- ChimeraX-users - RBVI Mailing Lists

bundle_info.xml API changes
by Eric Pettersen 01 Apr '20

01 Apr '20

Any non-developers feel free to skip this message. Even for developers, unless you are writing a toolshed bundle that uses the DataFormat, Open, Save, and/or Fetch tags in the bundle’s bundle_info.xml file, you could skip this message. For the two of you that are left, in anticipation of the the ChimeraX 1.0 release sometime this year we are changing some APIs we are unhappy with. Namely, the tags in the in bundle_info.xml that I mentioned in the previous paragraph. As they stand, they are not easily extensible and it is not obvious without looking at the documentation what the various fields do. On top of that, it is difficult to take the information in those tags and present interfaces for options in ChimeraX’s Open/Save file dialogs. Also, there is nothing preventing keywords added to the open command by one bundle from conflicting with keywords added by another bundle. We will be migrating those tags to use bundle_info’s Manager/Provider architecture (described here <https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/bundle_info.html>). Instead of fixed fields, you have keyword/value pairs, which is slightly more self-documenting. Also, a manager can ask a provider for various things, so in one case the manager can provide a partially processed “open” command along with the “rest of line” for the provider to handle its options, if any, and actually open the file, whereas in another the manager can ask for a widget containing options to show in an open or save dialog. In brief, the change allows us to solve some issues that looked pretty intractable with the old scheme. The exact details of the managers and providers supporting these functions are not detailed in that link (just the generic mechanism), but details will be added as implementations are completed. For convenience, there will some period of time when both the old scheme and new scheme will both work, but we anticipate dropping the old scheme before the 1.0 release. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Keep coordinates and radii of atoms
by Aritz Roa Eguiara 31 Mar '20

31 Mar '20

Dear ChimeraX Team, I am trying to represent a channels in ChimeraX. The output of Mole 2.5 is a .py for Chimera and I am trying to manually transfer to ChimeraX. Is there any easy way to do that? I would need that the coordinates and the radii of each atom is respected, but if I save it from Chimera in PDB the radii is not saved and saving the different atoms manually and then adding a script to give the the proper radius is extremely time consuming. Any suggestion? All the best, Aritz

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upgrading ChimeraX Toolshed
by Greg Couch 30 Mar '20

30 Mar '20

We're modernizing the ChimeraX Toolshed code base. There is a chance that it won't be accessible for day or two. And there's a chance it will be fixed in the next hour. :-) -- Greg

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volume onesmask usage question
by Alexis Rohou 30 Mar '20

30 Mar '20

Hi there, I was trying to use "volume onesmask" to go quickly from a dusted surface of a low-pass-filtered volume to a mask volume with the same dimensions, spacing, etc. as the input map. I thought "fullmap" might be a way to achieve this (the doc says "The remaining options are the same as described for volume mask"), but I don't think that option actually works with "volume onesmask": volume onesmask #3 fullmap true *Expected a keyword* Is there a "onesmask"-like operation or set of options that creates an output volume that's on the same grid as the input volume? Thanks, Alexis

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ToolInstance context menu displaying help
by Anthony James Schaefer 27 Mar '20

27 Mar '20

Hello, can tools' "Help" option in the context menu be changed to use `ToolInstance.display_help` instead of running the `help` command? I'd like to keep most of my documentation on GitHub. The `help` command cannot open URLs, so I thought I'd overwrite my tools' `display_help` methods to use `open` instead. However, I discovered this method isn't used anywhere. I've tried changing `_show_context_menu` in chimerax.ui.gui (around line 2087) to `help_action.triggered.connect(ti.display_help)`. It seems to behave the same for all built-in tools. I understand there might be reasons to not do this (e.g. users might not be able to connect to the internet). I'd like to keep stuff on GitHub because I can make a page on a GitHub wiki page faster than an HTML doc. Regardless of how tools' help pages get shown, I'd like to have examples of what my bundle can do on the GitHub wiki. To that end, my GitHub wiki could serve a dual purpose: a showcase and documentation. Best, Tony

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Coloring of atomic model surfaces
by Rasmus Kock Flygaard 27 Mar '20

27 Mar '20

Dear ChimeraX developers, I have a question regarding coloring of a surface representation of an atomic model. I open the pdb file and turn on surface representation with the command, surface #1 resolution 6 This works just fine. Then I color the surface by command, color #1 skyblue This also works fine. And then I want to color the surface of only a range of residues using the command, color #1:50-86 indigo target s But nothing happens. The reply log says that 1 surface was colored but no color changes is seen in the surface representation. Am I missing something in the color command for surfaces?? Any help is appreciated! Best, Rasmus Kock Flygaard

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addAtom
by Aritz Roa Eguiara 26 Mar '20

26 Mar '20

Dear ChimeraX team, Maybe it is a silly question but I have been trying to add atoms on ChimeraX but I have not found the way, is there any possibility? I need to plot a channel on my protein but I do not manage to do it without that. Thank you in advance. Best wishes, Aritz

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Loss of image quality
by Lucas Tafur 26 Mar '20

26 Mar '20

Hi, I hope everything is going well considering the circumstances. I've been enjoying ChimeraX but have now encountered an annoying issue. Without any apparent reason, the quality of my rendered images becomes very bad, eventhough I'm using the same command and sampling. I've been saving using the following command: save C:\Users\XXXXX.png transparentBackground true supersample 3 It always worked fine until this week (actually, two days ago the quality was still good). Suddenly it started getting bad. I'm using version 0.93. Any help would be appreciated. Best, Lucas

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NMR CSPs
by Bohg, Claudia 25 Mar '20

25 Mar '20

Hey, is it somehow possible to use this attribute in Chimera X? http://www.cgl.ucsf.edu/chimera/data/nmrcolor-nov2017/nmrcolor.html Best, Claudia

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ChimeraX VTK Export
by Angelos Angelopoulos 19 Mar '20

19 Mar '20

Hello, It would be absolutely great if ChimeraX supported exporting to a VTK file like Chimera did. Are there any plans to port the VTK export functionality from Chimera to ChimeraX? If not, please consider doing it. Thank you very much. Sincerely, Angelos Angelopoulos

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Re: [chimerax-users] Making movies and fitting structures into cryoEM
by Elaine Meng 13 Mar '20

13 Mar '20

Dear Madhan, My previous message already explained how you would move only one model in ChimeraX (you have to select part of it with Ctrl-click and then use the mouse mode "translate selected models" etc.). For example clicking the "translate selected models" icon in the Right Mouse toolbar assigns this mode to the right mouse button (= trackpad + Alt on Windows, trackpad + command key on Mac). See here for which Right Mouse icons go with which functions: <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> It sounds like even when you are moving everything together, you don't know how to translate models (up, down, left right) in either program. In Chimera, the default for translation is middle mouse button, or touchpad + option key on Mac (the key may be different on WIndows, just try the ones to the left of the space bar to see which one works). See the Mouse Preferences (menu Favorites... Preferences, change to category: Mouse) for button assignments: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/preferences.html#Mouse> See also "using touchpad or 1-button or 2-button mouse" <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#2button> In ChimeraX, use command "mousemode" if you want to change assignments. The "mousemode" manpage linked below also shows a table of the default assignments, e.g. translation is middle mouse button, or Mac trackpad + Alt (or 3-finger drag if multitouch enabled), or Windows trackpad + Ctrl-Alt. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> I hope this helps, Elaine > On Mar 13, 2020, at 11:28 AM, Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> wrote: > > Dear Elaine > > Thank you again. > > In Chimera - am able to lock one model by unchecking the "A" box in the Model Panel - in the particular example am working with, its the Cryo-EM density map - the other model is the atomic model from the crystal structure (PDB file) - am not able to move the atomic model into the Cryo-EM density model. When I use the mouse, all am able to do is rotate the second (atomic) model at the same place - am not able to move it from its location on the screen. > > In ChimeraX - its the same problem and since it does not have the model planel, both models are moving at the same time - the commands are a bit confusing as well > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Sent: Friday, March 13, 2020 10:07 AM > To: Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM > > Dear Madhan, > I don't understand "not able to lock" in ChimeraX or "not able to move" in Chimera. > > In Chimera, you can control whether each model is hand-movable or not by checking/unchecking the "A" (activated) boxes in the Model Panel, as discussed here: > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef> > > Show the Model Panel from the Chimera Favorites menu. > > By hand you can then move the atomic model to roughly the correct place in the map before optimizing the fit with Fit in Map. > > The ChimeraX tool Fit in Map is basically the same as the Chimera tool. However, in ChimeraX, the way to move just one model is to select some part of it (Ctrl-click) and then use the mouse mode "move selected models" as discussed in this earlier post: > <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> > > Also if you additionally press Shift, that mode switches between rotate and translate. > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/mousemodes.html> > > 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 12, 2020, at 6:23 PM, Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> wrote: > > > > Dear Elaine > > > > Thank you - all those tips were useful. > > > > With ChimeraX, am not able to lock the Cryo-EM density map and then use the crystal structure to fit into it. > > > > Whereas Chimera allows me to do so - however am not able to move the crystal structure to superimpose on the CryoEM density to do the 'Fit in Map' > > > > is it something am not doing right? I follow these instructions - https://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#… > > > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > > Sent: Wednesday, March 11, 2020 5:22 PM > > To: Tirumalai, Madhan R <mrtirum2(a)Central.UH.EDU> > > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Subject: Re: [chimerax-users] Making movies and fitting structures into cryoEM > > > > Dear Madhan, > > Although ChimeraX doesn't yet have a movie-making dialog (GUI), you can make movies with ChimeraX command scripts. In a command script (plain text file named ending in .cxc), the "movie" command does recording and creating a movie file, whereas other commands (show/hide, color, turn, 2dlabel, etc.) can be used to control display, motions, and labeling... whatever you want to happen during the movie. Simply opening the .cxc file runs the commands. > > > > You can change volume thresholds with the "volume" command "level" option, for example: > > > > volume #1 level 0.08 > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#general> > > > > To gradually change the threshold over multiple display frames, you can combine the "volume" command with the "perframe" command, for example: > > > > perframe "volume #2 level $1" range 0.1,0.3 frames 120; wait 120 > > > > (those should be plain text quotation marks, although the e-mail display may change them to fancy quotation marks) > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> > > > > See ChimeraX "making movies" page and links therein: > > <http://rbvi.ucsf.edu/chimerax/docs/user/movies.html> > > > > ...including movie-making tutorials: > > <http://www.rbvi.ucsf.edu/chimera/data/sbgrid-apr2017/cryomovie.html> > > <http://www.rbvi.ucsf.edu/chimerax/data/movies-may2019/moviemaking.html> > > > > See also general information on ChimeraX command files: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> > > > > For your other question, if you are asking how to fit an atomic structure into a map, see the "Fit in Map" tool and/or "fitmap" command: > > <http://rbvi.ucsf.edu/chimerax/docs/user/tools/fitmap.html> > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/fitmap.html> > > > > Or to compare one atomic structure to another atomic structure, you can superimpose them with the "matchmaker" command: > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html> > > > > Chimera has a Matchmaker GUI, but ChimeraX does not have the GUI yet, only the command. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > >> 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

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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

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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>

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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> > > >

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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

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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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