June 2021 - ChimeraX-users - RBVI Mailing Lists

Troubles when saving a map
by Stéphane ROCHE 18 Jun '21

18 Jun '21

Dear Mr/Mrs, I am new to ChimeraX (v 0.7) and I have a trouble when saving a map. I am working with a .ccp4 map from an electron microscopy project. I would like to slightly change the pixel size that was inaccurately estimated during data processing and chimeraX seems to be the program for doing that. - Opening the map is fine. - Then I change the pixel voxelsize which is also fine. - I then save the modified map (I use the .mrc format here given that I do not find a .ccp4 format). - However if I then use the map with my usual softwares (phenix, coot) it looks like pure noise. But the map looks normal with some other softwares (e.g. pymol). I also have no problem usually with my .mrc maps with any software so I would assume the problem is with the .mrc map I created Do you know what I could do to solve this problem ? Thanks, Stephane Roche Institut de Biologie Intégrative de la Cellule 91198 Gif sur Yvette France

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listing all-by-all atom distances
by Elaine Meng 15 Jun '21

15 Jun '21

> On Jun 15, 2021, at 9:33 AM, Juliana Glavina <jglavina(a)gmail.com> wrote: > > Hi Elaine, > I am trying to calculate the distance between one residue and a set of residues (within a name selection). I couldn't do this in Chimera either and I couldn't find the answer online. > Thanks! > Juliana Hi Juliana, (We recommend using the chimerax-users address CC'd here for questions, so that the Q & A will be archived and searchable.) One way to do it in ChimeraX is with the "contacts" command or Contacts tool. In this case you aren't necessarily using it to find contacts, but instead to measure and list atom-atom distances. You say "residues" but really all the distances are measured from atom to atom. You will get all by all distances between two sets of atoms, where the first set is your first residue and the second set is all the residues in your named selection. In ChimeraX, you can name the current selection or some other specification with the "name" command. To name the current selection "blah" it would be command: name frozen blah sel See "name" help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/name.html> Then if you want to measure all atom-atom distances between (1) atoms in residue 55 of chain A of model 1 and (2) your named selection "blah" and show them in the Log, you could use a command something like contacts #1/A:55 restrict blah overlap -1000 log true The large negative overlap value is used to force measuring all the distances even if the atoms are 1000 Angstroms apart, instead of the usual behavior of finding only the contacts. The Log will have lines like the following, where the last column is the distance between atomic centers: 1728 contacts atom1 atom2 overlap distance /A BGC 310 C6 /A TYR 10 CE2 0.018 3.622 /A BGC 310 O6 /A HIS 152 NE2 -0.134 2.834 /A BGC 310 O4 /A TRP 183 CG -0.202 3.272 /A BGC 310 C3 /A TRP 183 CE3 -0.253 3.893 /A BGC 310 C2 /A PHE 16 CD1 -0.323 3.963 /A BGC 310 C5 /A HIS 152 NE2 -0.360 3.880 /A BGC 310 C6 /A HIS 152 NE2 -0.366 3.886 /A BGC 310 O4 /A TRP 183 CD2 -0.424 3.494 /A BGC 310 C5 /A TRP 183 CE2 -0.429 3.919 /A BGC 310 O6 /A HIS 152 CD2 -0.490 3.710 /A BGC 310 C3 /A TRP 183 CZ3 -0.495 4.135 /A BGC 310 O4 /A TRP 183 CD1 -0.499 3.719 /A BGC 310 O6 /A HIS 152 CE1 -0.556 3.776 /A BGC 310 C5 /A TRP 183 NE1 -0.596 4.116 [...] The lines are in order of largest VDW overlap which is similar to shortest distance but not exactly the same. If you save to text file you can then sort by column, for example, by the second residue number to group those together, or by the distance. The "contacts" command has a lot of options including saving results to text file, as detailed here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html> You can do the same thing in Chimera, name selection and use "findclash" but the exact commands and their syntax are slightly different. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Adjusting coil width
by Edgar A Hodge 15 Jun '21

15 Jun '21

Hello, I'm struggling to adjust the coil width. This seems easy to do using the "cartoon style" command, but I can't seem to figure it out with coils. Thanks! Eddie

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align peptide to model sequence
by Lagerwaard, I.M. (Ilse) 15 Jun '21

15 Jun '21

Hi everyone, I want to write a script that can align the sequences of peptides to a model sequence and return the identical residues. Because I am new to programming, I could really use some help to get started. Could I use the search() method of the Sequence class for this? And if so, how could I go about this? Kind regards Ilse Lagerwaard

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Mesh resolution/smoothness
by Saren Tasciyan 15 Jun '21

15 Jun '21

Hi, I am trying to generate STL files out of protein models. Often the problem is that the mesh doesn't as smooth as the models (see pics below). I wonder if this is an artifact of rendering in ChimeraX or the mesh is actually hard coded to have certain resolution, which makes it look like this? I tried to find out why and ended up in custom_x3d function but didn't notice anything. Post-export smoothing is an option but I wonder, if that's the optimal approach? Perhaps, smoothing can create collisions between 2 STL models, where a higher resolution export may avoid this. Best, Saren -- Saren Tasciyan /PhD Student / Sixt Group/ Institute of Science and Technology Austria Am Campus 1 3400 Klosterneuburg, Austria

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dual conformation
by Wen-Jin Winston Wu 15 Jun '21

15 Jun '21

Hi, I am trying to use Chimera X to display an amino acid with dual side chain conformations (PDB code: 7a5v) together with its cryoEM density map (EMDataResource: <https://www.emdataresource.org/EMD-11657> EMD-11657). For example, Tyr 66 have two side chain conformations, however using the command below, it only showed one conformation. resfit /a:66 map #1 (a very nice command, by the way) I then used Chimera 1.15 to view the PDB coordinate, and it showed two side chain conformations for Tyr66 (as I saw in PyMol); on the other hand, Chimera X only shows a single conformation. Is there any way to display the two alternative conformations using Chimera X? Thanks a lot for your time, and possible help! Best wishes, Winston ************************* ATOM 495 N ATYR A 66 124.799 162.717 112.222 0.50 11.67 N ATOM 496 N BTYR A 66 125.017 162.760 112.080 0.50 12.99 N ATOM 497 CA ATYR A 66 124.008 162.914 110.998 0.50 12.05 C ATOM 498 CA BTYR A 66 124.035 162.916 111.002 0.50 14.20 C ATOM 499 C ATYR A 66 124.638 164.062 110.190 0.50 11.84 C ATOM 500 C BTYR A 66 124.433 164.115 110.140 0.50 13.40 C ATOM 501 O ATYR A 66 125.008 165.077 110.788 0.50 11.86 O ATOM 502 O BTYR A 66 124.411 165.246 110.660 0.50 14.99 O ATOM 503 CB ATYR A 66 122.562 163.249 111.355 0.50 13.02 C ATOM 504 CB BTYR A 66 122.666 163.125 111.624 0.50 17.22 C ATOM 505 CG ATYR A 66 121.759 162.139 111.997 0.50 14.56 C ATOM 506 CG BTYR A 66 121.542 163.315 110.654 0.50 21.09 C ATOM 507 CD1ATYR A 66 121.860 161.839 113.348 0.50 16.21 C ATOM 508 CD1BTYR A 66 120.718 162.258 110.325 0.50 25.90 C ATOM 509 CD2ATYR A 66 120.832 161.436 111.248 0.50 17.74 C ATOM 510 CD2BTYR A 66 121.189 164.579 110.209 0.50 29.25 C ATOM 511 CE1ATYR A 66 120.974 160.942 113.960 0.50 18.53 C ATOM 512 CE1BTYR A 66 119.590 162.443 109.543 0.50 32.51 C ATOM 513 CE2ATYR A 66 119.990 160.494 111.824 0.50 18.57 C ATOM 514 CE2BTYR A 66 120.067 164.784 109.421 0.50 27.89 C ATOM 515 CZ ATYR A 66 120.076 160.228 113.177 0.50 20.29 C ATOM 516 CZ BTYR A 66 119.252 163.714 109.107 0.50 30.80 C ATOM 517 OH ATYR A 66 119.241 159.287 113.722 0.50 24.21 O ATOM 518 OH BTYR A 66 118.168 163.886 108.291 0.50 39.05

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using pandas
by Lagerwaard, I.M. (Ilse) 11 Jun '21

11 Jun '21

Hello everyone, Is it possible to use the pandas package in ChimeraX? I tried opening a Python script containing the line 'import pandas', but I get the error: 'ModuleNotFoundError: No module named 'pandas''. Kind regards, Ilse

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Independent centres of rotation
by Shahid, Taha (Dr.) 10 Jun '21

10 Jun '21

Hi, Is there a method, even if an indirect one via a long command or a series of commands, to set independent rotation centres for a series of (cryo-EM) maps that would then turn together. This could be easily achieved by 'set independent' in the original Chimera, and is much missed by our group of structural biologists. Kudos otherwise on a wonderful upgrade to the program. Many thanks, Taha

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Re: [chimerax-users] saving multiple .obj files from a morph
by Elaine Meng 09 Jun '21

09 Jun '21

On Jun 9, 2021, at 3:38 AM, Brett Murrah <murrahx5(a)att.net> wrote: > I’m trying my best to use the perframe command to save each frame / model out from a morph and slider animation after morphing some pdbs. It is exporting something.. but only 1k files. I’m not sure what I’m doing wrong. Any help? My command is this: > > perframe "save D:/Projects/OBJs/model$1.obj model #3.$1" frames 10 > > PS, I put model #3 because the ID’s for 1 and 2 are the models I used for the morphs. The final morph is #3. If I export each slider frame by hand.. that seems to work. Trying to automate it best I can. > > Thanks you for any help! > Brett Hi Brett, I'm guessing you meant to send this to chimerax-users(a)cgl.ucsf.edu (CC'd here, the recommended address for questions). The morph #3 is a trajectory model. It does not have the frames as submodels #3.1, 3.2, ... so your save command doesn't make sense. I don't know what you mean by "1k files" either... do you mean it makes 10 files but they are too small? You would use "perframe" in combination with "coordset" to replay the existing morph trajectory. E.g. put something like this into a command file (plain text named something.cxc) and then open it in ChimeraX: perframe "save D:/Projects/OBJs/model$1.obj models #3" coordset #3 1,10; wait 10 ~perframe <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/perframe.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html> The reason I say to put it in a command file is to make the commands execute instantly one afer the other. I expected it to work when I entered them all as one long line in the command line (with semicolon separators) but then I got a parsing error, possibly due to a bug. E.g. I tried entering this as one long line (the mail tool may choose to break it up): perframe "save D:/Projects/OBJs/model$1.obj models #3"; coordset #3 1,10; wait 10; ~perframe ... but that gave an "incomplete quoted text" error which I will report as a bug. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Change default volume display settings?
by Oliver Clarke 08 Jun '21

08 Jun '21

Hi, Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX. Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model? Cheers Oli

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ChimeraX-users June 2021