- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] video of digestion kinetics
by Elaine Meng 18 Jan '21

18 Jan '21

Hi Tynan, Besides abruptly hiding atoms and bonds, you could fade them in or out over time (spread hiding across multiple movie frames), or don't hide them but select them (shown as green outline), or color them differently, or show them with different styling like fatter or thinner sticks, etc. These are all things you can do with the commands of either program, normal stuff that people frequently do when making figures or movies. Or instead of (or in addition to) changing how the peptide is shown, you could show a 2D label that is an arrow pointing to the cleavage point (see 2dlabels command of either program). Elaine > On Jan 18, 2021, at 12:04 PM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: > > Hi Elaine, > Thank you for the very quick response. The info does help. I was thinking that I might be able to take this approach. And I don't mind learning the command line > > However, I was also wondering if there was a way to highlight the peptide bonds between residues to show the actual cleavage points and what gets added as time goes on. This would be a more accurate representation of my data because some peptides are "lost" due to limitations in mass spec rather than the digestion (a very short peptide might not have been digested, but also wasn't IDed by the instrument). > Thank you! > Tynan > > -------- Forwarded Message -------- > Subject: Re: [chimerax-users] video of digestion kinetics > Date: Mon, 18 Jan 2021 11:47:07 -0800 > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Reply-To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> > To: Tynan A. Becker <tabecker(a)alaska.edu> > CC: chimerax-users(a)cgl.ucsf.edu > > > Hi Tynan, > I'm not sure if you meant to send this to the chimera-users(a)cgl.ucsf.edu list or the chimerax-users(a)cgl.ucsf.edu list. Anyway, using either program, UCSF Chimera or UCSF ChimeraX, in general you would need to make a command file for what happens during the movie. The command file could include hide successive parts of the peptide, i.e. if residues 10-12 get cut off first, hide them, then several steps (movie frames) later hide the next set of residues to get cut off, etc. > > In either program, making a command script would require learning the commands, so you would need to invest some time. In Chimera, however, there is also a graphical interface to movie recording, so if you are able to use the menus instead of commands to get to various states you want in your movie (e.g. with more and more of the peptide hidden), with this Movie Recorder interface you can save them as scenes and place them on a timeline. Still, however, at a minimum it will require learning how to use the menus of Chimera to do all the coloring, styles, 2D labels etc. that you want in your movie. > ChimeraX "making movies" page: > <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> > > Chimera "making movies" page: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html> > Chimera Movie Recorder tool: > <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/recorder/recorde…> > > 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 18, 2021, at 10:32 AM, Tynan A. Becker <tabecker(a)alaska.edu> wrote: >> >> Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the cleavage sites that develop sequentially over time in a specific protein as it is digested? >> Thanks, Tynan >

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video of digestion kinetics
by Tynan A. Becker 18 Jan '21

18 Jan '21

Good morning, I have kinetics data from the in vitro digestion of a protein by several enzymes. For each enzyme, I have 8 time points with peptides that remain intact at that point of time (which also gives me the cleavage sites added between adjacent time points). I was trying to figure out to model this in Chimera, including being able to show the protein from multiple sides. Looking online, I see that you have some videos with proteins showing alternate conformations. Do you think it possible for me to show the */cleavage sites/* that develop sequentially over time in a specific protein as it is digested? Thanks, Tynan

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Black/Dark Theme
by Petrychenko, Valentyn 13 Jan '21

13 Jan '21

Dear ChimeraX Developers Team, Do you have in your features list an dark or black GUI theme? I understand that stylistic features have lover priority than a really useful ones, but during many hours of work every day in ChimeraX white GUI eyes getting tired especially at late hours and especially when it contrasts with dark interface of the rest of the system and other dark themed software. I really looking forward to see a dark theme feature in future updates. Respectfully yours, Valentyn Petrychenko

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Question about the comparative homology modelling tool
by Moradkhan, Tiglath A 12 Jan '21

12 Jan '21

Hi I have two questions about the homology modelling tool: 1. Why is the default number of models to be built five? Does having five models provide a better choice for choosing the best model? 2. In evaluating a protein model which of the following parameters plays a much more dominating role: zDOPE, predicted RMSD or the predicted native overlap? Or do all three measures contribute the same effect on model evaluation? For instance a model might have a low zDOPE score but have a higher RMSD while another model might have a much more positive zDOPE score but a lower RMSD. Based on this, would the first model be the better one to pick or do both models have equal weight in terms of overall model quality? I would be very glad for advice. Thanks Tiglath

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high results tiff
by Fabian Glaser 10 Jan '21

10 Jan '21

Dear experts, I am sorry to bug with this issue again, but I dont’ find a good tutorial or clear instructions about the right way to prepare figures with high quality for publication with chimeraX, and I find myself again and again making them with chimera, since it seems I am able to produce 300 dpi with chimera on tiff for example using the save image dialogue, but on chimeraX I am only able to produce them with 72 dpi using the save command. I have tried all kind of sizes but… well for me it does not work yet. Again, may this is trivial, but I am not an expert in graphics, and if somebody could guide me would be really thankful. Thanks in advance, Fabian Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701

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Re: [chimerax-users] Stereo mode error
by Tom Goddard 07 Jan '21

07 Jan '21

Hi J.C., Since Chimera works in stereo and ChimeraX does not I think the problem is almost surely that ChimeraX requires a "core" OpenGL context (ie using modern OpenGL) while Chimera requires a "legacy" OpenGL context. I assume ChimeraX is working for you not in stereo. So it can get a core context, but apparently not a core stereo context. It looks like the Nvidia driver is not providing a core OpenGL stereo context. But Nvidia has clearly stated that it does support this in their 3D Vision FAQ https://nvidia.custhelp.com/app/answers/detail/a_id/4845 "Without 3D Vision, will NVIDIA Quadro GPUs still support OpenGL Quad-buffered Stereo? Absolutely YES. OpenGL Quad-buffered Stereo is not affected by changes to the 3D Vision driver." ChimeraX is asking for quad-buffered stereo core context and "core" contexts are the standard of current OpenGL. So if we believe Nvidia's statement then their driver will give this kind of context. And that suggests that you have a driver configuration setting that prevents it. It is certainly also possible that the Nvidia driver you are using is simply broken in its ability to provide core stereo contexts. But I think it is more likely you have it configured to not give such a context, possibly your X server "Option "Stereo" "10"" setting is the cause. When the Nvidia driver provides a core OpenGL stereo context this does not mean your 3D Vision glasses will work. In fact the above 3D Vision FAQ very clearly says it will not work with a current Nvidia driver unless a separate 3D Vision USB driver is installed. "NVIDIA announced it is no longer supporting 3D Vision. What does this mean? Hardware: NVIDIA is no longer selling the 3D Vision emitters and glasses. Drivers: R418 graphics drivers will be the last driver to contain the 3D Vision driver package. The R418 branch will be supported until January 2020. In addition, NVIDIA will decouple the 3D Vision USB driver from the graphics driver. NVIDIA will provide the 3D Vision USB driver package as a separate installer on NVIDIA.com moving forward - see Quadro Advance Options <https://www.nvidia.com/object/quadro-advance-options.html>. This will allow users to upgrade the graphics driver while continuing to use the standalone 3D Vision USB driver." If this statement from Nvidia is true then the 3D Vision emitter on your computer can only work if you have installed a separate 3D Vision USB driver. If the emitter does not work the screen will show a double image and stereo software like ChimeraX, Chimera and Coot will not complain but you will not see it in stereo through the glasses because the glasses cannot synchronize to the interleaved in time left and right eye images without the infrared emitter. It is possible that that separate 3D Vision USB driver does not work with a core OpenGL context. Kenneth Satyshur has several legacy Nvidia stereo systems and may know how to make ChimeraX work in stereo with 3D Vision. Ultimately, you are trying to use no longer supported hardware. Honestly Nvidia never supported 3D Vision well, and Windows is much more likely to work than Linux. It probably can be made to work with ChimeraX if enough hours are sunk into it, and will certainly be easier if you use old graphics software such as Chimera or Coot which was written based on the legacy OpenGL that 3D Vision originally worked with. Tom > On Jan 7, 2021, at 5:53 AM, Jean-Christophe HAESSIG <haessigj(a)igbmc.fr> wrote: > > Le mardi 05 janvier 2021 à 10:31 -0800, Tom Goddard a écrit : >> Hi Jean-Christophe, > Hi, > > That was a *very* insightful answer, thank you vey much. But at the > same time it's a bit saddening because it sounds like there will be no > way to use ChimeraX fully on this setup. > > My tests indicate that for the time being, 3D Vision still works with > the latest Nvidia driver on Linux. Despite nvidias decision to retire > 3D Vision, it only means they will stop producing shutter glasses. The > following FAQ entry makes that a little clearer : > https://nvidia.custhelp.com/app/answers/detail/a_id/4845 > Still, that doesn't explain how standard OpenGL calls would not be > supported on a recent driver. Maybe using 'Option "Stereo" "10"' in X > selects an alternate code path where only legacy contexts are > available. On the other hand, it seems this is the only way to get the > glasses to work. In fact, I tried every single stereo mode of the > nvidia driver, and all of them except one gave the same results : the > programs using the legacy contexts worked and ChimeraX crashed. > I also tried Chimera and indeed, it works as you suggested. > > In mode 14 (dubbed "Generic Stereo for DP") however, I couldn't get any > of the programs to work. Stereo is reported as disabled in nvidia- > settings but that could simply be beacuse there is no DP screen > attached. Anyway, it sounds more like this mode could support one of > the more recent GL calls. > > I guess I will keep the older 3D vision sets to run coot and chimera, > and seek more recent hardware for chimeraX. > > J.C. Haessig -- systems administrator, IGBMC > >

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Stereo mode error
by Jean-Christophe HAESSIG 05 Jan '21

05 Jan '21

Hi, I'm in charge of software packaging for our users at IGBMC. I'm trying to make stereo mode work since we still have several 3D vision sets. Even if that hardware has been retired, it seems that there isn't a more practical solution to 3D visualization ATM. We are going to test how it goes with a VR headset, but it already seems that not being able to look at anything else while using it will be a hindrance. I found a message on that subject dating back to June 2017, but I get the same errors even with the 0.1alpha2 version which seems to match what would have been current at that time : An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 73, in draw_new_frame view.draw(check_for_changes = False) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/view.py", line 165, in draw self._draw_scene(camera, drawings) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/view.py", line 205, in _draw_scene camera.set_render_target(vnum, r) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/camera.py", line 442, in set_render_target render.set_stereo_buffer(view_num) File "/usr/lib/ucsf-chimerax/lib/python3.7/site- packages/chimerax/graphics/opengl.py", line 1206, in set_stereo_buffer GL.glDrawBuffer(b) File "src/errorchecker.pyx", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glDrawBuffer, cArguments = (GL_BACK_RIGHT,) ) The host computer runs ubuntu 20.04 with the latest nvidia drivers (455). ChimeraX is deployed through a singularity container based on ubuntu 18.04. I got glxgears and coot running on the same setup (in 0.8.2 since latest coot also has a known bug in hardware stereo rendering as of now) Can anyone make sense of the error above ? I have a programming background so I can have a look but I have no idea where to start. Thanks, J.C. Haessig -- systems administrator, IGBMC

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VR for DICOM images
by Tom Goddard 04 Jan '21

04 Jan '21

H Gabriel, I am glad you were able to get ChimeraX to work with the Oculus Rift to look at DICOM images. I think this could be a useful feature but it has a long ways to go. ChimeraX is primarily used for molecular visualization, electron microscopy, and 3d light microscopy. The DICOM medical imaging capabilities have had very little development. As you found out the "volume appearance" settings are almost all useless. That was a first try to borrow some image rendering settings from other software that is designed for medical imaging data, but as you saw it does not look good at all. The trouble is that the ChimeraX volumetric rendering is different than other medical imaging software and I have not had enough time to figure out the differences. I have not looked at Invesalius -- thanks for that suggestion. Although some of the volume appearance presets have the brightness curve as a horizontal line, they use different transparencies and colors along that horizontal line. Still I am not surprised that they don't work right. They probably should not have been added to ChimeraX because they are not working correctly. If you can figure out useful presets in Hounsfield units by manually adjusting the curve in ChimeraX Volume Viewer and setting colors for each node, I could add your specific presets to ChimeraX (and probably take out those old broken presets that were translated from other software). You can add vertices to the brightness curve on the histogram in Volume Viewer by right clicking and choosing menu entry "New Threshold". The color button above the histogram changes the color of the last vertex on the curve that you clicked on. This is easiest not using VR. If you get a useful setting you can use the command "volume settings #1" (if your DICOM model is #1) and it will report all the settings including "image levels" and "image colors" which describe the brightness curve. Those are the values I would need to add a volume appearance preset. Did you see this ChimeraX VR DICOM tutorial? Maybe it has some useful info for understanding the current limited capabilities. https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tutorials/dicom-vr.html> And this documentation page on ChimeraX DICOM page summarizes the features (not specific to VR). https://www.rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html I agree with you that there is great potential for VR for medical imaging. It will take years of software improvement to make it work reasonably well, and since it is far from our primary audience for ChimeraX I cannot promise it will ever get those improvements. Tom > On Jan 4, 2021, at 12:31 PM, Biomodelos 3D <unidadbiomodelos3d(a)gmail.com> wrote: > > Tom, thanks for your answer, I finally was able to use ChimeraX with Oculus Rift and it's absolutely amazing!. (I may have issues with some USB contacts in my notebook, don't know really). > My first concern is about DICOM images, as we produce Biomodels (VR, AR and 3D printed). I've been playing with ChimeraX Volume Viewer and Oculus. I found a lot of advantages to accelerate and improve our workflow for VR Biomodels and online demonstrations, I'd like to share: > -We can enter a VR environment immediately, no need of complex segmentation and post processing. This is really fast! and allows us to face emergency cases (usually our job can't face emergencies). > -We can directly measure in 3D and see those measures in real time. > -Doctors can have a much more realistic sense of the problem, in a much faster way, and relate it to different tissue densities. > -Working in VR over original dicom images, many dimensional errors are avoided (any segmentation process implies dimensional errors). > -Also, interpretation errors (biomodelist's most important problems) are avoided, as doctors can see the study in VR by themselves, over an unaltered set of dicom images. > So I think ChimeraX VR capabilities are a complete game changer for doctors and surgeons. > > Beside, I have some questions: > I created a .txt to load a buttonpanel having Volume Appearances Presets (file attached). It works really fine, but I noticed some issues: > Black & White does not work > Glossy II and Glossy have all points over an horizontal line > High Contrast and Low Contrast have no difference (and have all points over an horizontal line) > Pencil does not work > Soft Skin II and Soft Skin III are the same > Soft on Blue and Soft on White have no difference (and all points over an horizontal line) > Appearances Presets look pretty different in ChimeraX compared to other Dicom Viewer software, can it be improved? > We use Invesalius, an open source brazilian software, as our mainstream workflow to produce volumetric renderings and .stl or .obj surfaces from dicom images. Unfortunately, it has no real time VR or AR tools. But is really good in Volumetric Rendering and segmentation of surfaces based in Hounsfield scale thresholds. So I wonder if some kind of knowledge-interchange may be useful for both developments? Please let me know if you think so. > > Thanks again! > > Gabriel Massano > Biomodelos 3D, Hospital de Ninos, Córdoba, Argentina > www.biomodelos3d.com.ar <http://www.biomodelos3d.com.ar/> > <ChimeraX Volume_Presets.txt>

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Deleting lipid molecules
by Moradkhan, Tiglath A 04 Jan '21

04 Jan '21

Hi Elaine Thank you for the help. I figured out what I was doing wrong. I wasn't using the proper syntax to delete the lipid molecules. Thanks Tiglath

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Bottleneck Large Surfaces
by Anderson, Jacob 04 Jan '21

04 Jan '21

With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay? ~jacob

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Sequence viewer Background color
by Y. Mutum 02 Jan '21

02 Jan '21

Hi This is a quick question, which I couldn't find online. I'm using ChimeraX-0.93 and was looking at the sequence of a protein chain. The background of the sequence viewer is black (picture attached) - is there any way to change it to some light color, as I can barely see the letters? I tried background color -but that changes for the molecule in display not the sequence. I also checked settings for the sequence viewer but there doesn't seem to be a setting specifically for the background sequence viewer either. Thanks Yaikhomba

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Computing protein cavities
by Y. Mutum 29 Dec '20

29 Dec '20

Hi This question is on calculating empty cavities of large protein complexes (~2 MDa) For example, the pdb-id: 6J5K. I have tried a few webservers and they are ignoring to calculate such large protein-pdb files as a whole. Does ChimeraX have tools that can be installed from the 'More-Tools' or an inbuilt one to calculate protein cavities in ChimeraX? If you could suggest external programs for computing cavities, that are reliable for such large protein-inputs, it would be also of a great help. The cavities need not be sealed by proteins all around - they can still be open to the bulk solvent. Thanks Yaikhomba

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ChimeraX "color by conservation" tutorial
by Elaine Meng 29 Dec '20

29 Dec '20

In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser. <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-…> Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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setting up mousemode - translate z - set pivot
by Helge Paternoga 22 Dec '20

22 Dec '20

Hi Elaine and Tom, Thanks for the explanations, that was very helpful. The build-in shift functionality indeed explains the translate/rotate behaviour! For me the shift button + "reversed" translate/rotate functions work perfectly, so I guess I will keep it that way. Is there anything else that speaks against it? For fitting, I am dealing with ribosomes and I have come to align the map I am fitting into in a way that makes the features clearly distinguishable (i. e. the straight solvent side of the large subunit viewed from the side), then I just move in my new map rotate to align the features and dump it using the z translate until it is in the other map, followed by fit in map. I was contemplating on how much I should stick to my old habits vs. trying new behaviours that might be more effcient in the long run. It is clear that ChimeraX offers many new opportunities for improving the workflow, but for now I like to keep my old logic (which cleary comes from using Chimera for a long time). I like to have three separate keys for rotating - xy translating - z translate that can be modified for the selected model (or dragged, will look into that). Therefore, I came up with the following setup: mousemode shift leftMode 'translate selected models' mousemode shift middleMode 'rotate selected models' mousemode shift wheel contour mousemode setting contour speed 0.1 mousemode control wheel 'translate selected models' mousemode setting zoom speed -1 fun F1 cofr sel camera ortho set bgColor grey lighting soft This actually leaves the right mouse button completely free and I was already wondering what could be a good function to map here! An unrelated observation that I had was that with grey background the selection rectangle while holding control is not visible on the background anymore (It works with white and black). Helge

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setting up mousemode - translate z - set pivot
by Helge Paternoga 21 Dec '20

21 Dec '20

Dear ChimeraX users, I am currently using the homeoffice time to finally get into ChimeraX, coming from Chimera. I just discovered "mousemode" and am trying to set up the controls to my liking. My goal is to make the fitting process of models and volumes into cryo-EM maps as smooth as possible. Currently, I use the following commands which are entered in the "execute these commands at startup" option in the settings => Is this the best way to permanently change the key-mapping? I could not find an .ini file, yet. mousemode shift leftMode 'translate selected models' mousemode shift middleMode 'rotate selected models' mousemode rightMode zoom mousemode shift wheel contour mousemode setting contour speed 0.1 My idea is to have the following set up: left mouse - turn all models (default) middle mouse - translate xy (default) right mouse - zoom shift left mouse - turn selected model shift middle mouse - translate xy selected model shift right mouse - translate z selected model scroll wheel - contour volume control right mouse - set pivot on selected model Turning and translating the models works well, also while holding shift for the selected model. As a side note, 'translate selected models' rotates the selected models in place whereas 'rotate selected models' translates in xy, is this intentional? => I would like to move the selected model in the z direction with the right mouse button while holding shift, is there an option for "translate z" ? => I am often re-setting the pivot point, therefore I would like to bind this function ("Set Pivot") to the mouse as well, does this option exist? I tried "pivot" but it did not work for cryo-EM volumes. Many thanks for reading, Helge

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Showing waters changes lighting
by Daniel Asarnow 18 Dec '20

18 Dec '20

Hi all, I have a few maps and models loaded, which have a couple hundred water molecules. When I display all the waters using 'show :HOH' the lighting changes. It makes "soft" look like "flat" and creates what looks like more ambient reflection in "full" or "simple." I embedded some screenshots below. My guess is something about a depth or lighting calculation is affected by all the waters, does anyone recognize what setting would need to change to correct this? Soft, shadows false: [image: image.png] Same after show :HOH [image: image.png] Full, shadows false [image: image.png] Same after show :HOH [image: image.png] Best, -da

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Holiday greetings from the ChimeraX team!
by Elaine Meng 18 Dec '20

18 Dec '20

The Chimera(X) team at the UCSF RBVI wishes you a safe and happy holiday season! Our holiday card is virtual this year: =-=-=-=-=-= Atoms of Apoferritin At a miraculous 1.22 Å resolution, the electron microscopy map of mouse apoferritin (right, EMDB 11638) can be mistaken for an atomic model (left, PDB 7a4m), with each atom standing out. The map from Nakane et al. (2020 Nature 587:152-156) shows glimpses of the lightest atoms, hydrogen, directly revealing the hydrogen-bonding network. Ferritin stores iron, as many as 4500 ions (Fe3+), as crystallites within its shell of 24 proteins. Apoferritin, ferritin without its iron cargo, has rock-like stability, making it ideal for divining the limits of electron microscope resolution. The images were made with UCSF ChimeraX, using ambient-occlusion lighting, coloring to delineate trimeric subunits within the dodecahedral shell, and curved helix tubes. Best wishes for a happy and healthy 2021! Conrad, Greg, Elaine, Tristan, Tom, Scooter, Eric and Tom =-=-=-=-=-= Full-resolution image: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png <https://www.rbvi.ucsf.edu/Outreach/card-gallery/2020-apoferritin/2020a.png>> Gallery of previous cards back to 1985: <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html <https://www.rbvi.ucsf.edu/Outreach/card-gallery/index.html>>

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inaccurate color box in the Models panel
by Daniel Larsson 17 Dec '20

17 Dec '20

Hi all, I'm trying to color multiple models in the same color using the color column in the Models panel. When I use the eye-droppper in the macOS colors panel, which pops up when I click on the color box, and then sample the middle of another color box, it gives me a slightly different RGB value. For example, if I start out with (209,35,16), what I get is (206,31,0). Another way of saying it is, if I sample the same color box with the eye-dropper repeatedly, the color changes. I can start out with a bright red color and then repeatedly sample the same box over and over and the color becomes a dark brown. What's up with this? Is it the macOS doing something with the colors of the boxes? Related, is there a way of getting the current RGB color of a model (or all models)? Thanks in advance! Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Extract TIFF images from a density map
by Andrea Dallapè 15 Dec '20

15 Dec '20

Hi all, I really hope that you all are healthy and safe. I would like to ask you if there is a method/command script to extract TIFF images from a density map. Basically, I used the "plane" option in Volume Viewer to see all the planes contained in the map. Now I would like to extract all the planes in TIFF images. Is this possible? Could you suggest to me how to deal with it? Thank you for your kind attention. Have a great day, Andrea

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Batch save the image of each chain
by Yong Liu 12 Dec '20

12 Dec '20

Hi All, I would like to save the image of each chain in one command. I have wrote following python code, but it is not working. Is anybody know how to fix it? # save the image of each chain def batchSave(session): chainID_list = info chains for x in chainID_list: chainID = chainID_list.split() ID = chainID[-1] save "Desktop/ID.png" width 4000 height 4000 transparentBackground true def register_command(session): from chimerax.core.commands import CmdDesc, register desc = CmdDesc() register('batchSave', desc, batchSave, logger=session.logger) register_command(session) Best, Yong Liu

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Superimpose overall structure
by Zheng, Fengwei 11 Dec '20

11 Dec '20

Dear ChimeraX developers, Thank a bunch for developing this so gracious and powerful software for our community! May I ask how to superimpose the overall structures of two analogues? e.g., the E. coli sliding clamp beta is a ring-shaped homodimer (two chains), while the yeast sliding clamp PCNA is a ring-shaped homotrimer (three chains), and their overall structures are quite similar, but when I use the matchmaker to superimpose them, it seems always only use the chain A, but not the all chains, pls see figures below~ Stay safe and warm, Many thanks! [cid:d0647b0e-e6db-459b-9f0b-72ee21eb06c7] Best, Fengwei

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Saving models in ChimeraX
by Moradkhan, Tiglath A 10 Dec '20

10 Dec '20

Hi I have a question about saving homology models in ChimeraX. Does the save command allow saving homology models as pdb files? If so then how is it possible to specify which folder to save homology models? Thanks Tiglath

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Handling gltf file
by Suzanne Duce (Staff) 10 Dec '20

10 Dec '20

Hi, When I import a .glb gltf file that I generated in ChimeraX into Blender to reduce its file size. The colouring seems to be lost. Is there a way to reduce the .glb file size in ChimeraX (or using another program)? Or not to lose the colours when importing it into Blender? Regards, Suzanne The University of Dundee is a registered Scottish Charity, No: SC015096

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Change AltGr
by Daniel Esteban Palma Igor 09 Dec '20

09 Dec '20

Hi, pressing AltGr takes the cursor to the command line, is there any way to change this key? I can't write some characters when the ipython shell is docked. Regards, Daniel Palma Igor

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Move model from position
by Lara Koehler 09 Dec '20

09 Dec '20

Dear chimeras users and developers, I would like to translate and rotate a model according to the rotation and translation matrix given by a fitmap. More precisely : I fit model #2 in map #1 and save the corresponding translation and rotation matrix with the save command. Then, I want to turn and move a model #3 so that it has the same position and rotation as model #2 (each correspond to the same pdb file). However, I want to do this automatically, so I need to do it from the matrix that is saved in a .positions file, and not from the (axis, axis point, rotation angle and shift along axis) values given by fitmap, but from the Matrix rotation and translation values. So far, - I compute the axis of rotation and the angle from the rotation matrix given by fitmap models #2 inMap #1 - I turn #3 around this axis and angle, in coordinateSystems #1 - I apply the translation also measured by fitmap models #2 inMap #1 to #3 (with three calls of the move command, for each axis x,y,z) However, there is a small gap between model #2 and model #3, whereas both should be at the exact same position. Maybe this has to do with the rotation center that is used in fitMap, but it cannot be saved in a .positions file, and I don't know how to recover it from the matrix rotation and translation given by fitmap. Do you have any idea of what I'm doing wrong, or how I could place model #3 at the same exact position as model #2 from the .positions file of model #2, and by moving and rotating model #3 ? (What I want to do then is re-apply this same transformation to build a chain of the same protein) Thanks, Lar Lara KOEHLER Laboratoire de Physique Théorique et Modèles Statistiques Bureau L123 - Bâtiment 530 - Rue André Rivière 91400 Orsay [ http://www.universite-paris-saclay.fr/ | www.universite-paris-saclay.fr ]

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multiple isosurfaces for one map
by Daniel Larsson 07 Dec '20

07 Dec '20

Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Plugin developers switch from PyQt5 to PySide2
by Tom Goddard 02 Dec '20

02 Dec '20

For those who develop ChimeraX plugins with graphical user interfaces, today we switched ChimeraX from using PyQt5 to using PySide2. These are nearly identical Python interfaces to the Qt window toolkit. In your code you will probably only need to change imports of PyQt5 to instead import PySide2. There are a few other small differences (e.g. pyqtSignal becomes Signal, and QAction callbacks may not have the same arguments) and more details about the differences are in this ChimeraX ticket <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635#comment:34>https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635> We made the switch because PySide2 has a bigger community development team, part of the Qt project, and has less restrictive licensing. Tom

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Add Chain to AtomicStructure
by Daniel Esteban Palma Igor 02 Dec '20

02 Dec '20

Hi, is there a way to add a Chain object to an AtomicStructure? Regards, Daniel Palma Igor

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BUG - NotADirectoryError when start Chimerax
by 江文宏 01 Dec '20

01 Dec '20

Hi, I am a phD from Peking University, Beijing, China. And I downloaded the latest version(1.1) of Chimerax for Centos. And I installed the chimerax in the linux (centos7) by yum install ucsf-chimerax-1.1-1.el7.x86_64. And everything went well for the install/compiling process. However, when I started the chimerax in the terminal, the terminal returned this error: Do you have any idea about such errors? I also tried the older version(1.0), but I got the same error. BTW, I used python3.8. Thanks! All the best, Wenhong Jiang

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New color picker alpha channel and custom color
by Daniel Asarnow 30 Nov '20

30 Nov '20

I noticed in a recent ChimeraX build the color picker has been simplified: [image: image.png] It seems we can still set the alpha channel within the "custom" color dialog, but the default color there is some shade of red regardless of the currently selected color. Could the custom dialog start at the current color by default? Setting the alpha channel via the picker is the fewest number of clicks, and starting at the current color will make slight adjustments much easier as well. Best, -da

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Problem with C2 symmetric assemblies
by Y. Mutum 30 Nov '20

30 Nov '20

Hi I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command. >>> sym #1 assembly 2 newModel false The idea is to superimpose Chain /C of 1be3 and its symmetry partner with that of 3cx5 (corresponding chains -C and N) to get of deviations b/w the chains. However, when I try to 'match #1/C with #2/C, then I am getting only half of the C2 symmetric assembly superimposed. Is there a way to superimpose both of the chains-C of 1be3 to 3cx5? I could open the model 1be3 twice and then superimpose to the equivalent subunits (chains C and N) of 3cx5, one at a time. But the resulting superimposed assembly 1be3 (from 2 different models) is not going to be the C2 symmetric. In short, for 1be3: pdb, is it possible to rename the symmetry mate with different chains and get the C2 symmetric assembly as a single model? Say, for this new 1be3 C2-symetric assembly, you rename the second symmetry partners chains - Chain C as C1, Chain B as B1 for example in that new model. The idea is to have a C2 symmetric model with different chains, so that it can be compared with other models easily. Thanks Yaikhomba

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User defined color values for each residue/position
by Niccolò Arecco 30 Nov '20

30 Nov '20

Hi, I’m using ChimeraX to visualise the structure of a complex of 4 proteins. I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. The input “colouring” file could be something like this tab delimited file: #POS AA SCORE 1 M 0.2 2 V 0.5 …. n N 0.8 But I can reshape it in a better format if necessary. If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this? In the end I’d like to be able to do something like ConSurf (https://consurf.tau.ac.il <https://consurf.tau.ac.il/>) does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least. Thanks a lot! Best wishes Nicco

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Coloring pdb surface by different colors
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow? I tried the surface command option but it seems to color the entire surface in a uniform color. Any suggestions would be very helpful. Thanks Yaikhomba

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Measuring Angles in ChimeraX
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I am trying to measure angles between three atoms using ChimeraX by typing >>> angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C However, the log reports: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C Unknown command: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C I have also tried to check if 'angle' is a valid command in the ChimeraX window I have opened. >>>usage angle In Log ---> "angle" is not a command name However, angle does seem to be a valid command in ChimeraX. In the documentation here -- http://www.cgl.ucsf.edu/chimerax/docs/user/commands/angle.html. I am using ChimeraX-1.0 ( version: 1.0 (2020-06-04)) I might have missed things out - Could you please give an idea of how i could measure angles using the command line in ChimeraX? Thanks Yaikhomba

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Build DNA structure in Chimera X
by Andreas Göransson 27 Nov '20

27 Nov '20

Dear Chimera X users, I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera? THanks in advance, Andreas Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping

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Use of EnumOption
by Daniel Esteban Palma Igor 26 Nov '20

26 Nov '20

Hi, when using the chimerax.ui.options.EnumOption, are you supposed to create a subclass that specifies the attributes "labels" and "values"? the documentation doesn't say anything about it. Regards, Daniel Palma Igor

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access to private chimeraX github
by Johannes Maier 25 Nov '20

25 Nov '20

Hi there, I really like chimeraX and I would like to have access to the github to play around more. Thanks so much in advance, Cheers, Johannes

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Specify GPU id for ChimeraX
by Shasha Feng 25 Nov '20

25 Nov '20

Hi, Is there any way to specify which GPU device for ChimeraX to run on? Currently, it uses the default GPU 0, which can disturb the existing jobs. Thanks. Best, Shasha

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Re: [chimerax-users] Set up to take pictures of structure with a specific angle
by Elaine Meng 24 Nov '20

24 Nov '20

Hi Emilie, How to use the command is shown in the "view matrix" help: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix> There is no colon, you would want a command something like the following, all on one line (the Mail app may show it as broken into multiple lines but it should all be one line): view matrix camera -0.97114,-0.2031,0.12509,57.651,-0.030537,0.62598,0.77924,221.24,-0.23657,0.75293,-0.61412,-21.353 I hope this helps, Elaine > > On Nov 24, 2020, at 10:31 AM, EMILIE MONTELLIER <emilie.montellier(a)univ-grenoble-alpes.fr> wrote: > > Dear Elaine, > > Thanks for your answers, it really helps me to understand how to use ChimeraX. > > For the question 2 > I manage to get the camera matrix by using view matrix in the command. Then I moved my structure and tried to apply the camera matrix I had, but I did not suceed. > I did view matrix :the number obtained in camera position > Here is a picture of the log : > Please do you know what I did wrong? > > Thanks by advance for your help, > Best regards, > > Emilie > > > De: "Elaine Meng" <meng(a)cgl.ucsf.edu> > À: "EMILIE MONTELLIER" <emilie.montellier(a)univ-grenoble-alpes.fr> > Cc: "chimerax-users" <chimerax-users(a)cgl.ucsf.edu> > Envoyé: Mardi 24 Novembre 2020 17:09:33 > Objet: Re: [chimerax-users] Set up to take pictures of structure with a specific angle > > Hi Emilie, > (1) Cartoon thickness. You would use the "cartoon style" command to change the ribbon dimensions and shape. It can be done separately for helix, strand, and coil. For example: > > cartoon style coil thickness 1.0 > > There are many options, see: > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style> > > (2) Multiple images from different sessions with same orientation. > > (A) If all your different sessions were made with either the same starting structure (same PDB file) or structures that were already fit on each other when they were opened, you could get matrix from the view that you want and apply the matrix to all the others. You would use "view matrix" without arguments in the session that already has the view you want, to report the camera matrix in the Log. Then you would use "view matrix" specifying that camera matrix in your other sessions to put them into the same view. > > (B) If all your different sessions were made with different PDBs that weren't already fit on each other, then I believe the only way is to include a reference structure in each one, make sure the reference structure is in the position you want as in (A) above, and match the structure for the image onto the reference structure (e.g. with matchmaker or align), and then hide the reference structure. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On Nov 24, 2020, at 12:45 AM, EMILIE MONTELLIER <emilie.montellier(a)univ-grenoble-alpes.fr> wrote: > > > > Dear ChimeraX users, > > > > I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure? > > > > Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)? > > > > Thanks by advance for your help, > > Regards, > > Emilie

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Set up to take pictures of structure with a specific angle
by EMILIE MONTELLIER 24 Nov '20

24 Nov '20

Dear ChimeraX users, I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure? Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)? Thanks by advance for your help, Regards, Emilie ------------------------------- Emilie Montellier, PhD MSCA Post-doctoral Researcher Institute for Advanced Biosciences - Grenoble, France Prof. Pierre Hainaut's laboratory Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Problems to save my file
by EMILIE MONTELLIER 22 Nov '20

22 Nov '20

Dear ChimeraX Users, I am a new user of ChimeraX and I struggled with saving my files. I have a very naive question. I have downloaded a PDB file for p53 protein structure, then I did some modifications of the structural representation using ChimeraX. Then, I would like to save my file, with this new representation to work on it later. The problem is when I save and open again, it shows the representation from the PDB I originally downloaded, but without the work I have been doing on it. In other words: which settings should I use to save my file to keep all the visual modifications I have been doing? I would like to open the file on Chimera later, and continue my work on this file. Thanks by advance for your help, Regards, Emilie ------------------------------- Emilie Montellier, PhD MSCA Post-doctoral Researcher Institute for Advanced Biosciences - Grenoble, France Prof. Pierre Hainaut's laboratory Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier(a)univ-grenoble-alpes.fr

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Animation feature in ChimeraX?
by Eric Pettersen 21 Nov '20

21 Nov '20

> Begin forwarded message: > > From: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Subject: Animatin feature in ChimeraX? > Date: November 20, 2020 at 10:05:00 AM PST > To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > > > Hi, > I have used Chimera for years for my publications and for generating animations for lectures and invited talks. I found the animation feature incredibly easy to use and intuitive. However I did not find a similar feature in ChimerX. I read about the Morph command but to me this seems much more complicated to use and much less intuitive. Is there a graphical interface to the Morph command or is this going to remain a command line feature only? I often use the animation feature of chimera to morph between two structural states, which is really easy. > Cheers, > Rodney Tweten, Ph.D. > George Lynn Cross Professor > Presidential Professor > > "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” > Isaac Asimov > > BMSB-1053 > 940 Stanton L. Young Blvd. > The University of Oklahoma Health Sciences Center > Oklahoma City OK 73104 > USA > Work phone: 405 271-1205 > Web page: https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney… <https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney…> > Skype: toxlab1

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ChimeraXClassifier platform attribute
by Daniel Esteban Palma Igor 21 Nov '20

21 Nov '20

Hi, I have a command that will work in mac and linux but not in windows, Should I create a separate ChimeraXClassifier for linux and mac with the corresponding platform attribute or there is a way to create only one ChimeraXClassifier for both? Regards, Daniel Palma Igor

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Transparency for atoms selected only
by Gabriele Cerutti 21 Nov '20

21 Nov '20

Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele

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Saving biomt record for generated icosahedral
by Moustafa, Ibrahim M. 20 Nov '20

20 Nov '20

Hi all, I built a full icosahedral model from ASU in chimeraX, how can I save the coordinates and BIOMT record of the generated full-model? Thanks for helping. Ibrahim

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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tips on how to use the "bond rotation" right mouse tool
by M. Elizabeth Stroupe 19 Nov '20

19 Nov '20

Hi all, I am working on a little side project to use ChimeraX with high school students to explore protein structures. I am looking for tips on how to make the program as intuitive as possible! I can't seem to make the "bond rotation" tool work easily. I gather you should be able to just highlight that, depress the right button, and move the mouse over the bond you want to move. Sometimes it works and sometimes it doesn't. What am I doing wrong? (and other tips besides having students do some of your tutorials before starting the activity would be very welcome!) Thank you! Beth

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General question about MODELLER
by Moradkhan, Tiglath A 19 Nov '20

19 Nov '20

Hi I have a question about using MODELLER. I've built models of a protein that I'm currently studying and wanted to know if it's necessary to minimize regions of the protein that may have poor quality based on the QMEAN score. Or does MODELLER minimize these regions when building homology models? Thanks Tiglath

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question about lighting options
by Ryan Cammarota 18 Nov '20

18 Nov '20

Hi, I am wondering whether there is a simple way in ChimeraX to set one point (or atom) as a light source, which could allow for the shadows cast by the surrounding atoms to be visualized? Thanks for your help, Ryan

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