- Chimera-users - RBVI Mailing Lists

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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Query
by Vani Pande 26 Sep '18

26 Sep '18

Hi, I am new to chimera. I want to superimpose a domain for the two protein molecules and get the rmsd for the non superimposed protein parts. How should i do it. Ihave superimposed domain of interest for my protein using match, but now i am not getting how to proceed further. Thanks Vani Pande Int PhD Biological sciences IISER Pune 20162013

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Command line equivalent to hide
by Ahmad Khalifa 26 Sep '18

26 Sep '18

While the command line equivalent to show is "modeldisplay #modelnumber", what is the equivalent for hide? Regards.

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Re: [Chimera-users] Chimera-users Digest, Vol 185, Issue 16
by Vani Pande 26 Sep '18

26 Sep '18

Hello, I did not receive a reply to the message I sent. Could you kindly help me out. Thankyou Vani Pande Int PhD Biological sciences IISER Pune 20162013 On Wed, Sep 26, 2018 at 5:50 PM <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Fitmap: correlation about the mean for global search > (Michele Lunelli) > 2. Re: Fitmap: correlation about the mean for global search > (Tom Goddard) > 3. Command line equivalent to hide (Ahmad Khalifa) > 4. Re: Command line equivalent to hide (Elaine Meng) > 5. Re: [chimera-dev] Auto set threshold boundaries and colors > (Benjamin Looker) > 6. Query (Vani Pande) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 25 Sep 2018 18:02:38 +0200 > From: Michele Lunelli <michlun23(a)gmail.com> > To: chimera-users(a)cgl.ucsf.edu > Subject: [Chimera-users] Fitmap: correlation about the mean for global > search > Message-ID: > < > CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear people, > > I want to do a global search of an atomic model into an EM map, using the > correlation about the mean (cam) as metric. I use a command like this: > fitmap #0 #1 resolution 6 metric cam search 100 radius 150 > > However, only the correlation about zero is reported in the final fit list > (and used to rank the solutions). Where can I find the cam values for all > the fits? > > Thank you > Michele >

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