[Chimera-users] mouse does not report potential values after change of surface transprency

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Fri Dec 14 15:40:28 PST 2012


When I colour a surface according to the potential (read from a delphi or apbs map) and change the surface transparency (in order to show some residues below the surface), the mouse no longer reports the potential values  as I walk over the surface. I have to re-colour the surface in order to get back this functionality but the surface is opaque now. Is that how it's supposed to be?



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

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Today's Topics:

   1. Re: mask command (Tom Goddard)


Message: 1
Date: Thu, 13 Dec 2012 16:15:56 -0800
From: Tom Goddard <goddard at sonic.net>
To: Xiangan Liu <xiangan.liu at gmail.com>
Cc: Chimera BB <chimera-users at cgl.ucsf.edu>
Subject: Re: [Chimera-users] mask command
Message-ID: <50CA6FBC.6020202 at sonic.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Xiangan,

   The mask command is working fine in my tests.  It only sets the map
values to zero outside the surface.  The values inside the surface are
identical to the original map.  If that is not the case for you than use
menu Help / Report a Bug... and provide the exact mask command you used
and explain how you know that the new masked map values are different
from the original map.

   This sounds like the right approach to segmenting a subunit.  If
instead you had a fit atomic model you could use Color Zone and the
Split button on that dialog.


> Hi Tom,
> I am trying to use your MASK command to extract some interested
> volumes from a density map based on another reference density map.
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/mask.html
> I followed your guide line from the link above, but the extracted
> density is not the same as the original density.
> Is there anything I should pay special attention?
> It looks like the command was created many years ago, is it still good
> for the latest chimera version?
> Do I have any other way to segment map based on a known subunit
> density map, something similar to color zone?
> Thanks,
> Xiangan Liu


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