- Chimera-users - RBVI Mailing Lists

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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Chimera morph colors with morph conformations
by Ahmad Khalifa 28 Sep '18

28 Sep '18

Hello, I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other. Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic. Thanks.

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Loading multiple ligand mol2 files for AV
by Leif Peterson 26 Sep '18

26 Sep '18

Is it possible to load multiple mol2 files, and add H, equlibrate charges, then energy minimize all if the ligands in batch mode, then save all of them to pdbqt files? Then, loop through all of the ligands using AV on each to get sorted docking results. Reason I ask is because almost all resources available on multiple ligand use with AD and AV seem outdated, developers moved on, and am hitting dead ends and pages not found.

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