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Re: [chimerax-users] Applying symmetry operations to generate an oligomeric model
by Tom Goddard 07 Nov '22

07 Nov '22

Hi Rob, Hopefully you are using ChimeraX, not Chimera -- we have only done maintenance on Chimera for the past 6 years. The ChimeraX commands all work in physical coordinates (Angstroms), not grid index units (pixels), and usually they use scene coordinates, not local model coordinates which makes a difference if you have moved individual models relative to one another in the scene. Your Dn symmetry problems are because the two-fold symmetry that flips one Cn ring to the other stacked Cn ring needs to be aligned on the x-axis. In your map apparently it is not aligned with the x-axis. In general it is helpful to have your map aligned in a standard way if you will be applying symmetry. For dihedral symmetry the z-axis is the cyclic symmetry axis, the origin should be on that cyclic symmetry axis mid-way between the two rings, and the x-axis should be a two-fold symmetry axis. If you don't use standard map orientations for symmetric maps it is going to be very painful to make symmetric copies of atomic models in those maps. Tom > On Nov 6, 2022, at 12:58 PM, Robert Harkness <r.harkness(a)utoronto.ca> wrote: > > Hi Tom, > > Thank you for your detailed response! > > I think I am using an older version of chimera. When I use the center <map> command, I just get one line of output that corresponds to the center of the map in grid coordinates. I have been converting these into angstrom coordinates using the pixel size and applying those in sym. > > Sometimes when I open a model and a map, I have to rotate and translate the model into a reasonable position inside the map and then do a “fit in map” to get the initial placement for sym, so this means that the model’s coordinates will now be different relative to the scene and the map. If I save the fitted model to a new PDB and then re-open it, will it now have the same coordinates of the scene (and map if I haven’t moved the map at all)? I think that way I can use scene coordinates for all maps and models. > > I am finding for other cages I am working on that have Dn symmetry, in some cases they work beautifully if I just fit the model into the portion of the map that corresponds to one unit of the cage, then save that model as a PDB relative to the map, then open it and use sym <model> group <Dn> center <map center in angstrom units> coordinateSystem <map>. In other cases doing this same procedure, the first half of the cage units are made perfectly as sym goes from the initial model around the Cn axis placing copies in the density, but when it flips over the 2-fold axis to do the other half, the model units are out of alignment with the density. So I have been adding the axis option to get it closer but find it requires a little tweaking. I guess the axis command doesn’t always give the perfect axis of rotation because the map is not perfect. Will this also be alleviated by just using everything in scene coordinates? > > Best, > > Rob > >> On Nov 5, 2022, at 7:55 PM, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> >> You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> >> Hi Rob, >> >> It sounds like you did everything right. Using "measure center #1" where model #1 is the map should give the right center of the tetrahedron. When you use that command it reports the center in map grid index units and also in scene coordinates, for example, >> >> measure center #1 <cxcmd:measure center #1>Center of mass grid index for emdb 15560 = (279.52, 279.92, 253.25) >> Center of mass xyz coordinates for emdb 15560 = (289.20, 235.85, 185.32) >> >> >> In the sym command were you use that center to copy your atomic model with tetrahedral symmetry you should use the scene coordinates (the second line of output) not the grid index coordinates. The "sym" command expects scene coordinates for the "center" option and you should not use the "sym" command coordinateSystem option. The coordinateSystem option is used only if the center coordinates are given in the coordinate system of a specific model rather than the whole scene. The models start out with the same coordinate system as the whole scene, but if you move a model in the scene (e.g. when you fit an atomic model into the map) then that model has different local coordinates than the scene. >> >> I see another potential problem in your sym command. The "axis" option is supposed to be a 3-fold symmetry axis of the tetrahedron. You are giving it the symmetry axis of the asymmetric unit trimer which may or may not be a symmetry axis of the tetrahedron. To determine the symmetry axis of the tetrahedron open two copies of the map and rotate one copy by hand using the "Move Model" mouse mode (which moves only the selected model) to roughly align two different trimeric subunits then optimize the alignment with "fitmap #2 in #1", then use measure rotation #2 to #1 and it will report a symmetry axis of the tetrahedron. Another way to go about this is if you density map already has a standard orientation, such as tetrahedron 2-fold symmetry axes along x,y,z then you don't need to specify the axis in the sym command, just use "t,222" in the sym command. Or if it has a symmetry axis along z use "t,z3" with no axis specification. You can probably see if it has a standard symmetry using "measure symmetry #1". >> >> Sorry for the delayed answer. I was at a workshop all last week and did not have time for email. >> >> Tom >> >>> On Nov 3, 2022, at 4:35 AM, Robert Harkness via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> Hello, >>> >>> I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do >>> >>> sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) >>> >>> And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! >>> >>> Best, >>> >>> Rob >>> >>> _______________________________________________ >>> ChimeraX-users mailing list >>> ChimeraX-users(a)cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> >>> Manage subscription: >>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users> >>> >> >

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error saving session in v 1.5
by Yoda Muppet 07 Nov '22

07 Nov '22

Greetings. We're having an issue savings session with ChimeraX 1.5. Trying to save a session file results in the following error: [save] (help: user/commands/save.html) /data/processed/staggers/cryofib- tryps/process/YTAT9-1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs [save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs] (cxcmd: save /data/processed/staggers/cryofib- tryps/process/YTAT9 - 1 lamella4 0206 def -5 110e tilt-7/full seg session.cxs) Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 285, in process data = sm. take snapshot (obj session, self.-state flags) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/log/tool.py", line 542, in take snapshot "contents': self.page source, AttributeError: *Log' object has no attribute 'page source' The above exception was the direct cause of the following exception: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 262, in discovery self.processed[key] = self.process (obj, parents) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 290, in process raise RuntimeError (msg) from e RuntimeError: Error while saving session data for "tools' -> ‹chimerax.core. tools. Tools object at 0x7f90efeb0310> => <chimerax.log. tool. Log object at 0x7f90ee2b3c10> During handling of the above exception, another exception occurred: Traceback (most recent call last) : File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 896, in save session. save (output, version=version, include maps=include maps) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 625, in save mgr.discovery(self. state containers) File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py", line 266, in discovery raise ValueError ("error processing: %S: %S" % ( obj stack(parents, obj), e)) ValueError: error processing: "tools' <chimerax.core. tools. Tools object at 0x7 f90efeb0310> <chimerax.log. tool.Log object at 0x7f90ee2b3c10>: Error while saving session data for 'tools' -> <chimerax.core. tools. Tools object at 0x7f90efeb0310> <chimerax.log. tool. Log object at 0x7f90ee2b3c10> BUG: ValueError: error processing: 'tools' for "tools => -> ->: Error while saving session data File "/opt/cryoem/chimerax-2022.10.28/lib/python3.9/site- packages/chimerax/core/session.py" line 266, in discovery raise ValueError ("error processing: %S: %5" % (obj stack(parents, obj), e)) See log for complete Python traceback.

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Change luminance in color palette
by Scott, Brandon L. 07 Nov '22

07 Nov '22

I am coloring surfaces using palettes (purples or a custom green-white-magenta). These both have a single luminance value, is it possible to generate a color palette that also has changing luminance. The ideal palette would be green -> white -> magenta along the color axis, and 0 - > 255 scaling the luminance of the rgb. We would effectively have a color bar matrix that goes from dark green to black to dark magenta if the values are low and bright green to white to bright magenta if the values are high. Thanks for your insights! -Brandon Brandon Scott, PhD CZI Imaging Scientist, Assistant Professor Nanoscience & Biomedical Engineering South Dakota Mines EEP 229 501 E. Saint Joseph St., Rapid City, SD 57701 724.510.1253 | Brandon.Scott(a)sdsmt.edu<mailto:Brandon.Scott@sdsmt.edu> [South Dakota Mines]<https://www.sdsmt.edu/>

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Create command for subunit model
by tim smith 06 Nov '22

06 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Applying symmetry operations to generate an oligomeric model
by Robert Harkness 05 Nov '22

05 Nov '22

Hello, I am trying to generate a model of an oligomeric protein cage that consists of 4 trimers and has tetrahedral symmetry. I am using the asymmetric unit model consisting of one monomer (#0) and a density map (#1) as a starting point. My strategy has been to take the asymmetric unit and fit it into a portion of the map corresponding to one of the monomers within one of the trimer faces of the tetrahedron. Then I generate a copy of that asymmetric unit (#2) and fit it into the map for an adjacent protomer within the same trimer face. This results in the two asymmetric unit models being rotated 120 degrees relative to one another and part of the same trimer. Then I use the measure rotation command to measure the rotation of the second asymmetric unit relative to the first, giving me a rotation matrix and axis parameters. I then do sym #0 (first asymmetric unit) group t,z3 axis <axis from measure rotation> center <axis points from measure rotation> coordinateSystem #1 (the density map) And this generates the right looking trimers, so the 3-fold axis appears to be correct, but the center is off such that only one of the four trimers matches the density map and is placed at the top of the tetrahedron, while the other 3 trimers are off into the void of the scene but placed at the other 3 vertices. I am not sure how to appropriately define the center. My feeling is that it should be the center of the map, taken from the measure center #1 command, but implementing those numbers in sym doesn’t work either. Any thoughts on how these center coordinates are defined/should be measured, or if there is a better approach for doing this would be awesome! Best, Rob

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Create subunit model
by tim smith 05 Nov '22

05 Nov '22

Hi All, I would like to create a separate subunit model in chimeraX like create command in Pymol. In my PDB model, 3 subunits are present, I want to make each subunit as a model for representation. Thank you and best regards Tim

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Re: [chimerax-users] [Chimera-users] Jagged edges in chimera X
by Elaine Meng 03 Nov '22

03 Nov '22

Hi Prathvi, For ChimeraX questions, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu CC'd here. As per this recent post, ChimeraX does not have multisampling, but if you are saving an image you can use supersampling: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-September/004310.ht…> ChimeraX also has a "graphics quality" command to increase the number of facets used to draw atoms, bonds, and cartoons (ribbons), although I don't know if that is going to help your issue very much: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#quality> 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 3, 2022, at 4:59 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Elaine, > > Is there a way to smoothen the jagged edges seen around ribbons and sheets in ChimeraX? > The jagged edges can be removed in UCSF chimera by setting the subdivision value to 20 and enabling multisampling but I do not see these features in chimeraX. > > -- > Prathvi Singh, > Research Fellow, > Department of Biological Sciences & Bioengineering, > Indian Institute of Technology, Kanpur-208016 > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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How to discover hydrophobic between two chains
by McClean, Phillip 02 Nov '22

02 Nov '22

Hi Everyone, I ran AF2 multimer and have a two-chain complex. I ran the mlp command on the two chains separately and together. The two chains seem to interact via hydrophobic residues where chain B fits into a pocket on chain C. Here are the chain residues: /b:72-124 /c:1-190 Is there any way to determine which residues (hydrophobic) in each of these two regions are interacting via hydrophobic interactions. Thanks for any help you can provide. Phil McClean

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Copy attribute value from one attribute to another
by Sean Connell 02 Nov '22

02 Nov '22

Hello, I have a question with a probably obvious answer but I cannot figure it out. Is there a command to copy an attribute value from one attribute to another, for example, seq_conservation to bfactor? The idea would be to save a pdb file with the conservation stored in bfactor (for sharing). In this case I guess there is the issue that one is an atom attribute and the other is residue attribute but one could assign all atoms of the residue the same value. Sorry in advance if I miss something obvious.

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Get atom from selection string in script
by Thibault TUBIANA 02 Nov '22

02 Nov '22

Hi! I would like to create a function to copy the torsion angle from a model to another one. The function would take in argument the model ID of the reference and target model (<int>) and the residue id (<int>). I looked a bit at the scripts available in [ https://rbvi.github.io/chimerax-recipes/ | https://rbvi.github.io/chimerax-recipes/ ] to have an idea of how to add function in ChimeraX, but I'm currently stuck at "how to get the list of atoms from a selection string ?". Here's my current script from chimerax.core.commands import run def copy_torsion(session, model1, model2, residue): selection = f"torsion #{model2}:{residue}@n,ca,c:{residue+1}@n" from chimerax.atomic import AtomsArg atoms = AtomsArg(selection) from chimerax.geometry import dihedral cur_torsion = dihedral([*a.scene_coord for a in atoms]) torsion=run(session, f"torsion #{model1}:{residue}@n,ca,c:{residue+1}@n {cur_torsion}") def register_command(logger): from chimerax.core.commands import CmdDesc, register, FloatArg, IntArg, BoolArg, Color8Arg, StringArg from chimerax.atomic import AtomsArg desc = CmdDesc(required = [ ('model1', IntArg), ('model2', IntArg), ('residue', IntArg), ], synopsis='Copy torsion angle') register('copyTorsion', desc, copy_torsion, logger=logger) register_command(session) Thank you for your help :) Best regards, Thibault. -- Thibault Tubiana, PhD Postdoctoral Fellow @ [ https://www.i2bc.paris-saclay.fr/equipe-interactions-and-assembly-mechanism… | IMAPP ] Institute for integrative biology of the cell ( [ https://www.i2bc.paris-saclay.fr/ | I2BC ] ) - CNRS UMR 9198 CEA Saclay, 91191 Gif sur Yvette - Bât 532 pce 34 Web Site: [ http://www.tubiana.me/ | http://www.tubiana.me/ ]

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