October 2023 - ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Chimera X menu "View" vs. "Focus"
by Eric Pettersen 23 Jan '24

23 Jan '24

Hi Christian, We named it “View” instead of “Focus” because it issues a “view” command, but your points have merit — “Focus” is more evocative of what the action actually does, and is less confusable with hide/show, so after some discussion we have renamed the menu item to “Focus” and the change will be in the next daily build. The menu item item still issues/logs a “view” command to do its work. We are aware that the direct equivalent of the “Fetch By ID” dialog is missing in ChimeraX and we intend to add it. It’s just a matter of implementation priorities, so it could still be a little while — but it’s useful to know that it’s definitely missed, which will make it more likely to get worked on sooner. Also, there is a list specifically for ChimeraX user issues — chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>, (cc’ed here), which would be better to discuss ChimeraX topics on than chimera-users… --Eric Eric Pettersen UCSF Computer Graphics Lab > On Sep 25, 2023, at 12:47 AM, C. Klein via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera Team > > first of all, thank you very much for your important and good work on the Chimera software. > > Two comments: > > I did some recent work with Chimera X. The menu item "Focus" was changed to "View", which I find less suitable. The term "View" is often applied in other contexts, in particular if a certain residue should be shown vs. not shown. In contrast, "Focus" is not ambiguous, it is not related to showing vs. hiding certain parts of the molecular representation but exactly indicates what is done by the command. > > The direct pdb download from rcsb or whatever repository is a highly useful tool which is more difficult to access than it used to be. Ok I know it is there, I type "open xxxx" and I use the command line quite a lot anyway, but for others who start with the menus it does not appear to be accessible. Perhaps I also missed something, but then others may not find it as well. > > Thank you and best wishes > Christian Klein > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 17 Nov '23

17 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

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Middle mouse click to center and move to atom
by Adrián González López 27 Oct '23

27 Oct '23

Hi, I do not know if this is possible already (I could not find it), but is there a way in ChimeraX to set the middle click mouse button (or any other button) to center and orient the atom you click? Similar to what happens on PyMOL by default. This helps so much when navigating around a structure. I know you can do it in some other way, but it takes more time and it is not so user-friendly. If there is no way to do this, could it be implemented? Many thanks! Best, Adrián När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Cap clipped atoms or bonds
by Daniel Larsson 27 Oct '23

27 Oct '23

Is it possible to have atoms or bonds capped when they are truncated by a near clipping plane, similar to how surfaces can be capped. Currently, you can see the interior polygons when you clip the middle of a molecule. See the attached image for an example. I tried to search the mailing list and the documentations, but could not find anything. Regards, Daniel [cid:image001.png@01DA08BB.1559BC80] När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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ChimeraX for WSL: release request
by Dmitry Semchonok 27 Oct '23

27 Oct '23

Dear Elaine and Eric, Since the number of Windows WSL systems is increasing do you consider releasing the compatible version of ChimeraX? Thank you Kind regards, Dmitry

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Chimera(X) website and web services down Oct 30-31
by Elaine Meng 26 Oct '23

26 Oct '23

Dear users, Due to system upgrades, the Chimera and ChimeraX websites, associated web services hosted by the UCSF RBVI (Modeller, Blast Protein, etc.), and the ChimeraX Toolshed will be unavailable -- the estimated downtime is from Monday, Oct 30 8:00 am PDT through Tuesday, Oct 31 11:59 pm PDT. Please pardon the inconvenience, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Re: Selection with coordinates
by Tom Goddard 26 Oct '23

26 Oct '23

Hi Siyoung, The movie recording needs a "wait" command to actually render frames. If you have 300 frames in your coordinate set it would be perframe "open select_atoms.py" movie record coordset #1 wait 300 movie encode test.mp4 Also I would suggest that your python code not use "atom.hide". That is an obscure attribute for hiding backbone atoms with ribbon display. Instead use atom.display = True atom.display = False It might be possible to record the movie entirely in Python, but I've never tried it. I would not suggest trying that approach unless you want to waste a lot of time since the movie recording code was not designed to work in a Python script. Tom > On Oct 24, 2023, at 6:01 PM, Siyoung Kim <kkssy141(a)gmail.com> wrote: > > Thank you very much for the helpful information. I think I am very close to what I want to do. > > I would like to make a video of a molecular dynamics trajectory and want to show only the atoms whose x coordinates are smaller than 0. Here is what I tried. > > a) I made a python script that can be applied to each frame and named it "select_atoms.py" > --------------------------------- > from chimerax.atomic import all_atoms > atoms = all_atoms(session) > for atom in atoms: > if atom.scene_coord[0] < 0: > atom.hide = 0 > else: > atom.hide = 1 > ---------------------------------- > > b) I opened up a trajectory in ChimeraX. > > c) In ChimeraX, I executed > --------------------------------------------- > perframe "open select_atoms.py" > movie record > coordset #1 > movie encode test.mp4 > ---------------------------------------------- > > Interestingly, if I just move a frame by myself using a slider, perframe is applied well. i.e., only the atoms whose x coordinates < 0 are shown in EACH frame > However, if I record a video like the above or click a play button, perframe is not successfully applied. Only the atoms whose x coordinates < 0 in the last frame are shown in all frames. Updating a selection in each frame does not work with this approach. > I have attached the video. Would you please help me with this? Thank you. > > I would be also curious if it could be done inside a python script. In the above, I made a script that should be applied to each frame and then called this script using perframe in ChimeraX. Would there be something like RED in the below? Thank you very much! > > RECORDING A MOVIE > for s in all_atomic_structures(session): > for cs_id in s.coordset_ids: > s.active_coordset_id = cs_id > atoms = s.atoms > atoms.selecteds = atoms.scene_coords[:,0] < 0 > atoms[atoms.selecteds].hide = 0 > atoms[~atoms.selecteds].hide = 1 > SAVE THIS IMAGE > ENCODING A MOVIE > > > On Mon, Oct 23, 2023 at 11:52 AM Siyoung Kim <kkssy141(a)gmail.com <mailto:kkssy141@gmail.com>> wrote: >> Hi Eric, >> >> Thank you very much for the very helpful information! I learned a lot. >> >> Best, >> Siyoung >> >> On Fri, Oct 20, 2023 at 8:58 PM Eric Pettersen <pett(a)cgl.ucsf.edu <mailto:pett@cgl.ucsf.edu>> wrote: >>>> On Oct 17, 2023, at 1:53 PM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>> >>>> Hi Tom, >>>> >>>> Thank you for your help. I can confirm that making a text file, select.py, that contains the below and running "run select.py" in the ChimeraX command line works. >>>> >>>> from chimerax.atomic import all_atoms >>>> for a in all_atoms(session): >>>> if a.scene_coord[0] < 0: >>>> a.selected = True >>>> >>>> I am quite interested in learning more about the chimerax.atomix library. Would there be any helpful resources about this? >>> >>> There is automatically generated documentation, but I don't recommend it because it is poorly formatted and littered with rarely used constants and functions from base classes (e.g. Structure inherits from Model and Drawing and therefore documentation for first_intercept_children() [from Drawing] is included). Instead, I'd browse through the code for atomic class definitions themselves. The Cython class definitions for Atom, Element, and Bond are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/atomic_cpp… . The definitions for the other classes are here: https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molobj… . The latter only has the base class definitions for Structure and PseudobondGroup (StructureData and PseudobondGroupData respectively). The final definitions are in structure.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/struct…> and pbgroup.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/pbgrou…> . >>> >>> Another approach is to find a bundle that does something similar to what you want to do and look at its code to see how it does it. All the ChimeraX source code is in the repository linked to above (and the Python code is included in every ChimeraX installation). >>> >>>> Would it be also possible to loop over a molecular dynamics trajectory and select wanted atoms in this way? >>> >>> Yes. A structure that is a trajectory will have multiple "coordinate sets" (sets of coordinates for the atoms). Therefore you can loop through the trajectory like so: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> for a in s.atoms: >>> a.selected = a.scene_coord[0] < 0 >>> >>> It may also be useful to know that the value returned by s.atoms is an "Atoms" instance (see molarray.py <https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/atomic/src/molarr…>) which in many ways can be treated as a vector for efficiency, which could definitely matter when processing a trajectory. So the above code could instead be: >>> >>> from chimerax.atomic import all_atomic_structures: >>> for s in all_atomic_structures(session): >>> for cs_id in s.coordset_ids: >>> s.active_coordset_id = cs_id >>> atoms = s.atoms >>> atoms.selecteds = atoms.scene_coords[:,0] < 0 >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>>> >>>> Thank you. >>>> Best, >>>> Siyoung >>>> >>>> On Tue, Oct 17, 2023 at 4:06 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >>>>> Oops. If you put this code in a file it needs to have a ".py" suffix, so call it select.py. The ".cxc" suffix is for ChimeraX commands. >>>>> >>>>> Tom >>>>> >>>>> > On Oct 17, 2023, at 12:58 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Hi Siyoung, >>>>> > >>>>> > Here is Python code to select all atoms with x < 0. >>>>> > >>>>> > from chimerax.atomic import all_atoms >>>>> > for a in all_atoms(session): >>>>> > if a.scene_coord[0] < 0: >>>>> > a.selected = True >>>>> > >>>>> > You can type this in the ChimeraX Python shell (menu Tools / General / Shell), or probably easier, put it in a text file "select.cxc" and open that in ChimeraX to run it. >>>>> > >>>>> > Tom >>>>> > >>>>> >> On Oct 17, 2023, at 9:04 AM, Elaine Meng via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >> >>>>> >> Hello Siyoung, >>>>> >> Sorry no, I can't think of a way to do it with a ChimeraX command. Maybe you could do it by using the initial orientation of the structure (just opening and not rotating) and veerrryyy carefully using the mouse to select a rectangle (Ctrl-click drag) but that is probably too difficult. Also you would need to know where X=0 is from just looking at the structure. >>>>> >> >>>>> >> Certainly you could do it with Python, but somebody else would have to advise on that. >>>>> >> >>>>> >> Best, >>>>> >> Elaine >>>>> >> ----- >>>>> >> Elaine C. Meng, Ph.D. >>>>> >> UCSF Chimera(X) team >>>>> >> Department of Pharmaceutical Chemistry >>>>> >> University of California, San Francisco >>>>> >> >>>>> >>> On Oct 17, 2023, at 5:33 AM, Siyoung Kim via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> >>> >>>>> >>> Hello, >>>>> >>> >>>>> >>> Would there be a selection keyword that selects atoms based on their coordinates? For instance, is there a way that I can select atoms whose x coordinates are below 0 (e.g., x < 0)? >>>>> >>> >>>>> >>> Thank you. >>>>> >>> Best, >>>>> >>> Siyoung >>>>> >> >>>>> >> >>>>> >> _______________________________________________ >>>>> >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> >> >>>>> > >>>>> > >>>>> > _______________________________________________ >>>>> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>>> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>>> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>>> > >>>>> >>>> _______________________________________________ >>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> > <test.mp4>

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crop the map
by Dmitry Semchonok 25 Oct '23

25 Oct '23

Dear colleagues, Could you advise on how to crop the map to the new 3D box size and save those changes? Thank you. Sincerely, Dmitry

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