- Chimera-users - RBVI Mailing Lists

Morphing code
by Minh Le 12 Oct '18

12 Oct '18

Hello there, I'm currently having trouble with the morphing code in chimera and I don't know how to use Python to make the morph.py. Is there any way you can help me with this? Thank you, Minh

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MD movie metafile
by Matthias Fellner 12 Oct '18

12 Oct '18

Good day I successfully loaded NAMD psf/dcd files into chimera (version 1.13.1) using the tools MD movie interface. As I have many runs and each has multiple dcd files I wanted to use a script to load the different runs, instead of manually picking all the files through the interface each time. I tried to follow the limited instructions of the MD Movie homepage but failed to get anywhere. I tried some versions of this command: md: D:\script.txt or movie: D:\script.txt The command md appears to try to start MDA (MultiDomain Assembler), the command movie wants some other unrelated inputs. I am also not sure if the script command would even work like this: namd(psf/dcd) D:\structure.psf structure_MD001.dcd - D:\ Any advice is appreciated Thank you Matthias Fellner

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Generating symmetry mates
by Vani Pande 10 Oct '18

10 Oct '18

Hello, I wanted to generate symmetry mates for the protein, I am not finding a way to do so in chimera.The protein is a monomer in an asymmetric unit. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

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C-N peptide bond within one peptide
by Emily Xu 08 Oct '18

08 Oct '18

Hello, Is there a way to join two ends of a peptide in Chimera? I am trying the create a peptide bond linking the C and N termini in a singular peptide to form a cyclotide. Is this possible in Chimera?

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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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