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 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@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

________________________________________ From: chimera-users-bounces@cgl.ucsf.edu [chimera-users-bounces@cgl.ucsf.edu] on behalf of chimera-users-request@cgl.ucsf.edu [chimera-users-request@cgl.ucsf.edu] Sent: Friday, December 14, 2012 10:00 PM To: chimera-users@cgl.ucsf.edu Subject: Chimera-users Digest, Vol 116, Issue 19

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Today's Topics:

1. Re: mask command (Tom Goddard)

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Message: 1 Date: Thu, 13 Dec 2012 16:15:56 -0800 From: Tom Goddard To: Xiangan Liu Cc: Chimera BB Subject: Re: [Chimera-users] mask command Message-ID: <50CA6FBC.6020202@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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