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Recipe: DistMap0
Created by jeff101 40 119
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Name: DistMap0
ID: 101659
Created on: Fri, 12/04/2015 - 02:42
Updated on: Fri, 12/04/2015 - 18:31
Description:

DistMap0c.txt 12/4/15 1220pm noon code



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jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
What does DistMap0 do?

DistMap0 finds the distances between every pair of alpha-carbons in the protein
and makes several maps of these distances. It gives output like below:

DistMap0: Puzzle 973: Post-CASP Tc853: Server Model Contacts with ID 998376
   at 12/03/15 20:33:23 has score 11250.722
   0 bands and 152 residues.
 
In the alpha-carbon distance map below:
   0 means distance is in range (-Inf,2).
   1 means distance is in range [2,4).
   2 means distance is in range [4,6).
   3 means distance is in range [6,8).
   4 means distance is in range [8,10).
   5 means distance is in range [10,15).
   6 means distance is in range [15,20).
   7 means distance is in range [20,30).
   8 means distance is in range [30,50).
   9 means distance is in range [50,Inf).
All nonzero distances range from 3.75 to 44.71
   for the Ca-Ca pairs 35-36 and 58-121 respectively.

L152d-6666778756777645787776554776567760
L147d-7776667567777774566677775254566506
L143k-8876556678778876654567776556665057
L138g-8887778778888887777567775564550567
L134t-7777778778888877776345665676305666
E129v-7766677767777766776555552675035655
E125v-8877778777788876777577775350564646
L120n-8887778788888887777778887305776557
E115n-8877677677778875666677775033665527
E111t-7766677667777765777566650575255654
L106d-5767778767777757887765405787567775
L102g-5545677767777666777754046787567775
H097k-7755567777777777776530456787557776
H093t-7766567778777777775403566777546677
H088e-8877677778778877775045775675535567
L083t-8876456788777887630556777677667467
L079d-8876545688667887503777787677777568
E074d-8776655477567775056777787677777657
E070d-7655657355566650577777675576677645
H065k-5556778624776505788777656787678774
E060p-5146777655664056788877677888788876
H056f-7455667566450466777877777888788877
L051n-7654555577405676667777777788788777
L047s-7655555266044675567777777787788777
E042y-6667778620676545788887777787788876
E038n-6556777602676525788777666787677765
E033t-7655545066255663467777776677777657
H028e-8776540578557787556777787788788678
L024i-7763204477556775545766777777777567
H019i-7753025577556776654655676677677567
H015k-7540336567545665666765576777677666
H010l-5304567556555455777765466787678776
E006t-5035777656664156788877577888778876
L001g-0557778766777557888877557888778876
      ||||||||||||||||||||||||||||||||||
      gtlkiietnysnfpkdddtetkgdtnnvvtgkdd
      0000000000000000000000111111111111
      0011122334455667778899001122233445
      1605948382716050493837261505948372
      LEHHHLHEEELLHEHEELLHHHLLEELEELLLLL
 
152-675785650 152 amino acids in all
133-767884605 min Ca-Ca dist=3.75 for 35-36
114-867876066 max Ca-Ca dist=44.71 for 58-121
095-757770645 Ca-Ca dist ranges chart key:
077-868807788 0 for 0-2, 1 for 2-4
058-677087887 2 for 4-6, 3 for 6-8
039-670787775 4 for 8-10, 5 for 10-15
020-707765667 6 for 15-20, 7 for 20-30
001-076687876 8 for 30-50, 9 for 50-Inf

The final map above is small enough to appear in the Recipe Output,
so it can be included in a snapshot of the protein when a puzzle ends.

Below is a sample snapshot made right after the DistMap0 run above.
You can click on the below image for a more detailed view.

jeff101's picture
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Joined: 04/20/2012
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See below for the original snapshot:
jeff101's picture
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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.

jeff101's picture
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Homologous proteins give similar-looking Contact Maps:

p.247 of the book "Proteins: Structures and Molecular Properties"
by Thomas E Creighton, Macmillan, 1993, ISBN 071677030X or 9780716770305
shows Contact Maps for the homologous proteins alpha-chymotrypsin and elastase
that look very similar to each other.

https://books.google.com/books?id=hu8T_kI1LrkC&pg=PA247
https://books.google.com/books?id=hu8T_kI1LrkC

jeff101's picture
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Joined: 04/20/2012
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DistMap0 output graphed using Matlab

Below is a Matlab image made from the full Distance Map made by the DistMap0 run above.
This map is a 152 x 152 grid of integers from 0 to 8. Note the resemblance between this
map and the Contact Map shown above. Click on the image below for more detail.

jeff101's picture
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Future versions?

It would be neat if we could use html code within the Recipe Output window.
Then I could use characters like █ ▓ ▒ ░ or █ ▀ ▄ ▌ ▐ ▙ ▛ ▜ ▟ ▚ ▞ ▖ ▘ ▝ ▗
from http://www.w3schools.com/charsets/ref_utf_block.asp
to make the above distance maps.

If you know how to use html code within the Recipe Output window,
please post here or at http://fold.it/portal/node/2001554 about it.

Thanks!

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
If you like this recipe, please try DistMap1:

DistMap1 (http://fold.it/portal/recipe/101679)
is a more elaborate version of DistMap0 that
can make *.eps image files like the Matlab image above,
uses a variety of shaded character sets to show distances
in the Recipe Output window and scriptlog.default.xml file,
and can make statistical charts suitable for input into
spreadsheet programs like Excel.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons