[Chimera-users] Chimera-users Digest, Vol 185, Issue 16
Vani Pande
vani.pande at students.iiserpune.ac.in
Wed Sep 26 06:35:25 PDT 2018
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 at cgl.ucsf.edu> wrote:
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> 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 at gmail.com>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Fitmap: correlation about the mean for global
> search
> Message-ID:
> <
> CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ at 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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> ------------------------------
>
> Message: 2
> Date: Tue, 25 Sep 2018 12:04:10 -0700
> From: Tom Goddard <goddard at sonic.net>
> To: Michele Lunelli <michlun23 at gmail.com>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Fitmap: correlation about the mean for
> global search
> Message-ID: <952A92E7-04EC-4D2C-A7C7-840240CF186E at sonic.net>
> Content-Type: text/plain; charset=utf-8
>
> Hi Michele,
>
> The Chimera fit list only reports correlation about zero. This is not
> great since you optimized for correlation about mean. A comment in the
> code mentions this problem. You can edit a Python file in Chimera to have
> it report correlation about mean instead. Change the following code
>
> def correlation(self):
> return self.stats.get('correlation', None)
>
> to read
>
> def correlation(self):
> return self.stats.get(?correlation about mean', None)
>
> in your Chimera distribution in file
>
> chimera/share/FitMap/search.py
>
> near line 134. On Mac this file will be in
> Chimera.app/Contents/Resources/share/FitMap/search.py.
>
> All our development effort is on ChimeraX now so we will remedy this
> problem in ChimeraX when we add the fit list to that program, but will not
> fix it in Chimera.
>
> Tom
>
>
> > On Sep 25, 2018, at 9:02 AM, Michele Lunelli wrote:
> >
> > 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
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription:
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 25 Sep 2018 12:19:03 -0400
> From: Ahmad Khalifa <underoath006 at gmail.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: [Chimera-users] Command line equivalent to hide
> Message-ID:
> <
> CAL1o8vMQLiULhWtJ-NYygO3Ftu-VuSZsg78Xdq-1Qh06EB5A4g at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> While the command line equivalent to show is "modeldisplay #modelnumber",
> what is the equivalent for hide?
>
> Regards.
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> ------------------------------
>
> Message: 4
> Date: Tue, 25 Sep 2018 12:45:15 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> To: Ahmad Khalifa <underoath006 at gmail.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Command line equivalent to hide
> Message-ID: <EF7A8861-7F3C-41BF-8F14-FE2FCC06845A at cgl.ucsf.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi Ahmad,
> Not too different! In your notation,
>
> ~modeldisplay #modelnumber
>
> for example: ~modeldisp #3
>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html>
>
> Regards,
> Elaine
>
> > On Sep 25, 2018, at 9:19 AM, Ahmad Khalifa <underoath006 at gmail.com>
> wrote:
> >
> > While the command line equivalent to show is "modeldisplay
> #modelnumber", what is the equivalent for hide?
> >
> > Regards.
>
>
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Tue, 25 Sep 2018 17:52:10 -0400
> From: Benjamin Looker <bgl44 at cornell.edu>
> To: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] [chimera-dev] Auto set threshold
> boundaries and colors
> Message-ID:
> <CAAgCWJvizba7=
> cAuSG3gGWWjcQhRPMfAaWFEnkgRh75CuxRutQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Elaine,
>
> Thank you so much for responding, the ability to create that alias in the
> program will be very useful, thanks!
>
> Best,
>
> Ben Looker
>
> On Mon, Sep 24, 2018 at 1:10 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:
>
> > 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 at 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/framevolumeviewer.html
> )
> >
> > >
> > > "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
> >
> >
>
> --
> Benjamin G. Looker
> Graduate Student
> Lancaster Group
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> ------------------------------
>
> Message: 6
> Date: Wed, 26 Sep 2018 17:31:14 +0530
> From: Vani Pande <vani.pande at students.iiserpune.ac.in>
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Query
> Message-ID:
> <CAA=Om-_wnVKJTRCwQ=
> ftFo1zhRuAaryz20+6Z8W-jJoT6bXRrQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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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> End of Chimera-users Digest, Vol 185, Issue 16
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