visualise3d.txt

To visualise the 3D structure using Absolut follow the following steps.

1. Create a 2 columns <name>.txt file and place the sequences like below:

0	HICAGFWHMPI
10	TDKTHPEVYTR
20	HYGMFLLPVGL
30	HGHMFFLHVIL
40	HFGMFELYVIL
50	HFVMFFLYVAL
60	HFVMPLLVLML
70	HFVMFYLVLML
80	HFTMFFLVLML
90	HFTMCFLVLML
100	FFIMFFLQLIL
110	FFIMFFLVLCL
120	FFIMFPLVLIF
130	PFIMFFLVLTL
140	FFIMFLLVLFL
150	FFIMFLLHLYL
160	CFIMFLLVLTL
170	FFIFFLSVLWL
180	FFIFFLLFTIL
190	FFIFFVLFLIL
197	FFYFYLLFLIL


2. On commandline run:

	repertoire <antigen> "C:/Users/pprobert/Desktop/Antbo/antboList.txt"

replace <antigen> by the antigen name. For e.g., in case of 1ADQ_A: replace <antigen> by 1ADQ_A.
The output is saved in a text file name <antigen>FinalBindings_Process_1_Of_1.txt


3. To visualise the binding

	visualize <antigen> "C:/Users/pprobert/Desktop/Antbo/1ADQ_AFinalBindings_Process_1_Of_1.txt"

The output is the name of the structures (and the two ways to name each structure from each end).

BLLDRDRRLR	128997	2	<=>	BDUDDRDRUU	132966		(70b, 190b)
BULRRURDRD	124769	1	<=>	DURURDRRLD	133024		(150)
LLLSLUSSUU	128933	1	<=>	UDDSSDLSLL	137060		(10)
LRRDURUUDU	128932	4	<=>	BDUDDRDURR	132966		(40, 70a, 120, 190a)
RRURSUUSLD	124837	9	<=>	BDRSUUSLUL	132966		(0, 20, 50, 80, 90, 110, 130, 160, 180)
SUULSLSLLU	124772	1	<=>	UDLLSLSLDD	124837		(30a)
UDLLSLSDLL	124837	1	<=>	DDDLSDSDDL	128869		(30b)
ULSDDLRRSU	124772	1	<=>	BDSRRLUUSL	132966		(100)
ULUUSLUUSD	124837	4	<=>	BDSUURSUUR	132966		(60a, 140, 170, 197)

Note: Above is an example of <antigen>=1ADQ_A, and on the right column we manually added sequence ID of each of the structure.


4. Export images from Absolut openGL window by moving between structures using (D/Q) and typing 'p' to print as a picture.