could make a symbolic link to that location, but the files would still really be in the same place. Probably the location can be changed by editing somewhere in the Python code, but somebody else would have to advise on that. You may be interested that there is a separate mailing list for ChimeraX, chimerax-users(a)cgl.ucsf.edu (CC’d on this message). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 13, 2020, at 4:00 PM, Martín González Buitrón <martingonzalezbuitron(a)gmail.com> wrote: > > Dears all, > Hope you are well. > > I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/). > > How can I change this to other of my own preference? > All the best, > Martín

3 2

Reverse color byhet
by Ahmad Khalifa 13 Feb '20

13 Feb '20

If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors. How to reverse byhet coloring? Regards.

3 3