How to show the electron density of just selected residues? Thanks
Hi, How to show the electron density of just selected residues? Thanks I followed the Chimera tutorial, but still the electron density of the whole protein was displayed. Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online. Thanks a lot. Best, Andy --
Hi Andy, You would select the residues, then as described in the tutorial, choose Features... Zone from the menu of the Volume Viewer dialog and click the Zone button that appears within the dialog. Make sure you have successfully selected something first (for example, the magnifying glass at the bottom right corner of the Chimera window should turn green), then click the Zone button, and move the slider to change the size of the zone. I assume you are referring to the "Density Display" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html> Now about "convexity," maybe you are looking at the attributes tutorial, part 2: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2> It is simply a geometric description of the surface shape. In some cases, people might use it to highlight the most exposed areas (high convexity is where the protein "sticks out") or possible binding pockets (low convexity = high concavity, where there are indentations in the protein). However, in this tutorial, it is mainly just an example of how you can use the Attribute Calculator to make new attributes out of existing ones. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 2, 2012, at 11:58 AM, Pingyang Liu wrote:
Hi,
How to show the electron density of just selected residues? Thanks
I followed the Chimera tutorial, but still the electron density of the whole protein was displayed.
Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online.
Thanks a lot.
Best, Andy
--
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Hi Elaine, Thanks a lot. Best, Andy On Fri, Mar 2, 2012 at 3:24 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Andy, You would select the residues, then as described in the tutorial, choose Features... Zone from the menu of the Volume Viewer dialog and click the Zone button that appears within the dialog. Make sure you have successfully selected something first (for example, the magnifying glass at the bottom right corner of the Chimera window should turn green), then click the Zone button, and move the slider to change the size of the zone.
I assume you are referring to the "Density Display" tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/density.html>
Now about "convexity," maybe you are looking at the attributes tutorial, part 2: < http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#pa...
It is simply a geometric description of the surface shape. In some cases, people might use it to highlight the most exposed areas (high convexity is where the protein "sticks out") or possible binding pockets (low convexity = high concavity, where there are indentations in the protein). However, in this tutorial, it is mainly just an example of how you can use the Attribute Calculator to make new attributes out of existing ones.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 2, 2012, at 11:58 AM, Pingyang Liu wrote:
Hi,
How to show the electron density of just selected residues? Thanks
I followed the Chimera tutorial, but still the electron density of the whole protein was displayed.
Another question: what does the convexity of a protein structure tell? I did not find much information about convexity online.
Thanks a lot.
Best, Andy
--
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Pingyang 0216 Newman Blacksburg, Virginia 24060-0011 United States ~~~~~~~~~~~~~~~~~~~~ L'important n'est pas de gagner, mais de participer. With malice toward none, with charity for all. 山中习静观朝槿，松下清斋折露葵。 "If you want to be happy, set a goal that commands your thoughts, liberates your energy, and inspires your hopes." - Andrew Carnegie
participants (2)
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Elaine Meng -
Pingyang Liu