Difference between revisions of "2022 Denovo tutorial 3 with PDBID 1X70"
From Rizzo_Lab
BrockBoysan (talk | contribs) (→System Preparation) |
BrockBoysan (talk | contribs) (→System Preparation) |
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Now load up Chimera: | Now load up Chimera: | ||
− | Tools > Binding/Surface Analysis > View Dock > Load | + | Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2 |
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[[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]] | [[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]] | ||
+ | Load fraglib_sidechain.mol2 | ||
− | [[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from | + | [[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from fraglib_sidechain.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715]] |
+ | |||
+ | Load both | ||
[[File:715_frags.png|thumb|center|800px|All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top) ]] | [[File:715_frags.png|thumb|center|800px|All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top) ]] |
Revision as of 12:19, 20 March 2022
System Preparation
Directory Setup
ATTENTION: This tutorial requires you to have first completed the 2022 1X70 VS tutorial: https://ringo.ams.stonybrook.edu/index.php/2022_DOCK_tutorial_3_with_PDBID_1X70
Make a new directory:
mkdir 09.focus_dn
Now inside 09.focus_dn, make the following DOCK6 input file:
Now load up Chimera:
Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2
Load fraglib_sidechain.mol2
Load both