- ChimeraX-users - RBVI Mailing Lists

pseudobond between atom and center of a ring
by Alexis Rohou 06 Mar '20

06 Mar '20

Hi all, Looking for ideas on how to achieve the following, if possible: I'd like to draw lines to represent favorable ring-ring stacking interactions (lines between the center of two arene rings), ring-ring edge-to-face interactions (between one atom of one ring and the center of the other ring), and between a regular atom (not part of a ring) and the center of an arene ring. So I'm guess what I'm looking for is a way to: 1. compute the center coordinates of a ring 2. place an invisible atom there 3. create a pseudobond between this virtual atom and other atoms/virtual atoms Any suggestions as to how I could achieve this? Cheers, Alexis

3 6

Depth cueing and silhouette
by Aritz Roa Eguiara 05 Mar '20

05 Mar '20

Dear ChimeraX team, I write you to ask about the depth cueing option. I have a structure with the silhouette true option and now I want to change the depth cueing to obtain a slice of the structure but with some of the fog coming from the background. The cartoon color disappear gradually as expected, however the black line of the silhouette is 100% or nothing, is there anything I am doing wrong or is it what I should expect? Is there anyway to obtain also that smooth disappearing of the silhouette? Thank you for your help. All the best, Aritz

4 6

not showing non-traced amino acids in sequence view after splitting a molecule
by Marta Perez Illana 05 Mar '20

05 Mar '20

Hi all When I open a cif in chimerax and press the sequence button the window shows up and there is everything within the molecule, including the non-traced amino acids (missing in the structure). Whereas if I do split the molecule to have just one chain, then the sequence view only shows traced amino acids, but not the non-traced ones anymore... Any ideas on this please? P.D. With cif files this was a bit confusing in regular chimera for me as well, since when saving the cif it was kind of converted and I guess some info regarding this non-traced aminoacids was missed... Thank you!!! Marta

3 4

Secondary structure display - pdb and cif
by Tetter Stephan 04 Mar '20

04 Mar '20

Dear ChimeraX users and developers, I am having an issue with secondary structure display. I am real-space refining a set of 120 chains in phenix. Of these, only 10 are unique, the rest is symmetry-related. Thus, I define secondary structure elements for the 10 unique chains only. The output pdb file header contains the secondary structure elements as imposed during refinement. Displaying this pdb file in ChimeraX shows the right secondary structure. The mmcif file instead, whether I use the phenix output or generate it from the pdb myself, displays different, non-sensical structures. Secondary structure is shown in loop regions, and some actual strands and helices not recognized at all. This artifact is only shown for the 10 subunits with secondary structure definitions, the other subunits show no secondary structure at all, thus something is read in, but not correctly, apparently. Any idea what the problem could be? Could the size of the complex be an issue? The attachments show the lines from the two file types concerning secondary structure definitions. Kind regards, Stephan

3 3

"zone" near MULTIPLE residues in ChimeraX
by Steve Chou 03 Mar '20

03 Mar '20

Dear ChimeraX team, I tried to use the zone command to display the atomic details and DENSITY near THREE residues of interest. These three residues are ligands and bind to the same place. https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/zone.html As the above manual said, the zone command can only display things near ONE residue. Is there a way to work around this? Many thanks, Steve -- Steve Chou

3 3

Bug: selection of atoms by attribute = color
by Pavol Bardy 393791 27 Feb '20

27 Feb '20

Hello, since version 0.91 I am experiencing problems with selecting atoms by color attribute "@@color=color". I am getting an error message "Expected an objects specifier or a keyword". In version 0.90 everything works fine. Other attributes like "bfactor" or "idatm_type" seems to work normally. Kind regards, -- Pavol Bárdy Laboratory of Microbial Molecular Diagnostics Department of Experimental Biology, Masaryk University Kamenice 5 / A25 Brno, 625 00, Czech Republic

2 1

change residues to helix
by Meinan Lyu 24 Feb '20

24 Feb '20

Dear cgl.ucsf.edu, In chimerax, Helix is disrupted for some reason, could I change the intermediate residues into helix? There are two ways I tried, 1: use 'dssp' command, 2: use 'setattr :467-469/A res ss_type 1'. But both didn't not work. Could you tell me how to change this? Best regards, Meinan [image: image.png]

2 2

Default mrc/ccp4 file opening by ChimeraX
by Kim, Doo Nam 20 Feb '20

20 Feb '20

I use mac (10.14.6). But when I double-click mrc/ccp4 file, chimera automatically opens it. I want to open it with ChimeraX (which is faster). However, even when I right-click on ccp4 file -> open with -> always open with -> ChimeraX_Daily, only that specific file is opened with chimera automatically. Does anyone know how to set up so that all (including future) .mrc and .ccp4 files are opened with ChimeraX? Thank you Best, Doonam

2 2

Error in reopening session
by Maximiliane Wieland 20 Feb '20

20 Feb '20

Hi, When I try reopening a session I have been using for two weeks now (so many saved view :( )and I get the following error: Unable to restore session, resetting. Traceback (most recent call last): File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/session.py", line 653, in restore obj = sm.restore_snapshot(self, data) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/statemgr.py", line 65, in restore_snapshot cmd.name_frozen(session, name, Objects(**value)) File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/basic_actions/cmd.py", line 54, in name_frozen raise UserError("nothing is selected by specifier") chimerax.core.errors.UserError: nothing is selected by specifier This is the error from the daily build, in the production release one I get the same error, only difference is in "cmd.py", line 52, in name_frozen When trying to open an older version (that I saved but did not open, since I kept using the same session and saved it to the latest version) I am asked to replace missing files, which are in fact not missing but still in the very same directory and with the very same name, so it feels like the real error lies elsewhere? Can I make it reopen the session without reopening the volume? The last version of the session I can open without a problem is close to two weeks old, I named some selections in the meantime, could that cause such an error? I use ChimeraX on MacOS X 10.12.6 I will also submit the bug but since it is kind of urgent I thought I would try submitting here, too, in hopes of a quick response. Best, Maxi

1 0

Set view
by Aritz Roa Eguiara 19 Feb '20

19 Feb '20

Dear ChimeraX, I am trying to produce a script .cxc to open on ChimeraX and I want to set a specific camera position coordinates that can be opened by anyone. I do obtain the position by just using the command camera, but then I do not know how to obtain that position without saving the view. How should this be written on the command line so that anyone can open it and get that view? For example, I know that PyMol allows the get view command to obtain all the information that later only need to be pasted on the script, is there anything similar? Thank you in advance for your help. Best regards, Aritz

2 2