October 2018 - Chimera-users - RBVI Mailing Lists

error opening .cif file
by Francesco Pietra 07 Oct '18

07 Oct '18

Hi With my /opt/UCSF/Chimera64-1.11.2/bin/chimera, I notice a mistake in opening 4i4t.cif.gz (as 4i4t.cif), i.e., residue 43 and 44 in chain D are mis-numbered 44 and 45, giving the wrong impression that residues 43 and 44 are missing. I have not checked anything else. cheers francesco pietra

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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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Chimera-users October 2018