[Chimera-users] Visualize dot_surface dat file in chimera

[Elaine Meng]

Only 7 lines shown in that message, but there was supposed to be a “.color” line before the first “.sphere” line, as in the file that was attached to the message.  I just cut-n-paste too quickly and missed it.  :-)

Elaine

> On Jan 22, 2019, at 3:57 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> 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
> 
> <dotsurf.bild>
>> 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
>> 
> 
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