- Chimera-users - RBVI Mailing Lists

Recording movie at 720p
by Ahmad Khalifa 05 Oct '18

05 Oct '18

I'm recording a movie in the command line using: movie record movie stop movie encode output ~/ I tried to include the option preset dvd for movie encode, I recieved the following error: "Error reading paper_movie.txt: AttributeError: 'module' object has no attribute 'standard_formats' File "/opt/UCSF/Chimera64-1.12/share/MovieRecorder/moviecmd.py", line 124, in encode_op settings = RG.standard_formats.get(preset) See reply log for Python traceback." What am I doing wrong and how can I record my movie at 720p? Regards.

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Maps/models display/activate checkboxes? [Feature suggestion]
by Oliver Clarke 04 Oct '18

04 Oct '18

Hi, It would be very helpful to have a way to undisplay all maps, or all models, at once. This would be particularly handy when inspecting the fit of a model in a map, as the residue tooltips don’t work when there is a surface in front of the atoms. Would it be possible to add two checkboxes in addition to the model specific checkboxes and the “all” checkbox that controls whether models, maps, or both are displayed? I would envision both the model and map checkboxes working as toggles, checked by default, but one could uncheck either to temporarily undisplay all maps/models, and then check the box again to return to the previous state. I know most effort is going into ChimeraX, so please disregard if this is difficult to implement. Cheers OIi

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Chimera pdb error
by 김민재 03 Oct '18

03 Oct '18

Hi! Thanks for all of your help, but I got another problem... I uploaded a picture of the Chimera error. The HG hydrogen atoms are not being shown in Chimera. When I extract just the CG and HG pdb lines and input them, Chimera works fine and can even calculate the surface. But, when I run it with the pdb file that I have right now, it keeps returning that error. I thought that maybe Chimera could only calculate the surface for atoms which are connected, and that the program was looking for mandatory bond between the atoms. I was wondering if there was a settings change I could make to fix this, or if there was any other way to go about straightening things out to calculate the solvent excluded area of this pdb file.

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MacOS Mojave
by Eric Pettersen 01 Oct '18

01 Oct '18

Hi all, MacOS Mojave will be released this Monday, Sept. 24. On Mojave, Chimera buttons and popup menus are not shown until the window containing them is resized. Therefore we advise against upgrading to Mojave until we come up with a fix for this issue — which we will announce on this list as soon as it is available. —Eric Eric Pettersen UCSF Computer Graphics Lab

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Hiding models one by one?
by Ahmad Khalifa 01 Oct '18

01 Oct '18

I'm trying to hide a range of models using ~modeldisplay #16-60. For display purposes, I want to to make them disappear one by one or in groups. I can of course write down a bunch of ~modeldisplay #16; wait 5; ~modeldisplay #17; wait 5;...etc. Is there a way to for loop that process in the command line or do it in a better way? Regards.

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Calculating surface area of a single atom
by 김민재 01 Oct '18

01 Oct '18

Hey everyone! I've been trying to calculate the solvent excluded surface area of a single hydrogen atom, but Chimera keeps returning an error "miscalc code 5" message whenever I run the "surface probeRadius" command. I would really appreciate anyone's help.

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FW: Contributing to ChimeraX ?
by Williams, Joanne 01 Oct '18

01 Oct '18

From: Nicholas Yue <yue.nicholas(a)gmail.com> Date: Sunday, September 30, 2018 at 3:40 AM To: "chimerax(a)cgl.ucsf.edu" <chimerax(a)cgl.ucsf.edu> Subject: Contributing to ChimeraX ? Hi, I took ChimeraX for a spin and when I save out to OBJ, the geometries looks connected up wrongly. I was hoping I can take a look at the source code to attempt to fix it myself. I see git being mentioned in the documentation. Is there a git repo I can clone and contribute to? If I need to sign any documents before contributing, let me know :-) I have other geometry format I'd like to write out to and also I am hoping to write out quads rather than triangles for use with OpenSubdiv in rendering software like RenderMan, Arnold, Mantra etc. Cheers -- Nicholas Yue Graphics - Arnold, Alembic, RenderMan, OpenGL, HDF5 Custom Dev - C++ porting, OSX, Linux, Windows http://au.linkedin.com/in/nicholasyue https://vimeo.com/channels/naiadtools

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Calculating surface for modified pdb file
by 김민재 29 Sep '18

29 Sep '18

Hi y'all, I've been trying to calculate the surface area of a modified pdb file. It is an extracted part from 3hgn. Although the file seems pretty small and simple, I keep getting a miscalculation-due-to-huge-chain error message from Chimera. I think it's because of the "WARNING: treat_rs_edge: third atom not found for edge 7 9" lines that get recorded on the reply log.I'm new to Chimera and using pdb files, so I would really appreciate advice on how to solve this issue. I took everything in a screen shot below. I can send anyone the actual files if they want to take a closer look. Thanks.

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Model color won't change
by Ahmad Khalifa 28 Sep '18

28 Sep '18

I have a structure with a biological unit. When I select the structure, click biological unit, it shows a surface. By selecting the surface I can show ribbon and then I have the entire biological unit fitted in my density. The original structure has the color #beb7beb7beb7. the biological unit geenrated from it has the color #beb8beb8beb8. In ribbon view, the structures look the same, but the chain trace shows a darker colored original structure (see the picture). None of them would allow me to change to the same color code #beb7beb7beb7 or #beb8beb8beb8. I want all of them to have the same color in chain trace view. How can I fix it?

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Displaying chain trace without atoms
by Ahmad Khalifa 28 Sep '18

28 Sep '18

I have some structures in chain trace view, I hid them via the command line ~disp, but when I reshow them with disp, all the atoms are present. How to show chain trace while hiding the atoms?

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