- ChimeraX-users - RBVI Mailing Lists

ChimeraX Side View
by Elaine Meng 19 Jul '19

19 Jul '19

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

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

19 Jul '19

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

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

18 Jul '19

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

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Molecular Dynamics Viewer
by James Starlight 16 Jul '19

16 Jul '19

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

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

15 Jul '19

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

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

12 Jul '19

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

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mesh lineThickness
by Yazan Abbas 12 Jul '19

12 Jul '19

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

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

11 Jul '19

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

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Appearance of thick edges
by Yazan Abbas 11 Jul '19

11 Jul '19

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

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feature request / suggestion
by Alexis Rohou 09 Jul '19

09 Jul '19

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

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

08 Jul '19

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

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

03 Jul '19

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

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

03 Jul '19

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

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

02 Jul '19

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

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

02 Jul '19

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

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

02 Jul '19

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

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

01 Jul '19

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

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

01 Jul '19

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

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

01 Jul '19

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

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

28 Jun '19

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

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Mouse modes
by Yazan Abbas 27 Jun '19

27 Jun '19

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

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

27 Jun '19

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

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

25 Jun '19

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

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

25 Jun '19

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

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

25 Jun '19

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

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