[Chimera-users] surface failures

[Elaine Meng]

On Mar 12, 2014, at 6:46 AM, Julian Marzi wrote:

> Dear Eric,
> I tryed the command surfcat c1 and surfcat c1 :.1 & ~:ohx, but this will also not work on my mac... The mac show for short time an activity, but nothing happens. The comand from Elaine molmap  :.1&~:ohx  5 worked and it looks great! Is there also a possibility to select a part of the sequence in the "surface" (molmap) presentation to show it in an other color? I select one part on the 25S-rRNa in green, but the molmap view covers it in grey and if I make a higher transparency, the selected part will be seen. But it would be better, if the selected part is colored in the molmap view. This would allow the marked spot directly recognize without transparency. If there is an answer for my question, please let it me know. If not, is not bad, you two have helped me incredibly much. 
> Thank you so much
> Regards
> Julian

Hi Julian,
The "molmap" surface can be colored to match atoms with the Color Zone tool.  The atoms can be hidden, it is just a step to the surface coloring that you want. After you color some atoms (for example, some part of the RNA that you selected) you can also color the part of the surface that is near the currently selected atoms with Color Zone (in menu under Tools... Depiction).

Color Zone is mentioned along with molmap in #3 in the surface workarounds page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html>

Also, you could color the molmap surface any overall color you want first, it doesn't have to be the default grayish color.  You could just click the color square on the Volume Viewer tool (that appears when you create the molmap surface) and then use the Color Editor, or you can select the surface directly in the main window and use the Actions... Color menu.

I hope this helps!

P.S. please send chimera questions to the chimera-users address instead of our individual addresses (to allow others to see the Q & A) - thanks!

Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco