[Chimera-users] [EXTERNAL] Re: Visualize dot_surface dat file in chimera

[Ashok Nayak]

Thanks a lot Elaine for the prompt response.


So do you have a script for reformatting the .dat file. I do have a number of PDBS to compare which makes it cumbersome.


But I guess the script made by oliver could be interesting whick I ll test.


-regards

Ashok

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, January 22, 2019 7:01:06 PM
To: Ashok Nayak
Cc: chimera-users at cgl.ucsf.edu BB
Subject: [EXTERNAL] Re: [Chimera-users] Visualize dot_surface dat file in chimera

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):
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.cgl.ucsf.edu_chimera_docs_UsersGuide_bild.html&d=DwIFaQ&c=pOo6bKNCxsIK6eGC4MYY4A&r=cYYeyUrqF3gVcprH69cY5ZZltMVZ9UxEHFna6lZ5TV8&m=SNJ8EsGWnpjNm5sxnUeTLwUSmFyn8il-XANrY1__XdM&s=fxHMPnWpD6hhWROy4bwu8Y3izej5617f9XrdTdJAQHw&e=>
>
> 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:
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_pipermail_chimera-2Dusers_2015-2DAugust_011373.html&d=DwIFaQ&c=pOo6bKNCxsIK6eGC4MYY4A&r=cYYeyUrqF3gVcprH69cY5ZZltMVZ9UxEHFna6lZ5TV8&m=SNJ8EsGWnpjNm5sxnUeTLwUSmFyn8il-XANrY1__XdM&s=ak9aTvN3hL46dOIGN169Di3VZerGvjNHf-n9kxtQUNM&e=>
>
> 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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