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

[Elaine Meng]

Hi Ashok,
No, I don’t have a script, sorry.
Elaine

> On Jan 22, 2019, at 4:12 PM, Ashok Nayak <Ashok.Nayak at vcuhealth.org> wrote:
> 
> 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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