- ChimeraX-users - RBVI Mailing Lists

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 >> > >

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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

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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.

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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

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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

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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

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