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Thu, 02/11/2016 - 21:13
#2
Default options
Jeff. It's impressing with the chart in the log. Could you set the default options so that we see these sharts by default please (without beeing obliged to export the output to external software)?
Fri, 02/12/2016 - 00:08
#3
Using the defaults outputs only ANSI characters.
I set the defaults to output only ANSI characters.
Mon, 01/25/2016 - 03:15
#4
DistMap1 can make *.eps plots:
Below are some *.eps plots made by DistMap1 for the same protein structure as above. Programs like GSview can display *.eps plots and convert them to other formats (like *.png). epsdim picks how many residues appear in the plot. epsway=1 uses 5 shades (5 distance ranges).
Mon, 01/25/2016 - 03:46
#5
DistMap1 can make 3 types of charts for input into Excel:
The first type of chart is a 'peel-the-onion' chart starting like below,
The second type of chart is an 'AA-stats' chart starting like below,
The third type of chart is an 'all-by-all-distances' chart starting like below,
All 3 of these charts can be delimited by commas (as above) or spaces,
Wed, 01/27/2016 - 00:42
#6
Why use Distance Maps?
Distance and Contact Maps show the protein in a way that does not depend on the protein's orientation in 3D space. If two structures for the same protein look different in 3D, it could be (1) because they are identical structures viewed from different directions or (2) because they are truly different structures. Looking at their Distance or Contact Maps can tell if the two structures are actually the same or truly different.
Wed, 01/27/2016 - 00:43
#7
Homologous proteins give similar-looking Contact Maps:
p.247 of the book "Proteins: Structures and Molecular Properties" https://books.google.com/books?id=hu8T_kI1LrkC&pg=PA247
Thu, 01/28/2016 - 23:41
#8
Where to get GSview?
My windows machine is using GSview 4.9 2007-11-18 and GPL Ghostscript 8.71 2010-02-10
Thu, 02/11/2016 - 21:29
#9
Tip: How to export?
Immediately after using the recipe, you can find the log of the script here: computer C:/Foldit/scriptlog.track (xml file) For instance, if my track is called evo, I'll find the log in the xml file From there, I can copy-paste the all log (or see it on the full windows), of copy-paste only the sectionin the right format (like excel etc).
Fri, 02/12/2016 - 00:33
#10
LuaRandom2 might make *.png images from DistMap1 output:
It may be possible to use part of the scriptlog file output by DistMap1 as input to the standalone Lua script LuaRandom2 (http://fold.it/portal/recipe/101669) to generate a Distance Map in *.png format, but I have not tried this myself. I would try chway=1,9, or 10, chart spacing=0 or 1, chart labels=0 or 1, and check the box for "Include a full-size chart" in DistMap1 for this.
Sat, 02/13/2016 - 17:56
#11
output for 1189
Hi all, Just getting caught up on this thread. 1189 output: http://fold.it/portal/files/chatimg/irc_476462_1455386022.png I'll look into a script that would create png files from the scriptlog. It would be a standalone script, as Jeff mentions. |
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DistMap1 was adapted from DistMap0 (http://fold.it/portal/recipe/101659).
DistMap1 finds the distances between every pair of alpha-carbons in the protein
and makes several maps of these distances. Its output includes lines like below:
The final map above is small enough to appear in the Recipe Output window,
so it can be included in a snapshot of the protein when a puzzle ends.
Below is a sample snapshot made right after the above DistMap1 run:
http://fold.it/portal/files/chatimg/irc_421719_1453688652.png