March 2020 - ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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

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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>

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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

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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

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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

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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

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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

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