- ChimeraX-users - RBVI Mailing Lists

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

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"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

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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

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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]

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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

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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

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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

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undo/redo move?
by Oliver Clarke 18 Feb '20

18 Feb '20

Hi, I like the expanded undo/redo capabilities in Chimerax - particularly having the capacity to undo selection/deselection and color commands is very helpful. However it seems like there is no undo/redo move functionality. I find myself using this a lot in Chimera, is there any possibility of incorporating this into Undo/Redo in ChimeraX? Basically adding the possibility to Undo/Redo translation, rotation and scaling? Cheers Oli

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workflow suggestions
by Joel Meyerson 17 Feb '20

17 Feb '20

Hi, I'm a reasonably experienced Chimera user making the shift to ChimeraX. So far I'm really enjoying it. I'm writing because the biggest challenge I'm having so far is that there doesn’t seem to be anything quite like the "activate" features in the original Chimera Model Panel. Are the "activate" features available in ChimeraX, or are there plans to implement them? If not, can you suggest a way to achieve a similar degree of agility for manipulating objects in ChimeraX? So far I have been clicking between Right Mouse modes which does not feel so fluid yet. Perhaps there are keyboard shortcuts or other workflow tricks that you could suggest to improve the feel of navigation. Thanks, Joel

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Re: [chimerax-users] [Chimera-users] Default storage folder, ChimeraX
by Elaine Meng 14 Feb '20

14 Feb '20

Hi Martín, Currently there is no way in the user interface to change the ChimeraX downloads location, described here: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> You could make a symbolic link to that location, but the files would still really be in the same place. Probably the location can be changed by editing somewhere in the Python code, but somebody else would have to advise on that. You may be interested that there is a separate mailing list for ChimeraX, chimerax-users(a)cgl.ucsf.edu (CC’d on this message). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Feb 13, 2020, at 4:00 PM, Martín González Buitrón <martingonzalezbuitron(a)gmail.com> wrote: > > Dears all, > Hope you are well. > > I have started to use ChimeraX in Ubuntu and I realised that one folder was created with my fetches and other things (i.e. ~/Download/ChimeraX/). > > How can I change this to other of my own preference? > All the best, > Martín

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