September 2018 - Chimera-users - RBVI Mailing Lists

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 Reason I ask is because almost all resources available on multiple ligand use with AD and AV seem outdated, developers moved on, and am hitting dead ends and pages not found.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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Re: [Chimera-users] [chimera-dev] Auto set threshold boundaries and colors
by Elaine Meng 25 Sep '18

25 Sep '18

Hi Benjamin, This only refers to intiial display. You can of course change the threshold (isosurface level) to whatever is appropriate for the specific data, by dragging the vertical bar in the Volume Viewer histogram or by using the “volume” command. It is not a preference, but you could create an alias that would be listed in the menu so that you could reapply it easily. For example, command: alias ^orbitals volume all level 0.05 color pink style surface … or there could be multiple levels and colors specified in the same command. Then your alias “orbitals” (or whatever you named it) would be listed in a top-level Aliases menu for easy reapplication to later datasets. I.e., choosing menu: Aliases… orbitals or typing the command “orbitals” would run it. Aliases are saved in the preferences: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> The volume command has many options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html> The 1% initial display (rather than a specific threshold value) was most useful for the wide variety of volume data where people often do not know what threshold will be best for viewing. It is surely adjustable by changing the code but others would have to advise on that matter. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Sep 23, 2018, at 10:18 AM, Benjamin Looker <bgl44(a)cornell.edu> wrote: > > Hello! > > My name is Benjamin Looker, and I have recently become acquainted with your software for visualization of molecular orbital calculations that my group does with some regularity. I was wondering whether the statement on this page refers to a specific preferences file in the Chimera program files. : > > (http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/…) > > "For unsigned data types, an initial threshold is set so that 1% of voxels" > > The reason I ask is because it would be much simpler, given a known color code and level, to standardize the import of files into Chimera for any sort of publication, especially in the event that many molecular orbitals needed to be visualized at once for a project. > > Best, > > -- > Benjamin G. Looker > Graduate Student > Lancaster Group

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Fitmap: correlation about the mean for global search
by Michele Lunelli 25 Sep '18

25 Sep '18

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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MatchMaker
by Ward, Miriam L. (CDC/OID/NCIRD) 24 Sep '18

24 Sep '18

Hello, I used MatchMaker to superimpose a couple of models. Now when I open any .pdb files, they automatically superimpose. How can I "turn off" MatchMaker so it doesn't automatically superimpose everything? Thanks, Leanne M. Leanne Ward, MEd. Microbiologist II Cherokee Nation Assurance contractor Rotavirus Surveillance and Molecular Epidemiology Team Gastroenteritis Viruses Branch Division of Viral Diseases, NCIRD, CDC Mailstop G04 1600 Clifton Rd. N.E. Atlanta, Georgia 30329 U.S.A. Phone: (404) 639-3265 Email: mrw0(a)cdc.gov<mailto:mrw0@cdc.gov>

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Hiding AutoDock Vina Search Volume (frame)
by leifepeterson＠sbcglobal.net 24 Sep '18

24 Sep '18

Using Select-->Chains-->(no ID), I can select the AutoDock Vina Search Volume structure after performing a docking, but once it's selected (highlighted in green), I can't seem to remove it from the molecular plot. What is the recommend way to remove the square frame?

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Re: [Chimera-users] Placing Autodock Vina Pocket around AA residues from RaptorX
by Leif Peterson 20 Sep '18

20 Sep '18

Hi Elaine, Thanks for the tip on the center command, and looking up the Swiss-Prot method. Leif Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10

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