<div dir="ltr">Hello,<div> I did not receive a reply to the message I sent.</div><div>Could you kindly help me out. </div><div>Thankyou<br><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr">Vani Pande<div>Int PhD Biological sciences</div><div>IISER Pune</div><div>20162013</div></div></div></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Sep 26, 2018 at 5:50 PM <<a href="mailto:chimera-users-request@cgl.ucsf.edu">chimera-users-request@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Chimera-users mailing list submissions to<br>
<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:chimera-users-request@cgl.ucsf.edu" target="_blank">chimera-users-request@cgl.ucsf.edu</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:chimera-users-owner@cgl.ucsf.edu" target="_blank">chimera-users-owner@cgl.ucsf.edu</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Chimera-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Fitmap: correlation about the mean for global search<br>
(Michele Lunelli)<br>
2. Re: Fitmap: correlation about the mean for global search<br>
(Tom Goddard)<br>
3. Command line equivalent to hide (Ahmad Khalifa)<br>
4. Re: Command line equivalent to hide (Elaine Meng)<br>
5. Re: [chimera-dev] Auto set threshold boundaries and colors<br>
(Benjamin Looker)<br>
6. Query (Vani Pande)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 25 Sep 2018 18:02:38 +0200<br>
From: Michele Lunelli <<a href="mailto:michlun23@gmail.com" target="_blank">michlun23@gmail.com</a>><br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a><br>
Subject: [Chimera-users] Fitmap: correlation about the mean for global<br>
search<br>
Message-ID:<br>
<<a href="mailto:CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ@mail.gmail.com" target="_blank">CADZjtDT0D2srWpLg3LDbeoPvReaO2mDAnqqCJisUuAKrBMZOwQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear people,<br>
<br>
I want to do a global search of an atomic model into an EM map, using the<br>
correlation about the mean (cam) as metric. I use a command like this:<br>
fitmap #0 #1 resolution 6 metric cam search 100 radius 150<br>
<br>
However, only the correlation about zero is reported in the final fit list<br>
(and used to rank the solutions). Where can I find the cam values for all<br>
the fits?<br>
<br>
Thank you<br>
Michele<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/85ebc7c8/attachment-0001.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/85ebc7c8/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 25 Sep 2018 12:04:10 -0700<br>
From: Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>><br>
To: Michele Lunelli <<a href="mailto:michlun23@gmail.com" target="_blank">michlun23@gmail.com</a>><br>
Cc: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] Fitmap: correlation about the mean for<br>
global search<br>
Message-ID: <<a href="mailto:952A92E7-04EC-4D2C-A7C7-840240CF186E@sonic.net" target="_blank">952A92E7-04EC-4D2C-A7C7-840240CF186E@sonic.net</a>><br>
Content-Type: text/plain; charset=utf-8<br>
<br>
Hi Michele,<br>
<br>
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<br>
<br>
def correlation(self):<br>
return self.stats.get('correlation', None)<br>
<br>
to read<br>
<br>
def correlation(self):<br>
return self.stats.get(?correlation about mean', None)<br>
<br>
in your Chimera distribution in file<br>
<br>
chimera/share/FitMap/search.py<br>
<br>
near line 134. On Mac this file will be in Chimera.app/Contents/Resources/share/FitMap/search.py.<br>
<br>
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.<br>
<br>
Tom<br>
<br>
<br>
> On Sep 25, 2018, at 9:02 AM, Michele Lunelli wrote:<br>
> <br>
> Dear people,<br>
> <br>
> 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:<br>
> fitmap #0 #1 resolution 6 metric cam search 100 radius 150<br>
> <br>
> 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?<br>
> <br>
> Thank you<br>
> Michele<br>
> <br>
> _______________________________________________<br>
> Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
> Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 25 Sep 2018 12:19:03 -0400<br>
From: Ahmad Khalifa <<a href="mailto:underoath006@gmail.com" target="_blank">underoath006@gmail.com</a>><br>
To: "<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
Subject: [Chimera-users] Command line equivalent to hide<br>
Message-ID:<br>
<<a href="mailto:CAL1o8vMQLiULhWtJ-NYygO3Ftu-VuSZsg78Xdq-1Qh06EB5A4g@mail.gmail.com" target="_blank">CAL1o8vMQLiULhWtJ-NYygO3Ftu-VuSZsg78Xdq-1Qh06EB5A4g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
While the command line equivalent to show is "modeldisplay #modelnumber",<br>
what is the equivalent for hide?<br>
<br>
Regards.<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/8c9da2e7/attachment-0001.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/8c9da2e7/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 25 Sep 2018 12:45:15 -0700<br>
From: Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>><br>
To: Ahmad Khalifa <<a href="mailto:underoath006@gmail.com" target="_blank">underoath006@gmail.com</a>><br>
Cc: "<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a> BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>><br>
Subject: Re: [Chimera-users] Command line equivalent to hide<br>
Message-ID: <<a href="mailto:EF7A8861-7F3C-41BF-8F14-FE2FCC06845A@cgl.ucsf.edu" target="_blank">EF7A8861-7F3C-41BF-8F14-FE2FCC06845A@cgl.ucsf.edu</a>><br>
Content-Type: text/plain; charset=us-ascii<br>
<br>
Hi Ahmad,<br>
Not too different! In your notation,<br>
<br>
~modeldisplay #modelnumber<br>
<br>
for example: ~modeldisp #3<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html</a>><br>
<br>
Regards,<br>
Elaine<br>
<br>
> On Sep 25, 2018, at 9:19 AM, Ahmad Khalifa <<a href="mailto:underoath006@gmail.com" target="_blank">underoath006@gmail.com</a>> wrote:<br>
> <br>
> While the command line equivalent to show is "modeldisplay #modelnumber", what is the equivalent for hide? <br>
> <br>
> Regards. <br>
<br>
<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 25 Sep 2018 17:52:10 -0400<br>
From: Benjamin Looker <<a href="mailto:bgl44@cornell.edu" target="_blank">bgl44@cornell.edu</a>><br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a><br>
Subject: Re: [Chimera-users] [chimera-dev] Auto set threshold<br>
boundaries and colors<br>
Message-ID:<br>
<CAAgCWJvizba7=<a href="mailto:cAuSG3gGWWjcQhRPMfAaWFEnkgRh75CuxRutQ@mail.gmail.com" target="_blank">cAuSG3gGWWjcQhRPMfAaWFEnkgRh75CuxRutQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Elaine,<br>
<br>
Thank you so much for responding, the ability to create that alias in the<br>
program will be very useful, thanks!<br>
<br>
Best,<br>
<br>
Ben Looker<br>
<br>
On Mon, Sep 24, 2018 at 1:10 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br>
<br>
> Hi Benjamin,<br>
> This only refers to intiial display. You can of course change the<br>
> threshold (isosurface level) to whatever is appropriate for the specific<br>
> data, by dragging the vertical bar in the Volume Viewer histogram or by<br>
> using the ?volume? command.<br>
><br>
> It is not a preference, but you could create an alias that would be listed<br>
> in the menu so that you could reapply it easily. For example, command:<br>
><br>
> alias ^orbitals volume all level 0.05 color pink style surface<br>
><br>
> ? or there could be multiple levels and colors specified in the same<br>
> command. Then your alias ?orbitals? (or whatever you named it) would be<br>
> listed in a top-level Aliases menu for easy reapplication to later<br>
> datasets. I.e., choosing menu: Aliases? orbitals or typing the command<br>
> ?orbitals? would run it. Aliases are saved in the preferences:<br>
> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html</a>><br>
><br>
> The volume command has many options:<br>
> <<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html</a>><br>
><br>
> The 1% initial display (rather than a specific threshold value) was most<br>
> useful for the wide variety of volume data where people often do not know<br>
> what threshold will be best for viewing. It is surely adjustable by<br>
> changing the code but others would have to advise on that matter.<br>
><br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
> > On Sep 23, 2018, at 10:18 AM, Benjamin Looker <<a href="mailto:bgl44@cornell.edu" target="_blank">bgl44@cornell.edu</a>> wrote:<br>
> ><br>
> > Hello!<br>
> ><br>
> > My name is Benjamin Looker, and I have recently become acquainted with<br>
> your software for visualization of molecular orbital calculations that my<br>
> group does with some regularity. I was wondering whether the statement on<br>
> this page refers to a specific preferences file in the Chimera program<br>
> files. :<br>
> ><br>
> > (<br>
> <a href="http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/1.8/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html</a>)<br>
><br>
> ><br>
> > "For unsigned data types, an initial threshold is set so that 1% of<br>
> voxels"<br>
> ><br>
> > The reason I ask is because it would be much simpler, given a known<br>
> color code and level, to standardize the import of files into Chimera for<br>
> any sort of publication, especially in the event that many molecular<br>
> orbitals needed to be visualized at once for a project.<br>
> ><br>
> > Best,<br>
> ><br>
> > --<br>
> > Benjamin G. Looker<br>
> > Graduate Student<br>
> > Lancaster Group<br>
><br>
><br>
<br>
-- <br>
Benjamin G. Looker<br>
Graduate Student<br>
Lancaster Group<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/a47d6edf/attachment-0001.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180925/a47d6edf/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Wed, 26 Sep 2018 17:31:14 +0530<br>
From: Vani Pande <<a href="mailto:vani.pande@students.iiserpune.ac.in" target="_blank">vani.pande@students.iiserpune.ac.in</a>><br>
To: <a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a><br>
Subject: [Chimera-users] Query<br>
Message-ID:<br>
<CAA=Om-_wnVKJTRCwQ=<a href="mailto:ftFo1zhRuAaryz20%2B6Z8W-jJoT6bXRrQ@mail.gmail.com" target="_blank">ftFo1zhRuAaryz20+6Z8W-jJoT6bXRrQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
I am new to chimera. I want to superimpose a domain for the two protein<br>
molecules and get the rmsd for the non superimposed protein parts. How<br>
should i do it. Ihave superimposed domain of interest for my protein using<br>
match, but now i am not getting how to proceed further.<br>
<br>
Thanks<br>
Vani Pande<br>
Int PhD Biological sciences<br>
IISER Pune<br>
20162013<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180926/50850f64/attachment.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180926/50850f64/attachment.html</a>><br>
<br>
------------------------------<br>
<br>
Subject: Digest Footer<br>
<br>
_______________________________________________<br>
Chimera-users mailing list<br>
<a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
Manage subscription:<br>
<a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
<br>
<br>
------------------------------<br>
<br>
End of Chimera-users Digest, Vol 185, Issue 16<br>
**********************************************<br>
</blockquote></div>