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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@gmail.com>
To: chimera-users@cgl.ucsf.edu
Subject: [Chimera-users] Fitmap: correlation about the mean for global
search
Message-ID:
<CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ@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@sonic.net>
To: Michele Lunelli <michlun23@gmail.com>
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Fitmap: correlation about the mean for
global search
Message-ID: <952A92E7-04EC-4D2C-A7C7-840240CF186E@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@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@gmail.com>
To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: [Chimera-users] Command line equivalent to hide
Message-ID:
<CAL1o8vMQLiULhWtJ-NYygO3Ftu-VuSZsg78Xdq-1Qh06EB5A4g@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@cgl.ucsf.edu>
To: Ahmad Khalifa <underoath006@gmail.com>
Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Command line equivalent to hide
Message-ID: <EF7A8861-7F3C-41BF-8F14-FE2FCC06845A@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@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@cornell.edu>
To: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] [chimera-dev] Auto set threshold
boundaries and colors
Message-ID:
<CAAgCWJvizba7=cAuSG3gGWWjcQhRPMfAaWFEnkgRh75CuxRutQ@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@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@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@students.iiserpune.ac.in>
To: chimera-users@cgl.ucsf.edu
Subject: [Chimera-users] Query
Message-ID:
<CAA=Om-_wnVKJTRCwQ=ftFo1zhRuAaryz20+6Z8W-jJoT6bXRrQ@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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