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

Tom Goddard goddard at sonic.net
Fri Dec 14 17:21:07 PST 2012


Hi Boaz,

 This is a bug.  Unfortunately I don't think it is simple to fix.  The underlying trouble is that Chimera treats color and transparency together.  Once you set the transparency, the surface color dialog decides it is no longer coloring the surface since some new "coloring" has been applied -- it has no idea it was just a transparency change.

 With some trouble you can get a transparent surface and report surface values by making the individual colors in the Surface Color dialog transparent. This is a pain since you have to press each color button and make each color have the desired transparency.

 I'll make a bug report for this problem.  But I think it won't be fixed soon because it involves having Chimera treat color and transparency as separate properties.

	Tom


On Dec 14, 2012, at 3:40 PM, Boaz Shaanan <bshaanan at exchange.bgu.ac.il> wrote:

> Hi,
> 
> 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?
> 
>  Thanks,
> 
>              Boaz
> 
> 
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> 
> 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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>   1. Re: mask command (Tom Goddard)
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> ----------------------------------------------------------------------
> 
> 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.
> 
>     Tom
> 
> 
>> 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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