From 744e762dc280851e32ca5b50b9a31cfa1a584101 Mon Sep 17 00:00:00 2001 From: hyginn Date: Sun, 27 Sep 2020 23:40:27 +1000 Subject: [PATCH] New script to demonstarte remote scripting of ChimeraX --- RPR-ChimeraX_remote.R | 148 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 148 insertions(+) create mode 100644 RPR-ChimeraX_remote.R diff --git a/RPR-ChimeraX_remote.R b/RPR-ChimeraX_remote.R new file mode 100644 index 0000000..fb16601 --- /dev/null +++ b/RPR-ChimeraX_remote.R @@ -0,0 +1,148 @@ +# tocID <- "RPR-ChimeraX_remote.R" +# +# Purpose: A Bioinformatics Course: +# R code demonstrating remote scripting of ChimeraX. +# +# Version: 1.0 +# +# Date: 2020-09 +# Author: Boris Steipe (boris.steipe@utoronto.ca) +# +# Versions: +# 1.0 First ABC units version +# +# +# TODO: +# %-encode and escape quotes, or just pass-through? +# +# +# == DO NOT SIMPLY source() THIS FILE! ======================================= +# +# If there are portions you don't understand, use R's help system, Google for an +# answer, or ask your instructor. Don't continue if you don't understand what's +# going on. That's not how it works ... +# +# ============================================================================== + + +#TOC> ========================================================================== +#TOC> +#TOC> Section Title Line +#TOC> ------------------------------------------------------ +#TOC> 1 ChimeraX REMOTE SCRIPTING 40 +#TOC> 1.1 Defining a Port 58 +#TOC> 1.2 Open ChimeraX 80 +#TOC> 2 WORKED EXAMPLE: SUPERPOSITION 100 +#TOC> +#TOC> ========================================================================== + + +# = 1 ChimeraX REMOTE SCRIPTING =========================================== + + +# One of the cool features of ChimeraX is that it can be driven by Python code, +# both within a running session and through Python scripts. What I find even +# cooler though is that ChimeraX can be driven from any programming language via +# its remote control function that can listen to commands sent from any other +# application. The interface that is used here is the standard REST (method) - +# the GET and POST verbs that ubiquitously underly the communication of clients +# and servers on the Web. + +# In order to establish the communication between this script and ChimeraX, all +# we need to do is: +# - open ChimeraX; +# - tell it to listen on a specific "port"; +# - send commands to that port via httr:: + + +# == 1.1 Defining a Port =================================================== + +# The httr:: package needs to be available + +if (! requireNamespace("httr", quietly = TRUE)) { + install.packages("httr") +} +# Package information: +# library(help = httr) # basic information +# browseVignettes("httr") # available vignettes +# data(package = "httr") # available datasets + +# We need to think od a port. Any available port number between 49152-65535 is +# fine. We'll choose 61803 because that's the fractional part of the golden +# ratio. But one could choose another. + +CXPORT <- 61803 + +# Check that our current version of R supports sockets (default since V 3.3) +capabilities("sockets") # MUST be TRUE. If not, don't continue. + + +# == 1.2 Open ChimeraX ===================================================== + +# - Open a fresh, new session of ChimeraX +# - type: +# +# remotecontrol rest start port 61803 +# +# ... or whatever the value of CXPORT is. + +# Now watch what happens in ChimeraX when you execute the following line: +( x <- httr::GET("http://127.0.0.1:61803/run?command=open+1BM8") ) + +# The .utilities.R script includes the function CX(), based on this principle, +# through which you can send commands to ChimeraX + +CX("camera sbs") +CX("lighting soft") +CX("color sequential #1 & protein target abc palette powderblue:orchid:white") + + +# = 2 WORKED EXAMPLE: SUPERPOSITION ======================================= + +# We superimpose the 1BM8 structure with the 1DUX crystal structure to be able +# to explore possible DNA binding regions in 1BM8 + +# The model for 1BM8 is already open as model 1 (#1) +CX("hide #1 cartoons") # hide chain a cartoon representation +CX("open 1DUX") +CX("hide #2") # hide everything ... +CX("show #2/a,b,c cartoons") # ... and show cartoons of chains a, b (DNA) and c +CX("view #2/c") # re-center the display +CX("select #2/a,b") # select the DNA chains +CX("color sel lightblue") +CX("surface sel enclose sel") # joint surface of both chains +CX("transparency 50") +CX("select #2/c") # select the protein chain +CX("color sequential sel target c palette palegreen:lightblue") + +# Now superimpose the 1BM8 chain onto 1DUX chain C +CX("show #1 cartoons") +CX("matchmaker #1/A to #2/C pairing ss") # the actual superposition +CX("select clear") + +# study the general layout, and the position of the 1mb8 secondary structure +# elements relative to 1DUX + +# Let's examine side chain orientations in more detail +CX("hide #2/c cartoons") # hide the 1DUX protein + +# select all residues in 1BM8 that are within 3.5 A of the DNA chains (a, b) +CX("select zone #2/a,b 3.5 #1 & protein residues true") +CX("~select sel & H") # de-select H atoms +CX("show sel target ab") +CX("size stickRadius 0.4") +CX("select clear") + +# The overall architecture of the Mbp1 APSES domain is a good match for the Elk +# transcription factor binding mode; the detailed conformations of side chains +# would need to change only to a minor degree. There is a very significant +# degree of structural similarity; remarkable, given that the DNA is not the +# target sequence of the Mbp1 transcription factor, AND the 1MB8 structure was +# determined without a DNA ligand. + +CX("remotecontrol rest stop") # release the socket +# Done. + + + +# [END]