- ChimeraX-users - RBVI Mailing Lists

cartoon highlight color?
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, Is there a way to customize the highlight color of helices and strands? For example, here is how it appears in Pymol. https://pymolwiki.org/index.php/Cartoon_highlight_color Thanks, Joel

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cxc script does not execute 'surface dust' command
by Joel Meyerson 07 Apr '20

07 Apr '20

Hi, I am observing inconsistent behavior in the ‘surface dust’ command. When I launch ChimeraX and execute the following commands one-by-one at the command line everything works as expected. However, if I place the commands in a cxc script, then double click the script ChimeraX launches and the script executes, but the ‘surface dust’ command does not hide the dust. In addition, within that same session I can then enter the ‘surface dust’ command manually and it works as expected. I’m running ChimeraX Daily 0.93 (2020-04-04) on Mac OS 10.15.1. Do you know why the command is not working inside a script? close all open map.mrc turn x 90 volume erase #1 center 175,160,314 radius 100 outside true surface dust #2 size 40 Thanks for the help. Joel

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Command "mlp"
by Cosmin Stefan Butnarasu 06 Apr '20

06 Apr '20

Hello, Hope to find you doing well. I am a PhD student in Pharmaceutical and Biomolecular Sciences and I am writing this email because I would like to better understand the mlp command. First of all, I have to say that I am a very novice on ChimeraX, I discovered this software basically few days ago, so I will write concepts that maybe are not properly correct. I would like to calculate the surface hydrophobicity of a protein. I saw that the mlp command graphically displays the molecular lipophilicity potential, which I suppose is somehow close to the surface hydrophobicity. However, when mlp command is compute, in the Log panel are shown three values, a minimum, a mean and a maximum, which I have not completely understood what they are for (see the picture attached). I searched on ChimeraX manual and I found that the SES surface could stand for “solvent-excluded surface” but I’am not sure about this. If so, could the mean SES value be a measure of the surface hydrophobicity of the protein? If not, can you suggest me a method to obtain not only a graphical display but also a value of the overall molecular lipophilicity potential? Thank you in advance! Cosmin Stefan Butnarasu ********************************************************* Cosmin Stefan Butnarasu, PhD Student Department of Molecular Biotechnology and Health Sciences University of Torino Via Gioacchino Quarello 15, 10135 email: cosminstefan.butnarasu(a)unito.it *********************************************************

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Questions about ChimeraX
by Yuhua Fang 06 Apr '20

06 Apr '20

Hi Recently I transferred to ChimeraX from the old version. I found: 1. Some SMILE strings copied directly from ChemDraw cannot be recognized by ChimeraX, such as O=C1NC2=C(/C1=C3NC4=CC=CC=C4C/3=C\O)C=CC(Br)=C2 2. Correct me if I am wrong but ChimeraX seems not able to do molecule docking/ligand minimization like the old version, right? Thank you Joshua Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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Show map only around certain selection
by Karim Rafie 02 Apr '20

02 Apr '20

Dear all, I was wondering how to show part of a map only surrounding certain residues, i.e. I have coordinates for a multiple-chain PDB but I only want to show the electron density surrounding one chain. Any help would be greatly appreciated. Best, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden

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ChimeraX equivalent to "Chimera web data"?
by Ben Webb 01 Apr '20

01 Apr '20

We have a number of web services and tools that generate web data (*.chimerax) files for legacy Chimera. (Typically they load in a PDB file and an alignment and apply some sort of custom view.) What would the equivalent be for ChimeraX? Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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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

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

select menu bundle tags
by Anthony James Schaefer 12 Feb '20

12 Feb '20

Hello Are there any plans to add bundle tags for putting selectors on the select menu? Thanks, Tony

3 2

Color by Conservation in ChimeraX
by Sean Moore 11 Feb '20

11 Feb '20

Hello, I read an older post that color by conservation is pending for ChimerX. Is it available now? When I open a sequence alignment that I generated elsewhere, it shows the alignment and conservation, it identified the correct protein chain, but there is no menu in that window to assign the colors to the protein. (no option to "Again from the Multalign Viewer menu, choose: Structure... Render by Conservation. This will call Render by Attribute, in which…”) Should I use Chimera for this instead of ChimeraX? Sean

3 4

Reproduce exact view
by Christophe Leterrier 10 Feb '20

10 Feb '20

Hi, I haven't been able to find how to - log - set - store - recall a precise view (ie get the same exact image if I do a snapshot). First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session. Thanks for your help! Christophe

4 7

Re: [chimerax-users] Crossfade rough transition while making a movie
by Elaine Meng 07 Feb '20

07 Feb '20

Hi Ahmad, This appearance of snapping to the position may not be very avoidable, because “view” transitions just take a linear path and it always looks somewhat abrupt (to me anyway) when it reaches the endpoint. There is currently no option to make it go slower when it is closer to the end. You could try saving an additional position along the way and using it as an intermediate and then going slower after the intermediate by using more frames per distance, and/or you could try adding a few extra wait frames between when it reaches the endpoint and when it starts the crossfade, for example: view pos6 50; wait 100 crossfade 50; view pos5; wait 50 (OR: crossfade 50 viewpos5 50; wait 50) However, I don’t know if either of those would help much. When I’m making a movie I usually end up experimenting a lot with numbers of frames in movements and waits, but the sharp endpoints of view transitions are not currently avoidable as I understand it. Best, Elaine > On Feb 7, 2020, at 1:10 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Hi Elaine, > > Sorry if my description was vague. With the modification you suggested, I still have the rough transition between pos6 and pos5 but with a slower crossfade into pos5. > > I attached my movie (made with script in the original post) to get a better idea of what I mean. At 0:2, pos6 appears like it snaps in place, then the crossfade into pos5 occurs. > > Is there a way to make the transition smoother? > > Regards. > > On Fri, Feb 7, 2020 at 12:18 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ahmad, > Not sure I understand what you actually want, but I’ll try to answer anyway… > > If you mean you want to see a gradual change in position from pos6 to pos5 then you would need to put a frames number after pos5, for example: > > crossfade 50; view pos5 50; wait 50 > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > (Crossfade does not interpolate the movement, you have to do it with the view command.) > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> > > Some minor notes on scripts. You do not need “;” at the end of any line; it is only needed to separate commands that are on the same line as each other, as in the example above. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Feb 6, 2020, at 11:59 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! > > > > view pos4 > > wait 30; > > > > movie record supersample 3 size 1920,1080 > > view pos6 50 > > wait 50; > > crossfade 50; view pos5 > > wait 50; > > movie encode IJ_movie3.mp4 quality high > > <IJ_movie3.mp4>

2 1

Crossfade rough transition while making a movie
by Ahmad Khalifa 07 Feb '20

07 Feb '20

I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! view pos4 wait 30; movie record supersample 3 size 1920,1080 view pos6 50 wait 50; crossfade 50; view pos5 wait 50; movie encode IJ_movie3.mp4 quality high

2 1

Command line interface is detached
by Ahmad Khalifa 04 Feb '20

04 Feb '20

My command line interface used to be attached at the bottom. Now it's floating on the screen and the only way I could attach it back is to place it in the right panel. How can I attach it back to the bottom of the screen, spanning the entire length of the ChimeraX window? P.s. I'm running Linux Centos 7.

2 1

Chimerax on a HPC cluster
by Thu Nguyen 31 Jan '20

31 Jan '20

Dear all, I administer a small HPC cluster (Rocks 7) at a bio research institute and a user has requested Chimerax to be installed on it. Has anyone successfully done so ? If yes, I wish to help some hints as to how it is done and an assessment of how it performs . Thanks and regards Thu D. Nguyen Systems & Computational Biology Platform Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne www.bio21.org

2 1

question about ChimeraX Hide Dust Feature
by Philip Schmiege 29 Jan '20

29 Jan '20

Hi I just downloaded the new ChimeraX, and was wondering where the Hide Dust option is located. I cannot find it. Any help is greatly appreciated! Philip _____________________________________ Philip Schmiege Graduate Student in Biophysics Li Lab, Dept. of Molecular Genetics, L5.162 philip.schmiege(a)utsouthwestern.edu ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 3

Fwd: Colors from snapshots
by Christophe Leterrier 29 Jan '20

29 Jan '20

Hi, I wonder why the colors in the snapshots (and movies) from ChimeraX are always washed-out compared to the colors I get live in the viewer. Attached is a screenshot with the viewer on the left, the corresponding snapshot on the right: one can see how the snapshot is desaturated compared to the viewer. From my limited tests it is the case when saving as both PNG and PPM, and I wonder if this could be corrected. I could saturate the screenshots afterward but it doesn't seem right to me to grossly mess with color levels post-hoc given how stunning the shaded rendering from ChimeraX are. Thanks, Christophe

3 5

Scripting Resources
by llehmann＠uoregon.edu 28 Jan '20

28 Jan '20

Hello, I am a teaching assistant with the University of Oregon for our Structural Biochemistry course. Currently, the course is taught using PyMOL, but we would like to transfer to ChimeraX in the future. A large portion of the course relies on publically available scripts designed for PyMOL that currently do not have equivalents for ChimeraX. We are wondering if there are plans to have a ChimeraX wiki with scripting resources similar to PyMOL at some point, or whether we'd need to write any python scripts ourselves? Of course I understand that ChimeraX is still developing, I'd just like to get a sense of whether we can reasonably transfer the course to ChimeraX in the future. Thank you for your time. Best, Lauren Lehmann Biochemistry Graduate Student University of Oregon

3 4

volume morph
by Karim Rafie 28 Jan '20

28 Jan '20

Dear all, I would like to create a morph movie between two volumes in ChimeraX, however I am having difficulties with generating it. I am using the following command (e.g.) to "create" the morph: volume morph #1,2 frames 50 After it has completed I get a new volume but I can't review the frames themselves, i.e. the output is a new map. I tried scouring the tutorials and command page but can't find a solution. I tried it with the ChimeraX Ubuntu 16.04 distribution as well as the generic linux version. Any help would be greatly appreciated. Best wishes, Karim ############################################## Karim Rafie; PhD, AMRSC Postdoctoral Research Fellow Carlson Lab Department of Medical Biochemistry and Biophysics Umeå University Umeå / Sweden

3 4

interface residue plot save as text file?
by Marta Perez Illana 28 Jan '20

28 Jan '20

Hi alI I have very recently started to play around with ChimeraX. I am trying to use the interface functionality as a substitute of traditional find contacts/clashes ( I am aware of the differences but I think for my purpose are both fine). I would like to save somehow the "interface residue plot", rather than the image of the plot per se, a kind of text file for example... is there a straight fordward way that am I missing? Thanks!! Marta

2 1

SMILES structures
by Eric Pettersen 27 Jan '20

27 Jan '20

Hi all, SMILES strings can now be translated to 3D structures (via NIH NCI or Indiana University web services), e.g. “open smiles:c1ccccc1”. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 1

dome camera mode
by James Hedberg 24 Jan '20

24 Jan '20

Hi, I see from previous threads (3/2019) that there are no plans to add the dome projection/fisheye mode for the camera control on ChimeraX: "It would take some days of work to add dome camera mode to ChimeraX. We have no funding for that and very few people will use it so I'm afraid that is not likely to be implemented.” I understand there is probably not a lot of current demand for this feature, however, in the spirit of Field of Dreams - if you build it, they will come. There is a growing interest in using planetariums/full domes for non-astro related sci-viz, yet very few tools available to do so. We’re currently using Chimera (regular) to do sci-viz in the planetarium for proteins and more. Knowing that this would be supported down the road when ChimeraX takes over (not sure when that will happen) would certainly be nice. You could make ChimeraX uniquely positioned to fill this deficit. Anyway, just a hand raised here for an informal poll of ‘who wants dome mode’. Thanks, James Dr. James Hedberg Physics Lecturer Director, CCNY Planetarium<https://ccnyplanetarium.org> City College of New York Department of Physics

2 6

ChimeraX and REST service interoperation
by Mungo Carstairs (Staff) 24 Jan '20

24 Jan '20

Hi, With your helpful hints, I have a version of Jalview interacting with ChimeraX in the same way it can already with Chimera, over the REST interface. Functionality includes loading structures, aligning, colouring, raising labels on structure on mouseover in Jalview, and exchange of residue features/attributes. I have just one interaction not working yet: highlighting residues in Jalview when a selection is made in ChimeraX. - Jalview starts listening for ChimeraX selections with (e.g.) info notify start selection jalview prefix SelectionChanged url http://localhost:49981/jalview/chimera1 - user makes a selection in ChimeraX - ChimeraX sends GET?chimerax_notification=SelectionChangedselection+changed - Jalview send 'info selection level residue' - no response / timeout; ChimeraX log reports 'broken pipe error' Exception happened during processing of request from ('127.0.0.1', 50714) Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 316, in _handle_request_noblock self.process_request(request, client_address) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 347, in process_request self.finish_request(request, client_address) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 360, in finish_request self.RequestHandlerClass(request, client_address, self) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 720, in __init__ self.handle() File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 426, in handle self.handle_one_request() File "/Applications/ChimeraX_Daily.app/.../http/server.py", line 414, in handle_one_request method() File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 97, in do_GET self._run(args) File "/Applications/ChimeraX_Daily.app/.../site-packages/chimerax/rest_server/server.py", line 174, in _run self.wfile.write(data) File "/Applications/ChimeraX_Daily.app/.../socketserver.py", line 799, in write self._sock.sendall(b) BrokenPipeError: [Errno 32] Broken pipe NB this is all before a response has been sent to the 'SelectionChanged' message. Any idea what the problem is here please? Do I need to reply to the first message before sending another? The same mechanism does work ok with Chimera. Thanks, Mungo p.s. I noticed the 'listinfo' command (undocumented) seems to behave like 'info'. Should I continue to use 'list' or switch to 'info'? * [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

2 3

PubChem
by Eric Pettersen 22 Jan '20

22 Jan '20

Hi all, As of tomorrow’s build, ChimeraX will be able to fetch PubChem entries, e.g. “open pubchem:2519” or “open 2519 from pubchem”. —Eric Eric Pettersen UCSF Computer Graphics Lab

1 0

Next/previous buttons for model display/activation?
by Oliver Clarke 21 Jan '20

21 Jan '20

Hi, I use the Next/Previous buttons in the lower portion of the Chimera GUI all the time for quickly cycling through maps/models (e.g. when inspecting the results of 3D classification). Would it be possible to bring these to the model panel on ChimeraX? Cheers Oli

2 1

Re: [chimerax-users] silhouettes on mesh in ChimeraX
by Tom Goddard 21 Jan '20

21 Jan '20

Hi Gabe, I agree the silhouette edges look bad on meshes. ChimeraX cannot turn off silhouette edges on just meshes. It uses the scene depth at each pixel to compute the edges and the mesh contributes to the scene depth. This is a different method than Chimera used. It has the advantage that it renders basically as fast as without silhouettes where Chimera renders about 2x slower with silhouettes. The Chimera method won't work in ChimeraX because ChimeraX uses modern OpenGL (core profile) which no longer supports drawing linewidth greater than 1. The Chimera algorithm worked by drawing the edges of every triangle in the scene with linewidth 2 and slightly behind the triangle. This linewidth 1 only limitation of modern OpenGL also is a problem with meshes on retina displays where the lines are too thin and hard to see. At any rate, there are ways to provide silhouette edges only on some models but not meshes. But they are hard to implement. I'll make a ticket for it but don't expect to be able to do it with our limited resources. https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2765 So the best advice I have is show the atomic model and mesh without silhouettes or use Chimera. Tom Examle of mesh with silhouette edges > On Jan 18, 2020, at 4:01 PM, Gabriel Lander <glander(a)scripps.edu> wrote: > > Hi Tom, > One of the "go-to" representations to demonstrate the quality of a modeled PDB in an EM density is sticks shown in a volume mesh. In Chimera when you turn on silhouettes they would only show around the atoms, but not the mesh. This is not the case in ChimeraX, and renderings with silhouettes and meshes look really messy. Is there a way to specifically turn off silhouettes on meshes but not atoms? > Thanks, > -gabe > >

1 0

How to batch process structures?
by jacky zhao 21 Jan '20

21 Jan '20

Hi everyone, I have tried to use chimeraX yesterday. It is vey cool! I just wonder how to batch process the structures? We will generate more than thousands of structures and will analysis the binding interface. Can I use chimeraX to instantly show the interface interactions one by one? Thank you for your time. Jacky

3 5

Exporting image in 300 DPI
by Hassan Ahmed 21 Jan '20

21 Jan '20

Hello, I wanted to ask if it is possible on ChimeraX to export image with 300 or 150 DPI? I can not find a possible selection tool as the older chimera versions. Is there a certain command or an option to do it? Thank you in advance, Regards, Ahmed -- Ahmed Hassan Institute of Plant Biology Braunschweig University of Technology Spielmannstrasse 7 38106 Braunschweig Germany Tel: +49 - 531 - 391 5885 e-mail: a-a.hassan(a)tu-braunschweig.de

2 1

Tile a vseries
by Sean Connell 17 Jan '20

17 Jan '20

Hello, I was wondering if it is possible to tile multiple volume series such that one can have 2-3 series playing side by side? If so could you suggest the syntax for the tile command I cannot seem to get it right? I have the two vseries loaded as #1 and #2 (and each series has 10 sub volumes). I have tried variations of tile #1,2 columns 2 spacingFactor 1 and get errors like this: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", line 258, in execute cmd.run(cmd_text) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2837, in run result = ci.function(session, **kw_args) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in tile spacing = max([m.bounds().radius() for m in models]) * spacing_factor File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in <listcomp> spacing = max([m.bounds().radius() for m in models]) * spacing_factor AttributeError: 'NoneType' object has no attribute 'radius' AttributeError: 'NoneType' object has no attribute 'radius' File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/std_commands/tile.py", line 27, in spacing = max([m.bounds().radius() for m in models]) * spacing_factor Thanks in advance for any suggestions you have. sean

2 1

Save scene like in "Chimera"
by Lau Kelvin 17 Jan '20

17 Jan '20

Hello all, Is there a save scene command like in chimera. I have found the command for positions via “view”. If not, its back to saving many sessions at the moment. Best, Kelvin -- Kelvin Lau https://people.epfl.ch/kelvin.lau Protein production and structure core facility - PTPSP EPFL SV PTECH PTPSP AI 2146 (Bâtiment AI) Station 19 CH-1015 Lausanne Switzerland Email: kelvin.lau(a)epfl.ch<mailto:kelvin.lau@epfl.ch> Phone: +41 21 69 30267<tel:+41%2021%2069%C2%A030267> If unreachable: +41 21 69 34494<tel:+41%2021%2069%C2%A030267>

3 4

Show active site metal and ligand in morph
by Yifan Wang 16 Jan '20

16 Jan '20

Dear chimeraX developer, I am a graduate student from university of Texas at San Antonio. I’m trying to make a movie to compare two of my structures (resting state and substrate bound) using the function “morph”. But there is a problem, I very appreciate if you can help me figure this out. As show in Figure 1, I have two structures superposed. The resting state (nude) contains an active site metal ion coordinated by three residues and 3 water molecules. And the substrate bound (blue) also contains a metal coordinated by the same residues, a remaining water molecule, and a new ligand as my substrate. After I entered command “morph #1,2 frames 60”, I got the result of Figure 2. However, the active site metal ion and the water and substrate are missing. I want to show the active site changes between model 1 and 2. Model #3.1 seems keep the metal coordination bonds but I can’t make it present even with “show”. So my question is how to show the metal and the corresponding ligands in morph? Regards, Yifan Wang [cid:143A130E-412D-4674-AB95-99EA0C21DF44@UTSARR.NET] [cid:90E28A3D-AB8F-402F-A982-8B40682176A1@UTSARR.NET]

2 6

Re: [chimerax-users] [Chimera-users] Chimera X commands
by Elaine Meng 14 Jan '20

14 Jan '20

Hi Drew, You may be interested that there is also a mailing list specifically for ChimeraX questions: <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> We’re glad you like Chimera! For ChimeraX we wanted to make various command-line improvements such as to make it easier to specify chains, to give several commands more obvious names or make them easier to use, etc. If you download ChimeraX the User Guide is in the Help menu, with the top page being an index of tools and commands that links to their individual pages. We also have a copy of the User Guide at our website: <http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html> The User Guide includes a page on the ChimeraX atomspec syntax and another on how it is different from Chimera’s. <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec-diffsum.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 Jan 13, 2020, at 9:53 PM, Andrew Waight <waight(a)msg.ucsf.edu> wrote: > > Hello all, > I've been an exclusive Chimera user for over 15 years. I have been scripting a lot in python lately and am super excited to learn that ChimeraX is written in python3. I totally want to import some chimera functions into my programs. Problem is, the ChimeraX command syntax seems all new (i can't even really figure out how to select properly, is there a ChimeraX command index that I am missing and is ChimeraX for me? ChimeraX looks beautiful by the way. Thanks you guys are amazing! > Drew

1 0

Show dashed lines after hiding atoms
by Ahmad Khalifa 09 Jan '20

09 Jan '20

How can I show the dashed lines that signifies an interruption in the structure after I do "Hide model-spec atoms"? Regards.

2 1

Chains with symbol ID such as % and $ cause errors
by Ahmad Khalifa 08 Jan '20

08 Jan '20

I can do "show #2/m cartoons" for a chain with ID m, but for a chain with ID % or $, I get: show #2/% cartoons Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword

2 2

Copy/combine function in ChimeraX
by Ahmad Khalifa 07 Jan '20

07 Jan '20

How do I duplicate (back up) a model that I already have open in ChimeraX? Regards.

2 1

ksdssp equivalent in Chimerax
by Elliott, Jabari 07 Jan '20

07 Jan '20

Dear users, I was wondering if there was a way to adjust the preset thresholds for betasheet and helix depictions in chimerax. Essentially, I am looking for a “ksdssp” command equivalent. - “Ksdssp –s 2” Best, Jabari

2 1

differentiating file category
by Anthony James Schaefer 02 Jan '20

02 Jan '20

Hello, Is there any way I can get a bundle to know that I'm trying to open a file from a certain category (e.g. Molecular structure vs. Molecular trajectory) from the File -> Open... menu? I'm trying to build a plugin that will allow me to open Gaussian log files in ChimeraX. I'd like to have it open the optimized structure when I go File -> Open... and change the file filter to "Molecular structure files". When I set the file filter to "Molecular trajectory files", I'd like it to open the log file as a trajectory with each frame being one of Gaussian's optimization steps. The file stays the same, I just want to have my 'open_file' method know that it should open the file differently. So far, I've tried having multiple 'Open' entries in my bundle tags. Here are some relevant tags from my setup.py: "ChimeraX :: DataFormat :: LOG :: Gaussian output file :: Molecular structure :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: DataFormat :: LOG trajectory :: Gaussian output trajectory :: Molecular trajectory :: .log :: :: :: :: :: Gaussian output file :: utf-8", "ChimeraX :: Open :: LOG :: Gaussian output file ::", "ChimeraX :: Open :: LOG trajectory :: Gaussian output trajectory :: :: coordsets:Bool", My 'open_file' definition line is: def open_file(session, path, format_name, coordsets=False): While I'm testing, I've set up my 'open_file' method to print the arguments that get passed to it. When I use File -> Open..., I can see that 'format_name' is always "Gaussian ouput file" (never "Gaussian output trajectory") and 'coordsets' is always False, regardless of the file filter. When I use the `open` command (`open asdf.log coordsets true`), 'coordsets' is True and 'format_name' is "Gaussian output file". I can work with the open command because of the 'coordsets' argument, but I'd like to know if there's something I can do with the File -> Open... menu. Thanks, Tony

3 2

Superimposition of Carbohydrate Molecules
by Rajarshi Roy 18 Dec '19

18 Dec '19

Dear ChimeraX, I am trying to superimpose multiple carbohydrate chains using chimeraX. Using match command, I am unable to do the same. Here is my command: *match #2:1-4 to #1:1-4* But I am getting the following error: Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'match' command to superimpose small molecules/ligands. Already I am using match command, still why the same error is showing? Please advise me on how to proceed? Thank you in advance. -- *with regards* *Rajarshi Roy* *PhD Research Scholar* *Biosciences and Biomedical Engineering* *Indian Institute of Technology, Indore* *India*

2 2

Amber trajectories
by Lewandowski, Jozef 16 Dec '19

16 Dec '19

Hi, Quick question. Are there any plans for ChimeraX to support opening also Amber trajectories (as Chimera does)? 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/>

2 1

Re: [chimerax-users] [Chimera-users] view MD ChimeraX
by Elaine Meng 16 Dec '19

16 Dec '19

Hi Fabian! The “Molecular Dynamics Viewer" tool is available on ChimeraX Toolshed from outside developers, i.e. it is not written by our group. However, the description on Toolshed pretty much says what it does: it is a simple graphical interface for showing multiframe PDB files as a trajectory. It doesn’t read other trajectory formats. <https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer> After you install it, it will be under Tools… General in the menu. Starting the tool from that menu will open a window in ChimeraX and then clicking the Open button in that tool will allow you to browse to and open a multiframe PDB file, like 1PLX.pdb downloaded from the RCSB PDB (NMR structure, so it has multiple conformations each as a MODEL in the single PDB file). Then you can use the other buttons, e.g. Start to play as a a trajectory. (I wasn’t sure what you meant by “not able to use it.”) However, *without* this tool: Just using ChimeraX without installing anything extra, you can read in a few trajectory formats and then play them with the “coordset” command or using a slider interface shown with “coordset slider". The trajectory formats known to ChimeraX are listed here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#trajectory> <http://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> See also “coordset” and “coordset slider” <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. There is also a chimerax-users(a)cgl.ucsf.edu mailing list, CC’d here. > On Dec 15, 2019, at 1:50 AM, Fabian Glaser <fglaser(a)technion.ac.il> wrote: > > Hi, > I installed Molecular Dynamics Viewer in ChimeraX but I am not able to use it, . I use it successfully in Chimera (no X). But in ChimeraX. > Can you please help me? > Best, > Fabian

1 0

SSL expiry
by James Walshe 13 Dec '19

13 Dec '19

Hi Guys, Hope you’re well. I’m trying to download some ChimeraX plugins. It appears the toolshed security certificate has expired. https://cxtoolshed.rbvi.ucsf.edu/ Just letting you know if you were unaware. Kind regards, James ______________________________________________________________________ The Victor Chang Cardiac Research Institute's Email is scanned by the MessageLabs Email Security System.

2 1

multiple conformations in one pdb chain
by Linda Schulte 12 Dec '19

12 Dec '19

Hi everyone, I have two conformation in a single PDB chain, see example below: ATOM 90444 N APHE z 9 253.604 183.844 259.994 0.50 47.28 N ATOM 90455 N BPHE z 9 253.778 183.499 258.715 0.50 47.28 N Chimera can read in this two conformations of the chain, while chimerax shows only the A atoms of the chain. How can I read in also the B atoms? Thanks a lot for your help. Best, Linda -- Linda Schulte Goethe-Universität Frankfurt am Main Institut für Organische Chemie und Chemische Biologie, AK Schwalbe Max-von-Laue-Straße 7 D-60438 Frankfurt am Main N160/300 +49 (0)69 / 798-29956 schulte(a)nmr.uni-frankfurt.de

2 1

Saving ChimeraX session error on macOS
by Yixiao Zhang 11 Dec '19

11 Dec '19

Dear all, I'm preparing a movie in chimeraX on macOS. There are more than 25 maps opened and also another 20 low-pass filtered maps generated within chimeraX by "vol gaussian". There are also ~20 pdb models, several positions saved by "view name" and ~20 2dlabels. I got the following error message when I save the .cxs file, and the session was not saved. RuntimeError: Unable to restore objects of LabelModel class in ChimeraX-Label bundle because the class name is not listed in the name to class table for session restore File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 142, in from_obj (obj_cls.__name__, bundle_info.name)) See log for complete Python traceback. The session is still alive, and I have no problem when I save other much simpler sessions. Is there a way that I can get this big session saved? Is the error related to 2dlabels? Many thanks, Yixiao

2 6

Starting ChimeraX programmatically with remotecontrol
by Mungo Carstairs (Staff) 11 Dec '19

11 Dec '19

Hi there, Jalview has the ability to launch Chimera with "--start RESTServer", capture the port number from the response, and drive Chimera with REST commands. I'm trying to figure out whether this mechanism is also provided with ChimeraX. I've read http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-July/000113.html and looked at http://www.rbvi.ucsf.edu/chimerax/docs/user/startup.html and http://www.rbvi.ucsf.edu/chimerax/docs/user/options.html#start but so far I can't see that "RESTServer" is a startable tool. Is this, or is it planned to be, possible somehow? Thanks, Mungo [University of Dundee shield logo]<http://uod.ac.uk/sig-home> Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK www.jalview.org<http://www.jalview.org> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> g.m.carstairs(a)dundee.ac.uk<mailto:g.m.carstairs@dundee.ac.uk> [University of Dundee Facebook]<http://uod.ac.uk/sig-fb> [University of Dundee Twitter] <http://uod.ac.uk/sig-tw> [University of Dundee LinkedIn] <http://uod.ac.uk/sig-li> [University of Dundee YouTube] <http://uod.ac.uk/sig-yt> [University of Dundee Instagram] <http://uod.ac.uk/sig-ig> [University of Dundee Snapchat] <http://uod.ac.uk/sig-sc> We're Scottish University of the Year again!<http://uod.ac.uk/sig-strapline> The Times / Sunday Times Good University Guide 2016 and 2017 The University of Dundee is a registered Scottish Charity, No: SC015096

3 3

Rotate bond move large/small option in VR
by Lewandowski, Jozef 09 Dec '19

09 Dec '19

Hi, Is there a way to change the option from the default “move small” to “move large” of the Bond rotation tool in VR? Ideally, it would be great if I could switch between these options on the fly with some combination of buttons on the controllers. If nothing like that is implemented is there a way I could change the “move” default for the Bond rotation tool in VR using the command line? 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/>

3 7

Relative paths to source files in saved sessions
by Christophe Leterrier 04 Dec '19

04 Dec '19

Hi, I'm working on multiple Chimera sessions on different computers, syncing the content of the folders and cxs files. However when opening a cxs file on a different computer, I have to manually relocate all the source files every time (in my case tif stacks, and even navigate for each of them from the cxs folder to the source files folder because the folder is reset at every source file selection). Would it be possible to somehow store the relative path between the cxs file and the source files in the cxs file, or try relative if absolute paths fail? I have no idea how this is done currently, so sorry if this is an unrealistic/undesirable proposal. Thank you, Christophe

2 1

Main interface does not start
by Thomas G. Laughlin III 04 Dec '19

04 Dec '19

Hi, I've been using ChimeraX 0.9 for a while, but today when I tried to open it, the group photo comes up and "initializing bundles" then disappears without starting the main interface/GUI. I recently installed items from the toolshed for the first time (2 days ago but ChimeraX worked the day of install) and I tried re-installing ChimeraX without success. This is on a Windows 10 OS with intel integrated graphics. Any suggestions on what to do to diagnose and correct the problem? Thanks for the help, -Tom -- Thomas G. Laughlin III PhD MCB (BBSB, Candidate) | *Univ. of California-Berkeley* | Present BS Biochemistry | *Univ. of Missouri-Columbia* | 2014 t.laughlin(a)berkeley.edu <thomas.laughliniii(a)gmail.com>

2 1

Fw: Multi-user sessions: development
by Williams, Joanne 02 Dec '19

02 Dec '19

________________________________ From: Grime, John M. <jgrime(a)ou.edu> Sent: Monday, December 2, 2019 1:12 PM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Multi-user sessions: development Hello! We have some use cases where multi-user VR sessions in ChimeraX would be very useful. We already have out own in-house networked VR software, and I was wondering if the source code to ChimeraX is available for academic users so we can see if we can add similar functionality? Thanks! John Grime, Ph.D. Emerging Technologies Developer University of Oklahoma Libraries

3 2

Segment map feature only available to Mac users ?
by WERNERT Florian 29 Nov '19

29 Nov '19

Hi ChimeraX users developers and maintainers, I've been able to experiment with the segment map<https://www.cgl.ucsf.edu/chimerax/docs/user/tools/segment.html> feature provided by Segger package on the Mac daily-build, on a colleague's Mac. However I downloaded the Linux daily build on my Linux machine and it appears that this function is not present in the menu. Is it a bug or is the "segment map" feature only available to Mac ? If this is the case, would someone be able to give some guidance on how to port the feature to Linux ? I'm quite experienced in C, C++, Java and Python coding, having the coding skills shouldn't be an issue in order to do it. Thanks, Florian W

2 2

ChimeraX stalls when trying to display surfaces from a (strange) group of atoms
by Christophe Leterrier 27 Nov '19

27 Nov '19

Hi, I'm trying to use ChimeraX to visualize Single-Molecule Localization Microscopy (SMLM) data. In short, the output of an SMLM acquisition and processing is a list of fluorophores XYZ coordinates with associated uncertainty, that can be used to reconstruct a 3D image. I have made a script that make a pdb file from these localization so that I can directly display the resulting structure as if it was a protein with a number of random atoms (the only difference is that angstroms in ChimeraX are really nanometers in my data). The rendered pqr file is here (I use a pqr pdb format to specify the radius to the localization uncertainty, hence the variable diameter of each sphere): http://www.neurocytolab.org/up/Example_File.pqr The rendering with the "Spheres" view of atoms works well, see a screenshot here: http://www.neurocytolab.org/up/Render.png However, when I try to get the enveloppe of the resulting object using the "Surfaces" display (click on Surfaces>Show), ChimeraX hangs (I'm on OSX and get the dreaded infinite rainbow beachball). Is there a chance that I can get ChimeraX to render the enveloppe object this way, or is it really too far from what it's supposed to do? I can imagine that I'm trying to use ChimeraX for something completely different than its intended use, but it definitely has a lot of potential for this. Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France

4 4

Color key
by Ricardo Righetto 18 Nov '19

18 Nov '19

Hi, Apologies if this has already been asked or documented somewhere, but I could not find it. Is there a way in ChimeraX to create a bar showing the color scale ("Color Key" in Chimera) e.g. when coloring a map by local resolution? Thank you! -- Ricardo Diogo Righetto

2 1

How to select one of ligands which is named in different numbers
by Meinan Lyu 11 Nov '19

11 Nov '19

Hi, I am having trouble in how to select one of the ligands which named LIG 1, LIG 2, LIG 3, LIG 4, etc. when I hide all of them and want to specifically show LIG 1, using "show LIG 1 target a" command does not work. How to deal with this that the ligand name have a space inside? Thank you very much. Best regards Meinan

2 1

surface cap transparent when surface dust on ?
by bertrand beckert 06 Nov '19

06 Nov '19

Hi All, I have been recently trying to color a volume by a map value... So far it worked really well using the color command.... color sample #1 map #2 offset 0.1 palette " values" But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera? Also another thing, I usually do is the following: open volume1.mrc volume surfaceSmoothing true surface dust #1 lighting soft Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes... Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent? Thanks for the hard work and the nice software! Best Bertrand

3 3

Catalina woes
by ubaumann 05 Nov '19

05 Nov '19

Dear all I am trying to use ChimeraX after a clean install upgrade to Catalina, OSX 10.15.1 I get the attached error message that the software can’t be scanned for malicious code Is there any way around this, please? Same holds for Chimera ( and other programs….) Thanks a lot! Kind regards, Ulrich

2 1

Trouble initializing ChimeraX on CentOS
by Brown, Alex 18 Oct '19

18 Oct '19

Hello and good morning, I have always had a great experience using Chimera and so I was hoping to try out ChimeraX for some of our larger cryo-em data sets. However, following download and an install that did not seem to produce an error message, I can not seem to initialize the program. I have copied the output from the command prompt below. Beyond that, I should probably also mention that we are running the centos-release-7-6.1810.2.el7.centos.x86_64 operating system with intel chips and nvidia graphics cards. [root@gaolab ~]# chimerax-daily NOTE: available bundle cache has not been initialized yet WARNING: could not retrieve bundle list from toolshed NOTE: Traceback (most recent call last): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/runpy.py", line 85, in _run_code exec(code, run_globals) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 871, in <module> exit_code = init(sys.argv) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/ChimeraX_main.py", line 580, in init check_available=opts.get_available_bundles) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 1681, in init _toolshed = Toolshed(*args, **kw) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/__init__.py", line 359, in __init__ if not available.has_cache_file(self._cache_dir): File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site- packages/chimerax/core/toolshed/available.py", line 109, in has_cache_file return os.path.exists(os.path.join(cache_dir, _CACHE_FILE)) File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType BUG: TypeError: expected str, bytes or os.PathLike object, not NoneType File "/usr/bin/../../opt/UCSF/ChimeraX-daily/lib/python3.7/posixpath.py", line 80, in join a = os.fspath(a) _See log for complete Python traceback._ Thanks in advance for any support you may be able to provide on this! -Alex Alexander Brown IV, PhD Postdoctoral Researcher Horae Gene Therapy Center Li Weibo Institute for Rare Diseases Research University of Massachusetts Medical School 368 Plantation Street, AS6-2011 Worcester, MA 01605 Phone: (508) 856-3316 Email: alex.brown(a)umassmed.edu<mailto:alex.brown@umassmed.edu> Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

2 1

problem of chimerax
by 陈柳青 18 Oct '19

18 Oct '19

Hello! I tried install either daily builds or release 0.9 of chimeraX on my win10 64 system, but both encounter the same problem showed in the attachment. After startup, i can't see any menu! but when i move mouse on the menu , it will appear sub menu. How can solve this bug? sincerely Liuqing chen

2 1

macOS Catalina gives PermissionError opening files
by Tom Goddard 15 Oct '19

15 Oct '19

If you are thinking of upgrading to the new macOS Catalina (10.15) and want to use ChimeraX on it you might hold off. We have found that opening files using the ChimeraX open command or the recent files thumbnails often causes PermissionError and fails to open the files. This is caused by a new macOS Catalina security feature when any app that tries to open a file under Desktop, Downloads, or Documents must first raise a permission dialog asking if the app is allowed to open files from that directory. When using the ChimeraX File / Open dialog (from the File menu) the permission dialog is shown and works. But if you use the ChimeraX open command of recent files thumbnails on directories that you have not granted permission for with the Open dialog, then those fail with PermissionError -- apparently those methods of opening are not able to show the permission dialog. Other applications (e.g. photo editing program Gimp) have the same problem. We do not yet know how to solve this. Tom

2 2

Re: [chimerax-users] [Chimera-users] surface color
by Elaine Meng 14 Oct '19

14 Oct '19

Hi Mike, So close! You’re only missing the “palette” keyword before “rainbow” … try: color height #1 center 0,0,0 axis z palette rainbow <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#distance> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> (By the way, there is a chimerax-users(a)cgl.ucsf.edu list CC’d here if you have questions specifically about ChimeraX.) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Oct 14, 2019, at 2:43 PM, Schmid, Michael F. <m-schmid(a)slac.stanford.edu> wrote: > > I’m trying to do the same thing as Chimera’s “Surface Color”, but in ChimeraX, on the command line. After reading the docs, I tried “color height #1 (the map designation) center 0,0,0 axis z rainbow”. It gave “expected a keyword”. What did I miss? > Thanks, > Mike

1 0

show stands' arrows a little werid
by Meinan Lyu 14 Oct '19

14 Oct '19

Dear Dr., The attached is a picture I saved which the stands' arrows are so wide when using chimeraX to draw some figures, could you please tell me how to make it normal? The problem showed after I put into these two command(not quite sure yet):1. zone #3:Lig residueDistance 5 label false 2. cartoon #3/b suppressBackboneDisplay true. Thank you very much！ Best regards, Meinan CWRU

3 5

Soft lighting changes when additional model is displayed
by Gabor PAPAI 14 Oct '19

14 Oct '19

Dear ChimeraX team, If I open a second model in ChimeraX (0.91) the ambient occlusion in soft lighting mode on the first model disappears or becomes diminished. How can I revert this effect? I attach an image to illustrate this phenomenon. The only change between the two displays that I opened a model of DNA and placed close to the first model. Best regards, Gabor [cid:6AAD58A0-1B6C-4362-8C29-57D033327EBF@igbmc.u-strasbg.fr] --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 4

issues with rotamers tool
by Llorente, Alejandro 09 Oct '19

09 Oct '19

Hi, I am new PhD student using ChimeraX and I am very interested in learning how to work with this program. I am trying to introduce some mutations in my protein in some specific amino acids that I have selected. When I introduce an Alanine in my position of interest (using dunbrack) I have no issues, but when I try any other amino acids (as Phe or Thy) the program has no problem giving me the prediction for the rotamers, but I have some issues. After select some of the most probable rotamers, all the amino acids of my protein change to that kind of amino acid (not just the specific one that I have selected). Another problem is that I have is that when I select a specific atom of an amino acid, the program also select similar atoms but in all the others amino acids of my protein. I really hope that someone can help me with these issues. Thank You very much Alejandro Llorente. Lab of Dr. Nancy Carrasco. Department of Molecular Physiology & Biophysics, Vanderbilt University. 2215 Garland Ave Nashville, TN 37232-0615, room 711. Mobile phone: +34 626586236

2 1

Unable to use Viewdockx
by Abhijeet Kumar 07 Oct '19

07 Oct '19

hi, I am a college student and I am working on a project on protein docking visualization and came across ChimeraX. I am not able to use Viewdockx and the user guide for viewdockx gives a 404 page not found error. So, can you help me with this? Thank you.

2 2

Cuved helix tubes
by Ernesto Arias Palomo 02 Oct '19

02 Oct '19

Good morning, We are using the modeHelix tube to represent the secondary structure. However, our structure contains some long and curved helices, and the representation does not follow their shape with enough precision. Is there any option to increase the fit of the tube to the overall shape of long helices? Thank you very much for your help. Kind regards, Ernesto. -- Ernesto Arias Palomo, PhD Group Leader Biological Research Center (CIB-CSIC) Ramiro de Maeztu, 9. 28040. Madrid. Spain earias(a)cib.csic.es +34 91 837 31 12 ext 4446

2 3

Calculation of polar and apolar surface area
by Gorman, Scott Daniel 02 Oct '19

02 Oct '19

Hi All, I was wondering if anyone has a preferred way of calculating the polar and apolar surface areas for a macromolecule with ChimeraX? I've tried deleting all of the solvent and then using the command "measure sasa @N @O @S" for the polar surface area and then "measure sasa @C" for the apolar surface area, but the calculation for either comes up with a number too close to the total surface area, i.e. apolarSASA + polarSASA > totalSASA. So clearly I'm not approaching this problem correctly. Scott Gorman PhD Candidate Boehr Lab PSU Chemistry

2 1

GUI not properly visualized
by Pascal Albanese UU 25 Sep '19

25 Sep '19

Hi Chimera staff, i just changed PC ad now i have huge visualization problems of the GUI, when opening is fine but when i open any pdb file or session all buttons and commands in the window disappear. Command line actually works but all i see is this: [image: image.png] do you have any explanation? i tried different releases (0.9 official, daily builds) I'm using W10 enterprise, 64bit, intel i9 9900, UHD graphics 630. Thanks for the support, best regards, -- Pascal Albanese Ph.D PostDoc Biomolecular Mass Spectrometry and Proteomics Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan 8 3584 CH, Utrecht The Netherlands Telephone: +31 30 253 6805 https://www.hecklab.com/

2 4

ray tracing
by Ahel,Juraj 24 Sep '19

24 Sep '19

Dear all, pardon me if this has already been answered elsewhere, but I failed to find any information about this in the publication, webpage, or the mailing list archive. Is there a way to generate images of ray-traced maps in ChimeraX? I was often using it in Chimera but I can't find the option to do it in ChimeraX. Was it not included as a feature? Many thanks! Juraj

2 1

Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

Hello I am having difficulty in manually imposing symmetry on a map (*.mrc file) and then extracting the unit cell for the subsequent fitting of PDB structures with fitmap. (1) When I use the command "Volume symmetry #1, C33 axis z centerIndex 107.5" I get the error message "No placements for #1" that I do not understand. (2) I cannot figure out from the help documentation on how to save and display one of the created segments. Any ideas? Thanks Shahid -- Dr Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

3 4

render buriedArea surface?
by Alexis Rohou 09 Sep '19

09 Sep '19

Hi all, I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. Is there a way to do this in ChimeraX? If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program? Thanks in advance! Cheers, Alexis

3 6

vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

Hello, In chimera one can display dot van der Waals surfaces for atoms. *vdw* *atom-spec* <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> What would be the equivalent command in ChimeraX? Thank you, Elena

2 2

Open days EPFL - ChimeraX VR
by Krapp Lucien Fabrice 05 Sep '19

05 Sep '19

Hello, We are creating some small VR demos in ChimeraX for the EPFL open days in a few weeks (https://www.epfl.ch/campus/events/celebration-en/portes-ouvertes/) It is an event to show to a broader audience what the university is doing. The demos consists of small proteins up to density maps of bacteriophage with a few simple animations and menus to interact with the structures. Everything is almost done, I'm currently trying to fix the last issue but I didn't find a solution in the documentation. For two of the demos we would like the user to move a selection in VR with one of the VR controller right out of the box without having to go in the VR menu and click on the "move selected" button. I was able to make it work on Linux by loading the session though the remote API with the right part selected but it doesn't seem to work on Windows. The log shows a status change when clicking on the button "move selected" in VR but not the actual command to change the mode. Do you know if there is a way to change the mode of the VR controller without having to manually go through the menu in VR ? In the mean time, I will try different saved sessions and (remote) commands to try and solve the issue. If the demos are a success we will most likely make them available online so that anybody can try and improve them. Thank you in advance for your help. best, Lucien

2 4

semitransparent volumes with ambient occlusion
by Sindelar, Charles 03 Sep '19

03 Sep '19

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! Here is a little request. For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful. What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off! I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like. I sure would like to have this option! I guess there must be some reason it is disabled? Best, Chuck Sindelar Opaque map + PDB (ChimX v0.6) (pretty but the PDB is obscured) [cid:image001.png@01D55FF9.D8266CF0] After adjust to 80% map opacity (ChimX v0.6) (pretty!) [cid:image002.png@01D55FF9.D8266CF0] After unshow/show PDB model (ChimX v0.6) (argh!) [cid:image003.png@01D55FF9.D8266CF0]

2 3

silhouette of transparent density
by YAO HE 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

5 10

silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

1 0

Chimera X and the Oculus Quest
by Thomas Gluick 28 Aug '19

28 Aug '19

HI First please excuse my computer language ignorance. My question is: Is the Oculus Quest compatible with Chimera X; if it is, is software available to link the program to the Quest. I am aware already that the Rift can be connected and also certain phones. Thank you for you time. Best Tom Dr. Thomas Gluick Assistant Professor of Chemistry School of Science and Technology 770-842-5532

2 1

Question about Calphas and line between them
by Yazan Abbas 21 Aug '19

21 Aug '19

Hi, While looking through the user guide, I came across an option to draw a line between consecutive Calphas that are displayed. I made a mental note to use that option in my figure, but I failed to bookmark it or write down what the command was. I've been through the user guide several times again, but can't seem to find it. Would appreciate it if someone could jog my memory. Thanks, Yazan

2 1

discontinuous helices in tube mode
by Yazan Abbas 19 Aug '19

19 Aug '19

Hi, Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success. Thanks, Yazan

2 3

Question about "color sample" command
by Sean Connell 19 Aug '19

19 Aug '19

Hello I have a question about the "color sample" command (Chimerax-daily version 0.91 2019-08-14) and its use in coloring a volume based on the values of a second volume (i.e. local resolution maps from relion) The command works great when I load the volumes in to chimerx but after I load them I want to transform them using matchmaker and the bring option so that all the volumes I want to view are in a common frame of reference. After I transform the volumes though if i re-issue the "color sample" command it seems to color the first volume according to the values in the un-transformed second volume I am guessing? Is this correct and expected or am I just doing something wrong? if this is what is happening is there a way to force color sample to read the transformed values or to re-sample the transformed maps so they are correctly read? Also the output of the color sample command reports the min,max and mean values, just to confirm this corresponds to the values of all the voxels displayed at the current threshold level right? Finally is there a way to show a key for the coloring in chimerax? Many thanks for any advice you can provide. Sean

3 3

Fly function in ChimeraX - 2
by Gabor PAPAI 16 Aug '19

16 Aug '19

Dear developers, I’ve seen that two years ago the fly command from Chimera was not implemented in ChimeraX. Is it implemented now? Or does ChimeraX have a similar function? I tried the view command inside the perframe function, unfortunately this didn’t result in a smooth transition between two named views. The only option I have now is to translate, zoom and rotate the scene with the individual commands, however this is quite tedious to set. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 1

RESMAP output superposition.
by chimerax-announce-owner＠cgl.ucsf.edu 15 Aug '19

15 Aug '19

From: Shahid Khan <outlook_CD0472DE47DC92D6(a)outlook.com <mailto:outlook_CD0472DE47DC92D6@outlook.com>> Subject: RESMAP output superposition. Date: August 14, 2019 at 7:33:59 PM PDT Hello The python script for mapping the RESMAP local resolution output does not work in ChimeraX. Has anybody modified it so that it does? Or written a new script with the same purpose for ChimeraX. Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

2 1

Understanding the output of the align command
by Yazan Abbas 14 Aug '19

14 Aug '19

Hi, I am trying to make a movie to rotate density in a manner that follows rotation between two atomic coordinates. To do that, I am aligning the two models and using the reportMatrix output to inform turn and move commands in order to transform the density. However, I am encountering some difficulty, and I'm not sure if this is related to bugs or my lack of understanding. For example, if I want to move from the position of model #1 to model #2, "align #1/b toAtoms #2/b move nothing reportMatrix true" produces the following: *Axis 0.11 -0.018 0.99Axis point 166 190 0Rotation angle (degrees) 108Shift along axis -0.24* I would think my turn command should be *turn 0.11,-0.018,0.99 108 models #1 center 166,190,0* But that doesn't work. I can get it to work if I assume that the reported axis is x,z,y instead of the expected x,y,z. Also, I have to use a rotation angle of -108 instead of 108. I'm not sure if I am using the axis point value correctly though, is it correct to use that as my center of rotation? It's location (166, 190, 0) places at the top of the box, which seems unusual to me. And finally, would I use this same information in a move command (i.e. move axis distance(shift), as reported by the align command? Many thanks in advance, I hope explained this clearly. Best, Yazan

3 5

Morphing atomic models and volumes in a single movie
by Yazan Abbas 05 Aug '19

05 Aug '19

Hi, I am trying to create a movie that is morphing between 3 atomic models while simultaneously morphing between the 3 corresponding volumes. The following is my script for recording this movie: *set max 25windowsize 1080 1080view frame1movie record supersample 3wait 1volume morph #12,13,14,15 frames 181 playStep 0.005524861878453038 constantVolume true modelId #16perframe "surface dust #16 size 40" frames 181coordset #10 1,181wait 181movie stopmovie encode test_full.mp4 quality high* There are 4 maps in my morph, but the fourth map is simply a copy of the first in order to mimic the *wrap true* option of the atomic model morph. I am encountering the following issue during the volume morph step: somewhere in between the morph between volume #14 and #15, the map disappears for a fraction of a second in the movie. I suspect its because of a calculation/waiting issue, because if I record the movie using filtered versions of the volumes (*volume guassian sDev 2*), I don't have the same issue. Am I correct in my interpretation of the issue? Is there a way to modify my recording script to avoid this? Thanks, Yazan

2 1

pixel size
by Yazan Abbas 31 Jul '19

31 Jul '19

Hi, I am trying to create a scale bar using the following method: 1. camera is set to ortho 2. save image image.png width 4000 height 4000 transparentBackground true 3. check pixel size in chimeraX using the zoom command (which shows Pixel size at center of rotation is 0.178) 4. in imageJ, set the scale to be 0.178Å/pixel which turns into 5.618 pixels/Å 5. Show scale bar of desired in length in ImageJ However, the resulting scale bar looks unusually small given the dimensions of my particle. Have I misunderstood something about the pixelSize settings? The user guide doesn't say anything about pixelSize when one of or both of width and height are specified in the same image command, so I assumed the pixel size of the saved image would be the same as in the graphics window. Thanks, Yazan

2 3

Runing multiple command lines in ChimeraX
by Marie Locard-Paulet 26 Jul '19

26 Jul '19

Hello, I am running ChimeraX version 0.9 (2019-02-16) on a Mac (macOS Mojave version 10.14.6). It works fine, and I can work by adding commandes in the command “box” in the bottom. But I would like to open a text file with multiple ChimeraX command lines (for reproducibility and gain of time). I saw the command “open” that should open a document with the suffix “.com” or “.cmd”. It doesn’t work in my hands. It says it does not recognise the suffix. Is there something I am missing? Could you please help? Kind regards, Marie. --------------------------- Marie Locard-Paulet NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen, Denmark

2 1

ChimeraX Side View
by Elaine Meng 19 Jul '19

19 Jul '19

In response to a question about Side View... From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: Side View Date: July 19, 2019 at 10:34:44 AM PDT Hi Zhijie, Thanks for your registration comments! You will be happy to know that ChimeraX does have Side View. You can choose it from the menu: Tools… General. <http://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html> To make a tool (Side View, etc.) start automatically every time you start ChimeraX, right-click in that tool (or Ctrl-click on some systems) to show the context menu, and from that menu choose “Start at ChimeraX Startup” <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#context-menu> <http://rbvi.ucsf.edu/chimerax/docs/user/window.html#tool-context>

1 0

Zalman 3D monitor support
by Tom Goddard 19 Jul '19

19 Jul '19

Hi Zhijie, We are not likely to support Zalman 3D monitors (row interleaved stereo mode) in ChimeraX. Those monitors were made 2009-2011 and then discontinued. We don't have the funding to support technology from long ago. Tom

1 0

Fw: Genentech ChimeraX source code inquiry
by Williams, Joanne 18 Jul '19

18 Jul '19

________________________________ From: Slaton Lipscomb <lipscomb.slaton(a)gene.com> Sent: Thursday, July 18, 2019 10:00 AM To: chimerax(a)cgl.ucsf.edu <chimerax(a)cgl.ucsf.edu> Subject: Genentech ChimeraX source code inquiry Hi, Genentech has a commercial license for ChimeraX. However we have run into challenges installing it for our high performance computing cluster because of the binary-only distribution model. We automate the build and deployment of applications for our HPC cluster using the tool EasyBuild. It's far easier to do this when working from source code. Is the source code for ChimeraX available to license holders? thanks slaton -- Slaton Lipscomb gRED IT Scientific Computing Support for gRED IT Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…> FAQs for gRED Scientific Computing services<https://urldefense.proofpoint.com/v2/url?u=https-3A__rochewiki.roche.com_co…>

1 0

Molecular Dynamics Viewer
by James Starlight 16 Jul '19

16 Jul '19

Dear ChimeraX users! I would like to make a movie of molecular dynamics trajectory that has been pre-converted to pdb format (totally 250 frames). 1) Firstly, I have a problem with the recognition of the SS elements of that ensemble in ChimeraX, where each snapshot looks just like a mixture of points ( i tried to use dssp but it did not solve the issue). At the same time the snapshots looks fine in another viewers including UCSF Chimera (not X) 2) If I have a pdb of the same protein with mapped B-factors and then I colored it using color byattribute bfactor palette rainbow range 2,100 2) would it be possible to map the trajectory to that pdb in order to see the motions (observed in MD) mapped onto the structure that has been coloured by b-factors? Thanks for help!

3 15

session files do not save "color zone" command actions
by Rasmus Kock Flygaard 15 Jul '19

15 Jul '19

Hi all, I'm using chimerax-daily-build (downloaded two weeks ago, Chimerax-0.91). I am using a model to color EM density maps per subunit using the "color zone ..." command, but when I save Chimerax session files these colored zones are not saved and I have to redo all of them to fully restore a session. Is there any way to include these colored zones in the saved sessions files? Kind regards, Rasmus ------------------------------------ Rasmus Kock Flygaard, Ph.D Postdoc, Amunts' Lab SciLifeLab, Stockholms University Sweden

2 1

MLP value of the ASP and GLU carboxylate
by Zhijie Li 12 Jul '19

12 Jul '19

Hello, I noticed that the lipophilic atomic potentials of OD2 and OE2 are set to very positive values in mlp.py: 'ASP': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CG': 0.54, 'N': -0.44, 'O': -0.68, 'OD1': -0.68, 'OD2': 0.53} 'GLU': {'C': -0.54, 'CA': 0.02, 'CB': 0.45, 'CD': -0.54, 'CG': 0.45, 'N': -0.44, 'O': -0.68, 'OE1': -0.68, 'OE2': 0.53}, As as result the hydrophobic surface representation always show hydrophobic patchs on the carboxylates, which look quite odd to me. Is there a justification for this setting? In addition, aren't the two oxygens in the carboxylate equal considerting that they are in resonance? Zhijie

3 5

mesh lineThickness
by Yazan Abbas 12 Jul '19

12 Jul '19

Hi, In chimera the volume mesh lineThickness option could be changed. I can't seem to find the equivalent option in chimeraX. Is it possible to change the thickness of mesh lines? Thanks, Yazan PS apologies if you received this message twice, there was an error in my browser when first sent...

2 2

WebGL apps still in the pipeline?
by Oliver Clarke 11 Jul '19

11 Jul '19

Hi, Loving the regular improvements to ChimeraX! Just wondering regarding a web viewer - the original roadmap for chimeraX mentioned “WebGL apps” (http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html <http://www.rbvi.ucsf.edu/chimera/data/adcom15/chimera2.html>), and original Chimera had a limited capacity to export scenes as interactive html files. Is this still something that is in the pipeline for ChimeraX? I would really love to be able to export ChimeraX scenes in a format that I can share on the web, without the need for users to download and know how to use ChimeraX. Ideally the user would be able to rotate, zoom and slab, but perhaps not translate - that is, the center of rotation would be fixed. The idea would be to enable sharing of “interactive figure” kind of views of the molecule/map (perhaps allowing switching between multiple scenes/views within one session). Cheers Oli

2 1

Appearance of thick edges
by Yazan Abbas 11 Jul '19

11 Jul '19

Hi all, While playing around with lighting settings, thick black lines appear on the edges of my model (picture attached) that do not go away when I reset lighting conditions. Is it a "feature" or a bug? I tried playing around with all or most of the lighting options to find one that would get rid of them, but that didn't work. Thanks, Yazan

3 5

feature request / suggestion
by Alexis Rohou 09 Jul '19

09 Jul '19

Hello, Apologies if this already exists, but I'd like to suggest a new option to the show/hide command: show /spec/ toggle which would behave like the toggle option of volume (one of my favorite chimeraX features by far), but would work on atomic models. Within the spec, anything currently shown would become hidden, and vice versa. Cheers, Alexis

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by James Starlight 08 Jul '19

08 Jul '19

Hi Greg, sorry for some delay :-) Actually I just checked and indeed, there is still problem with rendering of the images with chimera-X using here is the detailed output if it would help chimerax-daily --offscreen --nogui "${output}/!temp/chimeraX.${pdb_name}.cxc" INFO: Offscreen rendering is not available. INFO: module 'OpenGL.osmesa' has no attribute 'OSMESA_DEPTH_BITS' INFO: UCSF ChimeraX version: 0.9 (2019-04-03) INFO: © 2016-2019 Regents of the University of California. All rights reserved. INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/chimeraX.0476.cxc INFO: Executing: open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb INFO: Summary of feedback from opening /home_pers/novikov/Bureau/test/test/!temp/B-factors_0476.pdb --- _warning_ | Ignored bad PDB record found on line 2 REMARK THIS IS A SIMULATION BOX INFO: _B-factors_0476.pdb_ title: **Gallium Rubidium Oxygen Manganese Argon Carbon Silicon** [[more info...]](cxcmd:log metadata #1) INFO: Chain information for B-factors_0476.pdb #1 --- Chain | Description [ ](cxcmd:select :1-219 "Select chain") | [No description available](cxcmd:sequence chain #1/ "Show sequence") INFO: Executing: open /home_pers/novikov/Bureau/test/test/florence.pdb INFO: Chain information for florence.pdb #2 --- Chain | Description [ ](cxcmd:select #2:1-219 "Select chain") | [No description available](cxcmd:sequence chain #2/ "Show sequence") INFO: Executing: mmaker #1 to #2 INFO: Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 INFO: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: Matchmaker florence.pdb, chain (blank) (#2) with B-factors_0476.pdb, chain (blank) (#1), sequence alignment score = 1131.8 STATUS: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: RMSD between 194 pruned atom pairs is 0.859 angstroms; (across all 219 pairs: 2.266) INFO: INFO: Executing: hide #2 models INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: dssp #1 INFO: Executing: zoom 1.3 ERROR: turn x 15 y 15 z -40 ERROR: ..........^ ERROR: Expected an integer >= 1 or a keyword ERROR: Expected an integer >= 1 or a keyword INFO: Executing: wait ERROR: wait requires a frame count argument unless motion is in progress ERROR: wait requires a frame count argument unless motion is in progress INFO: Executing: preset "'overall look'" publication INFO: Preset expands to these ChimeraX commands: _set bg white; set silhouettes t_ INFO: Executing: set silhouettes true INFO: Executing: set silhouetteColor indigo INFO: Executing: set silhouetteDepthJump 0.02 INFO: Executing: color byattribute bfactor palette rainbow range 2,100 INFO: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 STATUS: 16875 atoms, 4661 residues, atom bfactor range 0 to 367 INFO: Executing: cartoon style width 2.4 thickness 0.50 xsection barbell INFO: Executing: 2dlabels create title text '"Cluster 0476"' color red font gothic xpos .01 ypos .90 size 36 INFO: Executing: lighting depthCueStart .4 depthCueEnd .8 INFO: Executing: lighting full intensity 1.4 shadows true qualityOfShadows finer INFO: Executing: save image /home_pers/novikov/Bureau/test/test/!plots/visu_0476.png format png width 600 height 600 supersample 4 transparentBackground false and this is my script open /home_pers/novikov/Bureau/test/test/!temp/B-factors_0472.pdb open /home_pers/novikov/Bureau/test/test/florence.pdb mm #1 to #2 hide #2 models wait dssp #1 #view zoom 1.3 turn x 15 y 15 z -40 wait # options for appearance preset 'overall look' publication # set bg powder blue set silhouettes t; set silhouetteColor indigo; set silhouetteDepthJump 0.02 color byattribute bfactor palette rainbow range 2,100 cartoon style width 2.4 thickness 0.50 xsection barbell # make info of the screen 2dlab create title text "Cluster 0472" color red font gothic xpos .01 ypos .90 size 36 # options for light light depthcuestart .4 depthcueend .8; lighting full intensity 1.4 shadows true qualityOfShadows finer save image /home_pers/novikov/Bureau/test/test/!plots/visu_0472.png format png width 600 height 600 supersample 4 transparentBackground false exit пн, 22 апр. 2019 г. в 23:38, Greg Couch <gregc(a)cgl.ucsf.edu>: > > Salut, > > Does ChimeraX work in offscreen mode for you now? I believe it is fixed. > > -- Greg >

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Re: [chimerax-users] [Chimera-users] Cylinder coloring extension
by Elaine Meng 03 Jul '19

03 Jul '19

Hi Thomas, Chimera “pipes” are always a single color each. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pipesandplanks/pi…> However, our new program ChimeraX has a cylinder-helix representation in which each residue’s segment can be a different color. Like Chimera, ChimeraX is a free download for noncommercial use. Commands are similar but not identical between the two programs. <http://www.rbvi.ucsf.edu/chimerax/index.html> In ChimeraX, if I open 2gbp and from the menu apply preset “cylinders/stubs” and then preset “publication” I get this: ... and then command “color by bfactor palette rainbow” gives this: Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Jul 3, 2019, at 3:48 AM, Thomas Marcellino <marcellino.tom(a)gmail.com> wrote: > > Dear Chimera Team, > > I am aiming to color a stucture according to the B factor and represent it as a cylinder (pipes and planks) is there any possibility to apply different colors within the same cylinder or assign the coloring scheme to the cylinder representation in the same way as doing it with surface ? > > Looking forward to an answer, > Thank you for your time reading my suggestion. > > Thomas M

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mclip - surface clipping per-model
by bertrand beckert 03 Jul '19

03 Jul '19

Hi Elaine, I just wonder if the option clipping per-model has also been introduced in ChimeraX like it is in chimera ( https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/per-model/per-mod…) ? Apparently the command mclip doesn't seem to exist... Has it been replaced? Best Bertrand

2 1

MacOS two-finger swipe on help window
by Alexis Rohou 02 Jul '19

02 Jul '19

Hi all, Not sure this is a bug, but on my MacOS laptop when I use two finger swipe motion while hovering over the help window (to browse up and down the page), the help page is scrolled as expected, but simultaneously the view in the main window is rotated. Is this expected behavior? It seems a bit counter productive to me. Cheers, Alexis

2 3

color a surface by volume data
by bertrand beckert 02 Jul '19

02 Jul '19

Dear all, I have been searching in the documentation for quite a while and I haven t yet found the solution of how we can in chimeraX color a surface/volume by a volume data like in chimera ... i.e: local resolution map in cryo-em... in chimera: volume viewer/Tools/Surface color/color suface by is it possible to do so in ChimeraX? Any Help would be really appreciated! Thanks also for the amazing software ! Best Bertrand

2 1

An error opening chimerax seesion
by Yehuda Halfon 02 Jul '19

02 Jul '19

Hi all, I'm using chimeraX 0.8 (2018-12-17) on centos 7 (can't remember the build). Sometimes when I load a session that was saved using this version of chimeraX it gives me this error: Unable to restore session, resetting. Traceback (most recent call last): File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/core/ session.py", line 593, in restore obj = sm.restore_snapshot(self, data) File "/software/graphics/chimerax/lib/python3.6/site-packages/chimerax/ std_commands/view.py", line 214, in restore_snapshot for k,v in data ['view attrs'].items(): TypeError: 'NoneType' object is not subscriptable After that I can't open the session again, so I need to remake it. Help, Yehuda Halfon

2 4

Placing markers using the VR wands
by Schmid, Michael F. 01 Jul '19

01 Jul '19

Hi- I don’t seem to be able to activate the Marker Placement functions in the menu that it called up by pushing the menu button (above the trackpad of the wand) to display a floating menu. It doesn’t seem to work with “vr off” either, using the mouse. I’d like to place markers in a tomogram, either in a density, or (preferably) at a specific 3D position with the wand. Thanks, Mike Schmid

3 4

suggestion for ChimeraX on MacOS
by Alexis Rohou 01 Jul '19

01 Jul '19

Hi there, I noticed that when I do "open browse", the native MacOS file browser is started, but when I click on File > Save..., a file browser from some other toolkit is used. I find this inconvenient because that file browser does not know about my recent history, bookmarks, etc. Any chance the File > Save... dialog could use the native OS file browser? Cheers, Alexis

2 1

Restoring views and how to use clip
by Yazan Abbas 01 Jul '19

01 Jul '19

Hi, Instead of using chimera sessions (which can get very big) to save my work when preparing figures for publications, I save all my commands in a .cxc file to be read by chimeraX later. Is there a single command that outputs all the necessary information in an appropriate format needed to restore a view? Currently what I have done is *alias myview view matrix; zoom *to output the information into the log, but the output needs to be re-formatted whenever I want to use that information with the view matrix and zoom commands. Is there a command that outputs that information in a format ready for copying and pasting? I know name view can partially fulfil what I am looking for, but it is only session specific. On a related note, I want to also restore the clipping for each figure/panel I create, but I don't seem to be using the clip command appropriately. For example, if I enter the command clip list, and the output is Using 2 clip planes: far -34.697, near -45.723, executing the command clip far -34.697 near -45.723 does not restore the same view. Am I missing something? Thanks, Yazan

3 2

Orientation and pre-superimposition of the PDB
by James Starlight 28 Jun '19

28 Jun '19

Dear Chimera Users! I am dealing with some script that use Chimera X to make a very nice images of the RMSF mapped to the PDB in B-factor column (produced by gromacs as the result of MD simulation). The problem that when I map RMSF onto structure for several different systems (e.g. the different conformations of the same protein) the pdb produced by gmx rmsf in different orientation so Chimera use it for image and the positions of the structure are not the same (thus not being aligned, see the image for example!) Would it be possible by means of some Chimera-X comands to orient pdbs in order to align them in the same way? E.g. I open (in bash loop) many pdbs (the same protein but in different states, which are not aligned before, but I need that on the final images the positions for each PDB would be the same (thus to avoid pre-align the PDBs before opening them in ChimeraX! Thanks in advance!

2 4

Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, Apologies if this has been posted before, still new to chimerax and the mailing list. Was wondering if there are plans to add support for modifying mouse keys with ctrl (similar to what is in chimera). I am also wondering if there are plans to create a recenter + change pivot button/function that is also part of chimera. Thanks, Yazan

3 4

Map issue after using color zone
by Yazan Abbas 27 Jun '19

27 Jun '19

Hi, I already submitted a bug report for this issue, but was wondering if there was a quick fix. After applying color zone to my map, parts of it appear broken where density is forming protrusion. An image example is attached. Using the latest daily build (jun 25). Thanks, Yazan

2 2

volume splitbyzone and color zone issues
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, I executed 'color zone #2 near #1 distance 5 sharpEdges true' to colour a map I loaded, followed by "volume splitbyzone #2', but repeatedly would get an error that the volume specified is not coloured by zone. Eventually after trying multiple times, it worked, however the log outputted the following: Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py", > line 130, in invoke > return self._func(self._name, data) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 3557, in _update_drawings > v.update_drawings() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 701, in update_drawings > self._update_surfaces() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 724, in _update_surfaces > s.update_surface(ro) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 1953, in update_surface > va, na, ta, hidden_edges = self._calculate_contour_surface(matrix, > level, rendering_options) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2048, in _calculate_contour_surface > rendering_options, level) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) > ValueError: not enough values to unpack (expected 3, got 2) > Error processing trigger "graphics update": not enough values to unpack > (expected 3, got 2): > ValueError: not enough values to unpack (expected 3, got 2) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/map/volume.py", > line 2071, in _adjust_surface_geometry > varray, tarray, narray = subdivide_triangles(varray, tarray, narray) I also get the following when using the color zone command, even though color zone works (most of the times, sometimes it fails) Traceback (most recent call last): > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/cmd_line/tool.py", > line 254, in execute > cmd.run(cmd_text) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", > line 2641, in run > result = ci.function(session, **kw_args) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/std_commands/color.py", > line 1248, in color_zone > color_zone(s, spoints, colors, distance, sharp_edges = sharp_edges, > auto_update = update) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 14, in color_zone > zc.set_vertex_colors() > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 84, in set_vertex_colors > replace = True) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 123, in color_zone_sharp_edges > ec = _edge_cuts(varray, tarray, i1, n1, points, colors, distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 147, in _edge_cuts > f = _edge_cut_position(varray, v1, v2, p1, p2, points, colors, > distance) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f) > ValueError: Cut fraction 1.8061 is out of range (0,1) > ValueError: Cut fraction 1.8061 is out of range (0,1) > File > "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/surface/colorzone.py", > line 181, in _edge_cut_position > raise ValueError('Cut fraction %.5g is out of range (0,1)' % f)

3 2

Distinguishing between upper and lower case chain IDs before and after splitting chains
by Yazan Abbas 25 Jun '19

25 Jun '19

Hi, My model (cif format) contains 34 chains, and so I've been using upper case and lower case letters for chain IDs. When I read in my model, the select command distinguishes between upper case and lower case, but after applying the split command on my model ('split #1 chains'), the select command no longer distinguishes between upper and lower case. I.e. 'select #1/D' will select both chains D and d. The split command works correctly, producing models 1.1-1.34. Also, is it possible to create a model from a selection? I can't find such a command anywhere, and the only thing I can figure out is to do the following: 'save *name* format mmcif models *selecion_name*; open test.cif' Thanks, Yazan

2 1

measure blob - persistent color?
by Alexis Rohou 25 Jun '19

25 Jun '19

Hi there, I absolutely love the new measure blob UI in the daily builds. Very useful. Thank you so much for putting it together. Is there a way to get the blob surface color to persist beyond hiding/showing the volume object? Obviously, in a script I could just re-measure the blob and re-color it, but is there another way to make the color "stick"? (Note, I don't plan to change the isocontour level) Cheers, Alexis

2 4

#2013: Trouble pip-installing Pyyaml prereq for bundle
by Andrés Giner Antón 20 Jun '19

20 Jun '19

Hello, two weeks ago we reported a problem regarding the installation of Pyyaml as a prereq of a bundle that we created, do you have any forecast of when we will get an answer? Here is the URL of the ticket: https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2013 Thanks for your attention. Greetings, Andrés Giner Antón

2 1

ISOLDE 1.0b3 now released for ChimeraX 0.9
by Tristan Croll 17 Jun '19

17 Jun '19

Dear ChimeraX users, Just letting you know that I've released ISOLDE 1.0b3 on the ChimeraX Tool Shed for use with ChimeraX 0.9. If you're not familiar with ISOLDE, you can get an overview at https://isolde.cimr.cam.ac.uk/. In brief, ISOLDE is designed to allow the high-fidelity, interactive remodelling/refinement of atomic models into low-medium resolution cryo-EM or crystallographic electron density maps. In designing ISOLDE, I've always had two groups in mind. The first is, of course, the experimental structural biologists whose job it is to solve the structures of new macromolecules and their complexes. The second (and, to my mind, equally important) group is the downstream *users* of such models. Like every other human endeavour, macromolecular model building is an imperfect field, and (particularly in the worse-than-2-Angstrom resolution range targeted by ISOLDE) many deposited models contain serious errors that are eminently fixable with modern tools. My hope is that ISOLDE will become a useful tool allowing you to directly inspect your model of interest in the context of its original data, providing you with a feasible pathway towards fixing any issues you find (or, failing that, moving to a new target) prior to committing serious resources to its study. Please enjoy. Constructive feedback is always welcome. Best regards, Tristan

1 0

Transparent background movie
by Norberto Escudero 14 Jun '19

14 Jun '19

Hi, I have succesfully created images with transparent background, but it seems is an impossible task for a movie. Is there any way around this? Thanks and regards, -- Dr Norberto Escudero Urquijo Prof. A. Warren's group Cambridge Institute for Medical Research (CIMR) Hills Road, Cambridge, CB2 0XY

3 2

Saving stereo pairs
by Gyunghoon Kang 14 Jun '19

14 Jun '19

?Hi, apologies if this information is available somewhere but all my searches returned information for the original Chimera. Is there a way to generate stereo pairs either in the command line or GUI? Best, Gyunghoon Kang

2 1

set silhouettes false for volume mesh only?
by Alexis Rohou 13 Jun '19

13 Jun '19

Hi there, Is there a way to set silhouettes false for volume meshes, but keep it true for other object types (ribbons, surfaces,...)? Cheers, Alexis

2 1

SMILES Input With ChimeraX
by Victor Blaga 05 Jun '19

05 Jun '19

Hello, I am just wondering if there is a way to input a SMILES string with ChimeraX, as with Chimera? I can't seem to find it in the documentation so I just want to confirm this functionality has indeed been dropped? Thank you, Victor Blaga Research Assistant McMaster University Department of Biochemistry and Biomedical Sciences

2 2

equivalent command for coloring elements specific colors?
by Liz Kellogg 30 May '19

30 May '19

Hi, There used to be this handy command in Chimera to color oxygen atoms and nitrogen atoms specific colors: color @O red,a color @N blue,a but I can't find the corresponding command in ChimeraX. Is there a way to color all nitrogen atoms blue and all oxygen atoms red? When I try what I think the equivalent command should be (I'm displaying cartoon backbone with stick side chains): color @O red target a color @N blue target a it says 'Colored 1120 atoms' but none of the sidechains are colored differently. Thanks for the help Liz

2 3

crossfade warps image when transitioning
by Liz Kellogg 23 May '19

23 May '19

Hi all OK I have a real problem this time (not a silly problem on my end). I'm trying to make movies in chimerax, and I used to be able to use the crossfade function in Chimera to smoothly interpolate two images to change the scene. However, in ChimeraX, when I use the crossfade function it either warps the first image or it somehow interpolates a zoomed in view of the lower left corner of the first image into the second, which makes for a jarring transition. Closing and re-opening ChimeraX seems to change the behavior, but I still can't get a smooth transition between image 1 and image 2. Any idea how to fix this? I thought perhaps setting the view size before starting to record the movie would help, but that doesn't seem to work. Thanks a bunch. Best Liz

2 2

nucleotides command not found in chimerax
by Liz Kellogg 22 May '19

22 May '19

Hi ChimeraX users, I am dabbling around in ChimeraX, and it seems that the documentation doesn't quite match up with the commands that are available. For example, this command: nucleotides https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/nucleotides.html would be useful, but when I enter this into the command line it says "unknown command" I downloaded the nightly chimerax build for mac, so it can't be a problem with an out of date version. Is this command not currently implemented? and if not, how many commands are listed in the documentation that aren't implemented? Best Liz

2 2

Re: [chimerax-users] tile command in chimeraX
by françois SERRA 22 May '19

22 May '19

Hi Elaine, thanks for the quick reply. my usual routine with 3D models involves loading tens of them, match them (now align :P) and then "tile", so yes its a bit tedious. I'll keep doing this in "old" chimera, and look forward for the advances in chimeraX. thanks again for the tool!! francois On Mon, 20 May 2019 at 19:25, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX > currently. If you don’t have too many structures, you could first > superimpose them all in the middle, zoom out somewhat (“zoom” command) and > then translate them individually up/down (y axis) and left/right (x axis) > with the “move” command, but it would be a little tedious and require some > trial and error as to spacing. It may be useful to save/restore positions > with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> > wrote: > > > > Hi, > > sorry for the stupid question, but I spent quite some time searching for > it. > > Is there some alternative to the "tile" command in chimera X? > > thanks! > > great tool :) > > francois > > -- *François Serra* **senior researcher - comparative epigenomics** *Computational Biology Group - *Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona *Tel: +34 934 137 97*

1 0

Fwd: tile command in chimeraX
by Elaine Meng 20 May '19

20 May '19

> > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Subject: Re: [chimerax-users] tile command in chimeraX > Date: May 20, 2019 at 10:25:27 AM PDT > To: françois SERRA <serra.francois(a)gmail.com> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > > Hi Francois, > Not a dumb question, but sorry, there is no “tile” equivalent in ChimeraX currently. If you don’t have too many structures, you could first superimpose them all in the middle, zoom out somewhat (“zoom” command) and then translate them individually up/down (y axis) and left/right (x axis) with the “move” command, but it would be a little tedious and require some trial and error as to spacing. It may be useful to save/restore positions with the “view” command. > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/zoom.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/move.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > >> On May 20, 2019, at 3:17 AM, françois SERRA <serra.francois(a)gmail.com> wrote: >> >> Hi, >> sorry for the stupid question, but I spent quite some time searching for it. >> Is there some alternative to the "tile" command in chimera X? >> thanks! >> great tool :) >> francois >

1 0

tile command in chimeraX
by françois SERRA 20 May '19

20 May '19

Hi, sorry for the stupid question, but I spent quite some time searching for it. Is there some alternative to the "tile" command in chimera X? thanks! great tool :) francois -- François Serra *senior researcher - comparative epigenomics* Computational Biology Group - Barcelona Supercomputing Center (BSC) C/ Jordi Girona, 29 08034 Barcelona Tel: +34 934 137 97

1 0

smoothen coils
by Gabor PAPAI 13 May '19

13 May '19

Dear developers, I would like to show helices as tubes (this I know how to do) and coils between them with smooth trajectories, more schematic, as it is drawn in Chimera using Pipes and Planks (or even more). I would appreciate your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

2 3

Feature Request: Dust ranges and new object as output
by Scott, Brandon L. 30 Apr '19

30 Apr '19

We can currently remove objects of a given size; it seems like it would be fairly straightforward to allow a range of object sizes to be kept from the middle, i.e. remove objects less than 20 and greater than 1000. Additionally, it would be really helpful if we could output the 'dusted' components as a new model so they could be individually colored and displayed, or be able to access the measured sizes of the objects for further analysis. Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

morph with molecular surface for part of molecule
by Susan Lea 30 Apr '19

30 Apr '19

How can I generate a morph with a molecular surface representation? many thanks Susan Prof. Susan M. Lea, FMedSci tel: +44 1865 275181 ------------------------------------------------------------------------------------------ Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

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Some preferences will reset
by Eric Pettersen 25 Apr '19

25 Apr '19

Hi all, In order to improve the modularity and maintainability of the ChimeraX code, the way some settings/preferences were handled was changed so that the code for that setting/preference could be kept in the appropriate tool bundle rather than in the ChimeraX core. A consequence of this change is that for settings/preferences that moved, they will revert to their initial default values rather than any values you may have saved for them. This will only happen for builds later than today, and furthermore if you go back to an older build it will still have your old values. For most settings/preferences this is not a big deal — you can easily just change them and save them again. The one setting that may be a little tricky is the “Startup commands” setting since there might be a lot of text saved in that one. Nonetheless, as long as you don’t delete your old build you can just start that and copy the commands from that into the new build. The preference categories that got moved are: Clipping Distances Labels Log Startup Trackpad Window —Eric Eric Pettersen UCSF Computer Graphics Lab

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ChimeraX python crush in no-gui mode
by James Starlight 16 Apr '19

16 Apr '19

Dear ChimeraX users! I am using a cxc script together with the following options to run ChimeraX in no-gui mode. chimerax-daily --offscreen --nogui test.cxc here is my scrript # chimeraX script windowsize 800 600 open ./test.pdb view; zoom 1.0; turn x 90; turn z -80; preset 'overall look' publication color byattribute bfactor palette rainbow range 2,100 # make info 2dlab create title text "B-factors for" color red font gothic xpos .04 ypos .90 size 30 # options for light light depthcuestart .4 depthcueend .8; lighting full save image ./test.png format png width 800 height 600 supersample 4 transparentBackground false This script works fine with GUI producing very good picture but with the --nogui it gave me error: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py", line 699, in init commands.run(sess, 'open %s' % arg) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 41, in open from_database=from_database, ignore_cache=ignore_cache, **kw)) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 117, in open models = handle_unknown_kw(session.models.open, paths, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw return f(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py", line 601, in open session, filenames, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 467, in open_multiple_data models, status = open_data(session, fspec, format=format, name=name, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 421, in open_data models, status = open_func(*args, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/scripting.py", line 115, in open_command_script run(session, text) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/run.py", line 31, in run results = command.run(text, log=log) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/cli.py", line 2616, in run result = ci.function(session, **kw_args) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/save.py", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/io.py", line 203, in export result = self.export_func(session, path, **kw) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/image.py", line 43, in save_image raise LimitationError("Unable to render images to save them") chimerax.core.errors.LimitationError: Unable to render images to save them could you help me how it may be fixed? Thank you in advance! Gleb

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Re: [chimerax-users] [Chimera-users] Using ChimeraX in no-gui mode
by Elaine Meng 15 Apr '19

15 Apr '19

Hi James, There is a different email address for asking ChimeraX questions (CC’d here). Yes, you can script imaging in ChimeraX with nogui if you are using Linux and start with the “nogui” and “offscreen” options on the system command line (they have dash-dash in front but my Mail keeps editing it to a long hyphen instead). <http://rbvi.ucsf.edu/chimerax/docs/user/options.html> In ChimeraX the command script filenames end in .cxc <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> The commands may be different than in Chimera. Open is with “open” save is with “save” and there is no publication preset but you can change to white background and show silhouettes with the “set” command. See the individual command help pages <http://rbvi.ucsf.edu/chimerax/docs/user/index.html#commands> making images <http://rbvi.ucsf.edu/chimerax/docs/user/images.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 Apr 15, 2019, at 2:14 AM, James Starlight <jmsstarlight(a)gmail.com> wrote: > > Dear Chimera users! > > Would be possible to use new ChimeraX for execution of some simple > scripts for structure visualisation and imaging via no-gui mode? > > I am using bash script to loop over pdbs and would like to > > 1) open each pdb which contains b-factors info in chimeraX > 2) apply preset publication > 3) colour the pdb using "color byattribute bfactor palette rainbow ave residue" > 4) save high quality image at the selected directory using chimera render > > Would it be possible to do these things directly from linux terminal > providing each time pdb and some script file with the list of the > applied commands? > > chimerax-daily ${pdb} ${script} > > Thank you in advance!

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Dome projection camera mode
by Tibor Füzik 10 Apr '19

10 Apr '19

Dear ChimeraX developers, I have not found the "dome" projection camera mode in ChimeraX (as it is in Chimera). Is there any equivalent projection (camera mode) or a workaround to get it? Would it be hard to implement it ChimeraX? Thanks. All the best, Tibor

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PDBe-KB ligand centric pages survey
by Lukas Pravda 04 Apr '19

04 Apr '19

Dear ChimeraX users, We are in the process of redesigning the ligand pages of PDBe and we would be grateful if you could fill out a short survey to help us understand what information about small molecules / ligands you would find useful. The survey is available at https://bit.ly/2FFmHFG. Recently, we have introduced protein-specific aggregated views on the structural data (pdbe-kb.org/proteins) as a part of Protein Data Bank in Europe Knowledge Base (PDBe-KB). We highlight the available information related to structures of specific proteins, including structural and functional annotations, domains, ligand-binding sites and interfaces. In the next step we would like to present a similar aggregated view from a small molecule / ligand perspective. Thank you for your time, Lukas -- Lukas Pravda, Ph.D. Bioinformatician/Scientific Programmer Protein Data Bank in Europe (PDBe) European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD United Kingdom

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Feature request: save cxc
by Zack Gainsforth 02 Apr '19

02 Apr '19

Hi, I am finding that saving my visualization as a cxc (scripting command) file leads to good reproducibility. Often, when I save a session (cxs) file, it doesn’t open again later (I think because directory path names change), but if I produce the visualization by coding a cxc file instead, then it hasn’t failed (yet!). In addition, I want to keep track of actions such as median filters, and filter parameters, pixel scaling, all that jazz. When I code this into a cxc file, all that info is in the code record. When I save a session file I often cannot find that information again later (was it a gaussian filter? median? What do I write in the paper!?) I would suggest a feature to save a cxc file or output a journal of all changes for a cxs file so I can see what I did at least for documentation/reproducability later. Cheers, Zack

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Re: [chimerax-users] Output motion prickle magnitude
by Scott, Brandon L. 02 Apr '19

02 Apr '19

Based on previous correspondence I added an output option in motion.py. Is there anyway to do a pull request or something similar, so that I don't have to make the changes everytime I stay up to date with the nightly builds? Thanks, -Brandon

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Transparency bugs with ribbons and density maps
by Pascal Albanese 27 Mar '19

27 Mar '19

Dear all, I'm haviong troubles with visualization of trasnparencies when using EM maps and PDBs. See in the example here: [image: image.png] The ribbon in the front is completely transparent (with silhouettes), the surface is set with a 50% transparency, and the pseudobonds inside or behind can be only visible when transparency of pbonds is set to 0 (at 5 already they disappear). Does anyone already experience these issues? Bests, Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Coulombic surface coloring
by Gabor PAPAI 27 Mar '19

27 Mar '19

Dear ChimeraX team, I would like to color a protein surface by electrostatic potential. Is there a way in ChimeraX to do that? My protein is too large (more than 20 000 atoms) to create a surface in Chimera, but ChimeraX has no problem to create it. Thank you in advance for your help! Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288

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Implement Crosslinks/pseudobond/distances subselections and/or export
by Pascal Albanese 22 Mar '19

22 Mar '19

Dear ChimearX Users and developers, I'm using ChimeraX for visualization and analysis of pseudobonds datasets from Crosslinking-MS and i found new features very useful (min max selection etc). I think it would be useful (but i don't know how much effort will be required) to be able to select subsets of distances (e.g. form 15 to 24 Angstroms, or involving chain A and B) and being able to create and export these subsets. for instance i have a Complex of A, B and C and i want to select all pseudo-bonds involving A and B and export them as pb file (to be able to load them as a separate model lateron). Or to sel min 15 max 24, and then export them as pb file (with "save" function). I think it would be really useful for both crosslinks visualization and analysis (i work with datasets of thousands of crosslinks on big complexes which make difficult to subselect them, i have to do it with pymol, then generate subsets and reformat them as .pb files). i had a look to previous threads, but i didn't found similar topics. If i'm wrong my apologize. Thank you! Pascal -- Pascal Albanese, PhD *Post-doc*, Politecnico di Torino Dipartimento DISAT, BioSolar Lab@Environment Park Via Livorno 60 10144 Torino e-mail: pascal.albanese(a)polito.it Phone number: +39 011 2257655 <+39%20011%20225%207655>

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Re: [chimerax-users] [Chimera-users] color key in chimera X
by Elaine Meng 18 Mar '19

18 Mar '19

Hi Pranav, ChimeraX does not yet have color-key drawing, sorry. One possibility for now is that even if you want to make the main image in ChimeraX, you could still make the color key separately in Chimera and then combine them in some image-editing program like Photoshop. In Chimera, you could use the “colorkey” command as Ibrahim suggests, or the GUI (Tools… Utilities… Color Key). Either way you would have to define the colors and set values “manually” to match the coloring in ChimeraX, so we understand it is not as convenient as when the image and key are in the same program. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels…> There is also a ChimeraX e-mail list chimerax-users(a)cgl.ucsf.edu that you can use if you have other issues/questions about ChimeraX specifically. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 18, 2019, at 12:13 PM, Moustafa, Ibrahim M. <ria2(a)psu.edu> wrote: > > Hi Pranav, > > Not sure about ChimeraX but in Chimera you can use 'colorkey' command line: > > colorkey x1,y1 x2,y2 value1 color1 value2 color2.... > > example: > colorkey 0.1,0.1 0.11,0.5 3.0 blue 4.0 cyan 5.0 green 6.0 yellow 7.0 orange 8.0 red > > You can use the colors and their values from the output of local resolution map. > > > Ibrahim > From: Chimera-users <chimera-users-bounces(a)cgl.ucsf.edu> on behalf of Pranav Shah <p.shah.lab(a)gmail.com> > Sent: Monday, March 18, 2019 2:56 PM > To: chimera-users(a)cgl.ucsf.edu BB > Subject: [Chimera-users] color key in chimera X > > Hi, > I have a isosurface rendering that I have colored by radius as well as > local resolution. I want to now place a colour key in the image to > indicate the relevance of the colors. Is there a way to achieve this > in ChimeraX? If not, is there a way to easily port the commands to > Chimera? > > Cheers, > Pranav > -- > Pranav Shah > Postdoctoral Research Fellow.

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Volume Rendering Issue
by Scott, Brandon L. 15 Mar '19

15 Mar '19

I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended? Thanks for the help, -Brandon [cid:1b1e95a3-2efc-477f-925e-74b92b367f68] [cid:56f70b34-d199-466f-a578-76fde802d5ec] ____________________ Brandon Scott, PhD SDSMT, Nanoscience

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OpenGL error running ChimeraX under VNC on CentOS 7
by Tom Goddard 14 Mar '19

14 Mar '19

Hi Alexis, ChimeraX is crashing in the OpenGL graphics driver (libGL.so.1) when the Qt window toolkit is trying to use it. This is certainly an OpenGL graphics problem with your VNC setup. Sometimes VNC is run mirroring an actual display connected to the server computer you are connecting to, and sometimes it displays a virtual desktop, for example, when connecting to a server that has no physical display. ChimeraX will very likely work if VNC is mirroring an actual display on the server, but will almost surely fail if it is using a virtual desktop on the server. This is because OpenGL rendering only works to a physical display directly connected to the computer running the app (ChimeraX). I think there have been efforts to send the OpenGL commands to another computer and have that client computer's graphics card render, but that is a very obscure capability, and I have only heard of it failing, never saw it work. Tom > On Mar 14, 2019, at 10:40 AM, Alexis Rohou wrote: > > Hi Tom, > > I am attempting to get ChimeraX running on a CentOS7 workstation with a > nice discrete GPU card for running ISOLDE. Unfortunately, I am having no > luck so far. Tristan Croll, who is helping me get started with ISOLDE, > suggested I send you directly this report and ask for guidance. > > Some details: > - I installed the daily CentOS7 RPM from yesterday (13-March-2019) > - I am connecting to this workstation using a VNC server/client. I do > not have physical access to the workstation, at least not any time soon > - Starting the binary under gdb gives the error & stack trace copied below > - it could be that this is just related to OpenGL over VNC not working > properly. If you suspect this is true, could you suggest some test I > could run to confirm this is the case? > > Any other hints would be most welcome! > > Thanks, > Alexis > > >> WARNING: QOpenGLShader::compile(Vertex): failed >> WARNING: QOpenGLShader::compile(Fragment): failed >> WARNING: Could not link shader program: >> "" >> >> Program received signal SIGSEGV, Segmentation fault. >> 0x00007fffe6e6a013 in ?? () from /usr/lib64/nvidia/libGL.so.1 >> Missing separate debuginfos, use: debuginfo-install >> ucsf-chimerax-daily-2019.03.13-1.el7.x86_64 >> (gdb) bt >> #0 0x00007fffe6e6a013 in () at /usr/lib64/nvidia/libGL.so.1 >> #1 0x00007fffe54e268a in () at >> /usr/lib64/nvidia/libnvidia-glcore.so.340.107 >> #2 0x00007fffe6eac1a0 in () at /usr/lib64/nvidia/libGL.so.1 >> #3 0x00007fffe0e4fc6f in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #4 0x00007fffe0df1842 in () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 >> #5 0x00007fffe0df2143 in >> QPlatformBackingStore::composeAndFlush(QWindow*, QRegion const&, >> QPoint const&, QPlatformTextureList*, QOpenGLContext*, bool) () at >> /opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/PyQt5/Qt/lib/libQt5Gui.so.5 > > >

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MOL2 import
by Marco J. Müller 14 Mar '19

14 Mar '19

Dear ChimeraX Team, when I try to load structure outputs of docking runs in .mol2 format into ChimeraX, it fails to load them, while the same can be imported by Chimera successfully. After a bit of playing around I found that the following section is relevant and fails in this format: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 SMALL USER_CHARGES The problem seems to be that ChimeraX requires explicit definitions of /#features/ and/#sets/ in the third line (apart from /#atoms #bonds #substructures/), while they are typically omitted in most programs. So the following lines could be imported: @<TRIPOS>MOLECULE MYCOOLMOLECULE 57 62 1 0 0 SMALL USER_CHARGES Can this case be addressed in a future version of ChimeraX? Thank you in advance, Marco -- Marco J. Müller PhD student Technische Universität Braunschweig Institute of Medicinal and Pharmaceutical Chemistry https://www.tu-bs.de/pharmchem Beethovenstr. 55 | 38106 Braunschweig | Germany

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How can I use command crosslinks with bonds?
by Jun Ha Song 04 Mar '19

04 Mar '19

Dear RBVI, I want to use few command lines that are exclusively available for pseudobonds. The problem is that my model is consisted of markers and links, and there seems like no possible way for me to simply transfer bonds into pseudobonds. What commands like *crosslinks histogram *provide seems way to good for it to be limited for pseudobonds only. Is there a technical reason why such command is only applicable with pseudobonds? Can commands in Chimera/ChimeraX that work with pseudobonds easily be adapted to work with bonds, or is that too much of technical difficulty? If it is not feasible, is there a way to turn bonds into pseudobonds? Best, Junha Song.

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matchmaker RMSD in ChimeraX
by Tom Goddard 04 Mar '19

04 Mar '19

> From: Martin Moncrieffe <mcm35(a)cam.ac.uk> > Date: March 4, 2019 at 1:15:06 AM PST > To: Tom Goddard > Subject: matchmaker in ChimeraX > > Hi Tom, > > Is it possible to get the rmsd as a function of residue position when using mm in ChimeraX? I’ve turned on the verbose flag and can see the residues used to match but not their respective rmsd’s. >

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Can we draw arrows in ChimeraX?
by Steve Chou 28 Feb '19

28 Feb '19

Dear ChimeraX team, I need to draw straight and curved arrows to show the straight and twisting forces on the molecules. See the attached images (cropped from ChimeraX interface) for details. Does ChimeraX have the functionality to do this? Steve -- Steve Chou

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equivalent to "define"?
by Alexis Rohou 28 Feb '19

28 Feb '19

Hi there, Having looked through the docs a few times, I'm pretty sure I know the answer, but here goes... Is there a ChimeraX equivalent to define <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> in Chimera 1? Or any other facility to draw geometric shapes (I'm particularly interested in calculating and drawing planes)? Cheers, Alexis

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, The single plane you are showing is the “solid” style, no different from if multiple planes are shown. You can use brightness value 1 for each color if you want, but it needs to be specified, it does not default to 1 (that usually is not what people want when using solid style rendering of more than 1 plane since it would be totally opaque). Also normally single planes are shown as partially transparent in both Chimera 1 and ChimeraX. Tom > On Feb 28, 2019, at 12:34 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > I’m also unclear why for an opaque plane it is necessary to set a brightness for each map value - surely a color palette with simple color,value pairs would be fine if there is no transparency issue as there is with a 3D solid representation? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

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Re: [chimerax-users] Color palettes for planes and solid data?
by Tom Goddard 28 Feb '19

28 Feb '19

Hi Oli, There is no capability to automatically use a palette and min/max range of map values that sets the levels and colors. That might be useful although when I have done this by hand I think equally spaced colors rarely produces what I want. The cryosparc image you attached is a good example of the color spacing not producing a very informative view. At any rate, if you want this feature in ChimeraX use the Help / Report a Bug… menu entry which is also for requesting features. I just tried setting the map threshold below the lowest value in the map and clipping in Chimera 1 and it only clips a cube for me. So I’m not sure what you mean when you say that works in Chimera 1. The streaks when you color the clipped and capped surface are because the cap is composed of triangles and only the vertices of the triangles are colored and the triangles are very long and skinny. Read about the Surface Capping mesh subdivision option in Chimera 1 if you want more explanation of it. ChimeraX does not yet support the cap subdivision, but if you follow my previous suggestion it is an alternative method that can work. Tom > On Feb 28, 2019, at 12:31 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi Tom, > > Yes I know it is possible to do manually, thank you, but it requires quite a lot of futzing about with brightness/color pairs to get nice looking results. I was wondering if it would be possible to add support for palettes, with color thresholds automatically distributed between a minimum and a maximum, so that one can for example color a map slice with a rainbow palette between a minimum and a maximum density value (e.g. as per the density slices from cryosparc that I attached to the previous email). > > Re the cube, I set the threshold to -10 so that when I clip the map, it exposes a face that I can color by density value. I do this in Chimera and it works as expected without altering anything, here I just see streaks. I’m still unclear why I just see streaks on the clipped face no matter the threshold - this doesn’t seem to be the intended behavior? > > Oli > >> On Feb 28, 2019, at 3:06 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Oli, >> >> To set the colors of different map values use the volume command >> >> volume #1 level 0,0 color white level 10,.9 color blue level 70,1 color green >> >> This says map value 0 has brightness 0 and color white, map value 10 has brightness 0.9 (on a 0 to 1 scale) and color blue, map value 70 has brightness 1 and color green. That is for using the “volume” or “plane” style as shown in the volume viewer panel. >> >> When you instead try to color a clipped map surface, your second screenshot has the surface threshold set to -10 while your map values range -.1 to .15 so you see just a cube surface — not sure what you are doing that for. In your third screen snapshot it looks better, but the colors are streaks on the clipped surface because the cap surface mesh subdivision is not fine. In Chimera you can set the cap subdivision in the Surface Capping dialog, but there currently is no control of the cap mesh subdivision in ChimeraX. Instead you could just crop the map either setting its bounds with the volume command “region” option or easier by using the crop mouse mode. Then the face of the cropped box will use a mesh that matches the map resolution and coloring should be ok. >> >> Tom >> >> >>> On Feb 28, 2019, at 11:35 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> Hi, >>> >>> Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! >>> >>> I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. >>> >>> Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). >>> >>> Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). >>> >>> Cheers >>> Oli >>> >>> <Screen Shot 2019-02-28 at 2.34.47 PM.png><Screen Shot 2019-02-28 at 2.32.03 PM.png><Screen Shot 2019-02-28 at 2.25.00 PM.png><Screen Shot 2019-02-28 at 2.26.03 PM.png> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu >>> Manage subscription: >>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >> > >

1 0

Color palettes for planes and solid data?
by Oliver Clarke 28 Feb '19

28 Feb '19

Hi, Would it be possible to add support for more convenient coloring of solid representation data and planes of density maps? E.g. by specifying a color palette? Apologies if this already exists and I’m just not finding it! I would like to be able to make nice looking slices of a density map, without surface contours, colored by density value (e.g. attached). This can be a good way of showing disordered regions of a EM reconstruction. Currently, when a density map is loaded as a plane or solid represntation in Chimera, there is no way to automatically assign a predefined palette, and the defaults do not convey much information (at least for typical EM maps - example attached). Also, when I attempt another way to do this, coloring the surface by map value and then clipping the surface, the results are odd, unlike in Chimera (see attached at different contours). Cheers Oli

1 0

Missing features in ChimeraX
by Tom Goddard 26 Feb '19

26 Feb '19

Hi Junha, Glad to hear you are trying VR with ChimeraX. Per-model clipping in ChimeraX is done with the clip command, or with the clipping mouse modes, atom radii are set with the size command, visibility is set with the show/hide commands, color is set with the color command, there are volume tracer mouse modes, and saving marker files should work, although you hit some bug and should press the Report a Bug… button when you get that traceback. ChimeraX does not have the selection inspector window yet. ChimeraX uses a different window toolkit Qt while Chimera used Tk so it requires all new code to move any graphical user interface from Chimera to ChimeraX. ChimeraX is a completely new program, modernizing every component of the 20-year-old design of Chimera so even moving commands from Chimera to ChimeraX requires substantial work. If you don’t find ChimeraX ready for your use, of course you should continue to use Chimera. We expect ChimeraX to replace Chimera in a few years. You might want to spend an hour skimming Elaine’s thorough ChimeraX documentation to understand what is in ChimeraX, including many new features like virtual reality that are not in Chimera. Tom > On Feb 26, 2019, at 2:03 AM, Jun Ha Song wrote: > > Tom, > > I recently got HTC Vive, and therefore started using ChimeraX. I have to say; the VR functionality is amazing. The ability to VR alone is sufficient reason for me to move over to ChimeraX. > > However, I noticed that key, crucial, irreplaceable features are (as far as I am aware) non-existent on ChimeraX. Below are function/tools that exist in Chimera that I use (literally) everyday, and I am wondering if these function/tools can also be implemented on ChimeraX or not. > > - per-model clipping (mclip) > - inspect selection (ability to change atom/bond/surface radius, visibility, color) > - volume tracer (ability to save markerset or atom/bond as .cmm) > > If the circumstance is so that implementing these onto ChimeraX is not feasible, then I must remain with Chimera until similar tools become available on ChimeraX. > > Also, is there any particular reason why all the tools of Chimera are not copied onto ChimeraX? Is ChimeraX trying to be another program that is different from Chimera? > > > > As for "ability to save .cmm", I tried saving atom/link using command > > save E:\LBNL\Stereocilia\ChimeraX_Markerset.cmm format markers models #1 > > but I got error saying that > > NotImplementedError: Slices are not implemented. > File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\markers\cmmfiles.py", line 39, in markerset_as_xml > rgb = tuple(r/255 for r in m.color[:3]) > See log for complete Python traceback. > > is this a simple bug during development, or have I typed wrong command? > > Best, > Junha Song.

1 0

How to zoom into a spot that is not located in the center gradually and straightly?
by Steve Chou 24 Feb '19

24 Feb '19

Dear ChimeraX team, Thanks for your fast and detailed responses to my questions! If a spot is in the center of view, we can zoom into the spot through a straight line. If it's not, it's really difficult to get there through a straight line. I tried something like this in a "movie" script, but it's still not straight. ========= move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 move y -20 zoom 1.25 wait 2 ========= Is there a way to zoom into a spot that is not in the center of view through a straight line. Steve -- Steve Chou

2 7

Can we change the lighting gradually in ChimeraX?
by Steve Chou 20 Feb '19

20 Feb '19

Dear ChimeraX team, Is it possible to change the lighting gradually in ChimeraX, e.g., from "soft lighting" to "lighting simple"? This sounds weird, but makes sense if we want to change the lighting method in a movie. Thanks in advance! Steve -- Steve Chou

2 1

help with chimerax wildcards
by Michael Lawrence 20 Feb '19

20 Feb '19

Hi, I am trying to use wild cards in chimerax but they appear not to work. I type the command color @N* blue and get as response Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword All I am trying to do is color all nitrogens blue. Version 0.5 (2018-02-05) running on macOS Sierra v10.12.6 what am I doing wrong? thanks Mike Lawrence

2 2

Blank lines in pseudobond files
by Tom Goddard 19 Feb '19

19 Feb '19

I made ChimeraX ignore blank lines and comment lines starting with “#” in pseudobond (.pb) files. Tom > On Feb 15, 2019, at 3:02 PM, Steve Chou wrote: > > Hi Elaine, > (1) I tried to read the pseudobonds from a file (.pb) , > ========================= > #1/A:13@NE2 #1/A:704@O > #1/A:13@NE2 #1/A:502@MG > #1/A:13@NE2 #1/A:501@PB > > #2/A:13@NE2 #2/A:704@O > #2/A:13@NE2 #2/A:502@MG > #2/A:13@NE2 #2/A:501@PB > ========================= > the program reported an error. > ============================= > ValueError: not enough values to unpack (expected 2, got 0) > File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file > aspec1, aspec2 = line.split()[:2] > See log for complete Python traceback. > ============================= > > (2) Then I tried to add distances on the ChimeraX terminal > ============================= > distance #1/A:13@NE2 #1/A:704@O > distance #1/A:13@NE2 #1/A:502@MG > distance #1/A:13@NE2 #1/A:501@PB > > distance #2/A:13@NE2 #2/A:704@O > distance #2/A:13@NE2 #2/A:502@MG > distance #2/A:13@NE2 #2/A:501@PB > ============================= > I was able to see the distance labels in the two structure. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. > Steve > > On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. You'd make a plain text file with name *.pb with lines like that and open it. > > You don’t have to read in pseudobonds from a file, however. If not too many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing>> > > > > For the case where composition changes, you could add in a fake Mg ion and water to the structure that’s missing them, but you’d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com <mailto:stevezchou@gmail.com>> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. > > > (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users> > > > > -- > Steve Chou > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

1 0

Fwd: [Chimera-users] Can ChimeraX morph between two surfaces?
by Steve Chou 16 Feb '19

16 Feb '19

Hi Elaine, (1) I tried to read the pseudobonds from a file (.pb) , ========================= #1/A:13@NE2 #1/A:704@O #1/A:13@NE2 #1/A:502@MG #1/A:13@NE2 #1/A:501@PB #2/A:13@NE2 #2/A:704@O #2/A:13@NE2 #2/A:502@MG #2/A:13@NE2 #2/A:501@PB ========================= the program reported an error. ============================= ValueError: not enough values to unpack (expected 2, got 0) File "/opt/UCSF/ChimeraX-daily/lib/python3.7/site-packages/chimerax/read_pbonds/readpbonds.py", line 27, in read_pseudobond_file aspec1, aspec2 = line.split()[:2] See log for complete Python traceback. ============================= (2) Then I tried to add distances on the ChimeraX terminal ============================= distance #1/A:13@NE2 #1/A:704@O distance #1/A:13@NE2 #1/A:502@MG distance #1/A:13@NE2 #1/A:501@PB distance #2/A:13@NE2 #2/A:704@O distance #2/A:13@NE2 #2/A:502@MG distance #2/A:13@NE2 #2/A:501@PB ============================= I was able to see the distance labels in the two structures. And I saw an new model (name: distances; ID:3) show up in the "Models" panels. Then I ran morphing again. The Mg and water molecules moved, but still didn't move together with the protein. Steve On Fri, Feb 15, 2019 at 11:31 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Steve, > Yes, if those are the correct specifiers for atoms in your structure. > You'd make a plain text file with name *.pb with lines like that and open > it. > > You don’t have to read in pseudobonds from a file, however. If not too > many, probably easier just to add distance monitors. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html> > <http://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context> > > Elaine > > > On Feb 14, 2019, at 9:49 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > Hi Elaine, > > Thanks for your detailed explanation! > > What's the format of the pseudobond file? Should it look like this? > > =============================== > > #1/A:13@NE2 #1/A:502@MG > > =============================== > > All the best, > > Steve > > > > On Thu, Feb 14, 2019 at 7:43 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > Hi Steve, > > Actually I’m surprised the Mg and water were included (even if present > at both ends) because I thought they had to be tethered by a bond or > pseudobond (like a distance measurement) to the biopolymer chain, as > described here under “Atoms in Common”: > > > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> > > > > For the case where composition changes, you could add in a fake Mg ion > and water to the structure that’s missing them, but you’d have to decide > where to put them. Also it was my understanding that they had to be > tethered to the biopolymer chain (e.g. add distance measurement, which can > then be hidden), but maybe that requirement has changed, or the Mg does > already have a metal-coordination pseudobond to the biopolymer. > > > > Or if you don’t care if the Mg or water move during the morph, you could > just display those atoms from the original model (that was input to > morphing) even though they are not present in the trajectory. > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Chimera(X) team > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > > On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou(a)gmail.com> wrote: > > > > > > Thanks, Elaine! > > > You command "rainbow structures" works beautifully. > > > There is "a Mg ion" and "a water molecule" in the two conformations. > > > (1) If the two conformations have exactly the same compositions (by > shifting the structure), the "Mg ion" and the "water molecule" do not > follow the same path as the protein. They move but separate from the > protein. > > > (2) If the two conformations have slightly different compositions, the > "Mg ion" and the "water molecule" do not show up in the morphed pdb > ensemble. > > > Is there a way to morph the specific components properly? > > > Steve > > > > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > > Manage subscription: > http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > -- Steve Chou -- Steve Chou

2 5

ChimeraX equivalent to ribinsidecolor
by Lukas Kater 15 Feb '19

15 Feb '19

Hi, is there a way to change the color of the inside of helices? Something like "ribinsidecolor" in chimera. see an example here (second picture from top): https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ribstyles.html Thanks for any feedback! Lukas

2 1

Can ChimeraX morph between two surfaces?
by Steve Chou 14 Feb '19

14 Feb '19

Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou

2 5

bug report: hide with silhouettes
by Alexis Rohou 11 Feb '19

11 Feb '19

Hi Elaine, ChimeraX team, When silhouettes is set to true, hiding all models causes a bug whereby the display panel is not responsive / redrawn. As far as I can tell other parts of the GUI are still working. Below is a minimal reproducer. Attached are screenshots of what I'm seeing when silhouettes true (bug) or silhouettes false (no bug). I am running this on MacOS 10.13.6 on a MBP with graphics "Intel Iris Plus Graphics 650 1536MB" (sorry not sure what might be relevant here), and the Chimera version is: UCSF ChimeraX version: 0.8 date: 2018-12-17 22:26:30 UTC branch: v0.8 commit: 412d62d1949722ed7f52b3e515ec0f3b70b6b7af Python: 3.6.4 Obviously there's a workaround to avoid this but this caught me a few times in the last couple of days and it'd be nice to not have to watch out for it because the only solution I've found so far is to quit ChimeraX and start again. Cheers, Alexis PS. here's the reproducer: open pdb:1tbq set silhouettes true # Hide stuff hide #!1 models # Wait a bit (alternatively stop here and return to interactive use before doing the next step) wait 100 # print version out version verbose # Try to show it again. This should work (and does if silhouettes false) show #!1 models

3 4

volume zone - unexpected behavior when newMap false
by Alexis Rohou 11 Feb '19

11 Feb '19

Hello, I've been playing with volume zone and having good fun, but... I've noticed that if I set newMap to false, then the invert option is ignored (behavior is as though invert is false, even when I specify invert true). When newMap is set to true, or not set at all, the invert option has the effect I expected from reading the documentation. Am I missing something? Hopefully description above is unambiguous but let me know if you need step-by-step. Cheers, Alexis

3 4

Can ChimeraX add noise (Brownian-like motion) in morphing?
by Steve Chou 11 Feb '19

11 Feb '19

Dear ChimeraX support, When morphing from one structure to another unaligned structure, ChimeraX follows a smoothly curved path? Can it add noise (Brownian-like motion) to the path? All the best, Steve -- Steve Chou

2 3

equivalent to "move cofr"
by Alexis Rohou 08 Feb '19

08 Feb '19

Hello, Switching to ChimeraX, I find myself looking for an equivalent to "move cofr <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html#cofr>". Is there one? The use case is: I'm working on a particular part of a map & structure, I open a structure of a homologuous domain from the PDB, but its coordinates are way off, and I want to move it to the region I'm working on without having to zoom out and drag it. My apologies if this is in the documentation somewhere, I'm still finding my way around. Cheers, Alexis

2 2

Output motion prickle magnitude
by Scott, Brandon L. 08 Feb '19

08 Feb '19

Using the measure motion command I am able to generate the prickles on the surfaces correctly, which is great for visualization. Is it possible to write the magnitude of those prickles, and the index to a file so we can do further analysis on the distributions? Cheers, -Brandon ____________________ Brandon Scott, PhD SDSMT, Nanoscience

2 1

How to align two molecules using a subset of atoms in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX support team, I tried the following command first - it worked well. ================== match #1/A to #2/A ================== Then I tried to align the two molecules using parts of them - it didn't work and complained that "No chains in reference structure PROT.pdb #2 compatible with BLOSUM-62 similarity matrix." ================== matchmaker #1/A:10-20@CA to #2/B:10-20@CA ================== System Info: ================== Platform: Linux-3.10.0-862.el7.x86_64-x86_64-with-redhat-7.5-Maipo ChimeraX version: 0.9 (2019-02-05) ================== Thank a bunch! Steven -- Steve Chou

2 3

How to re-define the secondary structure info in ChimeraX?
by Steve Chou 08 Feb '19

08 Feb '19

Dear ChimeraX developers and users, In Chimera, I can use the following commands to redefine the secondary structure info. ============================ setattr r isHelix false : setattr r isSheet false : setattr r isSheet true :8-12,16-21 setattr r isHelix true :55-61,78-92 ============================ What's the ChimeraX equivalent? By the way, I can also delete the hydrogen atoms using "delete element.H" in Chimera. Is there an equivalent in ChimeraX? Many thanks in advance! Steve -- Steve Chou

2 1

Bio-Formats with ChimeraX?
by Matthew Akamatsu 07 Feb '19

07 Feb '19

Hi, I just started using ChimeraX to render and save 3D time lapse microscopy data as a high-performance replacement of Fiji. I am wondering how flexible ChimeraX can be in opening different TIF-derived file formats - particularly hyperstacks (multi color, multi Z, multi time). Other desired formats would be proprietary formats like .nd2 and .sld . Bio-Formats does all of this in an open-source manner - how feasible would it be to have bio-formats type functionality in ChimeraX? Thanks, Matt

2 3

VR in ChimeraX and Dell Visor
by Lewandowski, Jozef 24 Jan '19

24 Jan '19

Hi, Has anyone tested Dell Visor for VR in ChimeraX? If yes are there any issues you have run into? I am assuming that the experience should be similar to what Tom has described for Samsung Odyssey but I would appreciate if anyone had specific feedback on this particular piece of hardware. Thanks, Józef

2 1

color by conservation
by George Ghanim 16 Jan '19

16 Jan '19

Hello, Is it possible to color amino acids by conservation from an alignment file? Thanks, George Ghanim —— PhD Student Rio Lab Molecular and Cellular Biology, University of California Berkeley

2 1

ChimeraX crashes from time to time on Lenovo Y530
by Yehuda Halfon 02 Jan '19

02 Jan '19

Hi All, I bought a new laptop, Lenovo Y530 which has GTX 1050Ti as well as the intel 8750H which has UHD 630 and 16 GB of ram with windows 10. Chimerax is installed on m.2 drive. Sometimes, without any correlation it freezes and crashes, when I restart the error in the picture. All the drivers are updated. I run chimerax with the GTX as the GPU. I think it's something with the dual GPUs, is there a fix for it? I tried both 0.7 and the new 0.8 (not daily). On my other laptop, an old Macbook pro it run perfectly. Thanks, Yehuda Halfon

3 2

Movie recording error
by Carlos Escalante 21 Dec '18

21 Dec '18

Dar all, Trying to make a morphing movie. Everytime I run it, it comes out with the following error: Unknown command: coordset #3 1,21 And there is no sign that is recording. The same error occurred when I created the morphing, but it did created the morphing. Also, if I try to change anything and run the command again, it says ‘already recording a movie’ Any suggestions? Thank you Carlos R. Escalante Assistant Professor Department of Physiology and Biophysics VCU School of Medicine 1220 East Broad Street MMRB 2040 Richmond VA 23298 carlos.escalante(a)vcuhealth.org 804-628-1202

2 1

version 0.7
by jingdong cheng 21 Dec '18

21 Dec '18

Hello, Could you provide me the older version 0.7? I tried the new 0.8, it is good, fixed a lot of bugs, but it runs super slow slow. It is better to change back to 0.7, but on your website I can’t find it anymore. Cheers! Merry Christmas! Jingdong

2 1

FW: hi
by Williams, Joanne 21 Dec '18

21 Dec '18

From: mosbah amine <aminemosbah(a)hotmail.com> Date: Thursday, December 20, 2018 at 11:24 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: hi dear colleague trying to download chimiraX , no way to get to the right page !!! would you please send me the zip file , i agrre to licesing requarements also i have a windows10 for compatibility regards Dr mosbah amine TN

2 1