[Chimera-users] A question about colouring a resmap output file in Chimera.

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 15 17:54:15 PDT 2016


Hi Thanos,
I’ve never used Resmap myself (it is a separate program from Chimera), but as I understand it, the output file contains the local resolution values calculated from the input map.  You would have both that original map and the resmap output map open in Chimera, show an isosurface of the original map, and color it by the values in the resmap map.

It is best to send Chimera-related questions to the list CC’d here (chimera-users at cgl.ucsf.edu) because often other people know more about something than I do.

>From this earlier post to the list, I thought Resmap also output a Chimera script that you could run to perform the coloring:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-October/011679.html>

However, even if you didn’t run such a script you could do the coloring using the Surface Color tool or the “scolor” command in Chimera.

Finally, there must be more information about how to use Resmap with Chimera, and how it calculates the values, in the Resmap manual and the Resmap paper in Nature Methods, see:
<http://resmap.sourceforge.net/#manual>

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 Jul 15, 2016, at 4:47 PM, T-I <ignatiou at gmail.com> wrote:

> Hello Elaine.
> My question today is:
> 
> I have run Resmap on my em-density map (.mrc) to calculate the local resolution
> 
> When i open both the original  .mrc  file and the _resmap.mrc file in chimera i don't understand how to then colour the map with the values found in the resmap calculation.
> 
> what do i do exactly?
> 
> also i don't understand where the resmap values are??
> many thanks
> Thanos
> 




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