Hi Ashok, No, I don’t have a script, sorry. Elaine
On Jan 22, 2019, at 4:12 PM, Ashok Nayak <Ashok.Nayak@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@cgl.ucsf.edu> Sent: Tuesday, January 22, 2019 7:01:06 PM To: Ashok Nayak Cc: chimera-users@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@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...>
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_piper...>
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@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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