[Chimera-users] Visualize dot_surface dat file in chimera

[Elaine Meng]

Hi Ashok,
One way is to reformat to BILD, a simple plain-text format (filename.bild) that can be opened in Chimera.  For example, your 4 lines would become these 8 lines:

.sphere 234.17638  238.94343  268.17244 0.1
.color 0.44800    0.47168    0.80000
.sphere 234.33047  238.06957  268.17244 0.1
.color 0.44800    0.47168    0.80000
.sphere 234.63396  237.23575  268.17244 0.1
.color 0.44800    0.47168    0.80000
.sphere 235.29419  242.56321  267.72878 0.1

Actually, you don’t need to repeat the color line except when it changes.  The last column in the sphere line is the radius, change as needed for larger or smaller “dots."

Format description (and I also attached the above as a file):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>

I also note that Oliver Clarke has used a script to convert HOLE output for Chimera and a different coloring method, as discussed in this thread:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2015-August/011373.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

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> On Jan 22, 2019, at 1:29 PM, Ashok Nayak <Ashok.Nayak at vcuhealth.org> wrote:
>   
> Hi,
> I have a HOLE dot surface fie exported from coot in the .DAT format. Unfortunately I cant display it in chimera.
> 
> Could you suggest me the compatible format in chimera to visualize the dot surface files
> 
> Its in X Y Z r g b Hexcol format
>      234.17638  238.94343  268.17244       0.44800    0.47168    0.80000  #7278cc
>      234.33047  238.06957  268.17244       0.44800    0.47168    0.80000  #7278cc
>      234.63396  237.23575  268.17244       0.44800    0.47168    0.80000  #7278cc
>      235.29419  242.56321  267.72878       0.44800    0.47168    0.80000  #7278cc
> 
> Any suggestion will be appreciated
>