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<p style="margin-top:0;margin-bottom:0">Thanks a lot Elaine for the prompt response.</p>
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<p style="margin-top:0;margin-bottom:0">So do you have a script for reformatting the .dat file. I do have a number of PDBS to compare which makes it cumbersome.</p>
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<p style="margin-top:0;margin-bottom:0">But I guess the script made by oliver could be interesting whick I ll test.</p>
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<p style="margin-top:0;margin-bottom:0">-regards <br>
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<p style="margin-top:0;margin-bottom:0">Ashok<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, January 22, 2019 7:01:06 PM<br>
<b>To:</b> Ashok Nayak<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> [EXTERNAL] Re: [Chimera-users] Visualize dot_surface dat file in chimera</font>
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<div class="PlainText">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. :-)<br>
<br>
Elaine<br>
<br>
> On Jan 22, 2019, at 3:57 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Ashok,<br>
> 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:<br>
> <br>
> .sphere 234.17638 238.94343 268.17244 0.1<br>
> .color 0.44800 0.47168 0.80000<br>
> .sphere 234.33047 238.06957 268.17244 0.1<br>
> .color 0.44800 0.47168 0.80000<br>
> .sphere 234.63396 237.23575 268.17244 0.1<br>
> .color 0.44800 0.47168 0.80000<br>
> .sphere 235.29419 242.56321 267.72878 0.1<br>
> <br>
> 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."<br>
> <br>
> Format description (and I also attached the above as a file):<br>
> <<a href="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=">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=</a>><br>
> <br>
> 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:<br>
> <<a href="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=">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=</a>><br>
> <br>
> I hope this helps,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> <dotsurf.bild><br>
>> On Jan 22, 2019, at 1:29 PM, Ashok Nayak <Ashok.Nayak@vcuhealth.org> wrote:<br>
>> <br>
>> Hi,<br>
>> I have a HOLE dot surface fie exported from coot in the .DAT format. Unfortunately I cant display it in chimera.<br>
>> <br>
>> Could you suggest me the compatible format in chimera to visualize the dot surface files<br>
>> <br>
>> Its in X Y Z r g b Hexcol format<br>
>> 234.17638 238.94343 268.17244 0.44800 0.47168 0.80000 #7278cc<br>
>> 234.33047 238.06957 268.17244 0.44800 0.47168 0.80000 #7278cc<br>
>> 234.63396 237.23575 268.17244 0.44800 0.47168 0.80000 #7278cc<br>
>> 235.29419 242.56321 267.72878 0.44800 0.47168 0.80000 #7278cc<br>
>> <br>
>> Any suggestion will be appreciated<br>
>> <br>
> <br>
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