166 lines
6.3 KiB
R
166 lines
6.3 KiB
R
# tocID <- "RPR-ChimeraX_remote.R"
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#
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# Purpose: A Bioinformatics Course:
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# R code demonstrating remote scripting of ChimeraX.
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#
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# Version: 1.0.1
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#
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# Date: 2020-09
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.0.1 2021 Minimal updates
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# 1.0 First ABC units version
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#
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#
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# TODO:
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# %-encode and escape quotes, or just pass-through?
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#
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#
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# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ------------------------------------------------------
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#TOC> 1 ChimeraX REMOTE SCRIPTING 41
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#TOC> 1.1 Defining a Port 59
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#TOC> 1.2 Open ChimeraX 81
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#TOC> 2 WORKED EXAMPLE: SUPERPOSITION 113
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#TOC>
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#TOC> ==========================================================================
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# = 1 ChimeraX REMOTE SCRIPTING ===========================================
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# One of the cool features of ChimeraX is that it can be driven by Python code,
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# both within a running session and through Python scripts. What I find even
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# cooler though is that ChimeraX can be driven from any programming language via
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# its remote control function that can listen to commands sent from any other
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# application. The interface that is used here is the standard REST (method) -
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# the GET and POST verbs that ubiquitously underly the communication of clients
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# and servers on the Web.
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# In order to establish the communication between this script and ChimeraX, all
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# we need to do is:
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# - open ChimeraX;
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# - tell it to listen on a specific "port";
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# - send commands to that port via httr::
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# == 1.1 Defining a Port ===================================================
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# The httr:: package needs to be available
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if (! requireNamespace("httr", quietly = TRUE)) {
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install.packages("httr")
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}
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# Package information:
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# library(help = httr) # basic information
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# browseVignettes("httr") # available vignettes
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# data(package = "httr") # available datasets
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# We need to think od a port. Any available port number between 49152-65535 is
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# fine. We'll choose 61803 because that's the fractional part of the golden
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# ratio. But one could choose another.
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CXPORT <- 61803
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# Check that our current version of R supports sockets (default since V 3.3)
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capabilities("sockets") # MUST be TRUE. If not, don't continue.
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# == 1.2 Open ChimeraX =====================================================
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# - Open a fresh, new session of recently updated version of ChimeraX
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# - type:
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#
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# remotecontrol rest start port 61803
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#
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# ... or whatever the value of CXPORT is.
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# Now watch what happens in ChimeraX when you execute the following line:
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( x <- httr::GET("http://127.0.0.1:61803/run?command=open+1BM8") )
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# The .utilities.R script includes the function CX(), based on this principle,
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# through which you can send commands to ChimeraX
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CX("camera sbs")
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CX("lighting soft")
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CX("color sequential #1 & protein target abc palette powderblue:orchid:white")
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# The command echos Chimera's response if the parameter "quietly" is
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# FALSE (default), and we can silence output with quietly = TRUE :
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CX("info models #1 attribute num_residues")
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CX("info models #1 attribute num_residues", quietly = TRUE)
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# Either way, the command also returns Chimera's responses "invisibly";
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# i.e. we can use the results by assigning the output to a variable:
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hBonds <- CX("hbonds #1 & protein makePseudobonds false log true", quietly=TRUE)
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x <- read.table(file = textConnection(hBonds), skip = 9,
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blank.lines.skip = TRUE, fill = TRUE)
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hist(x[,13], main="H-bonds", xlab="D···A (Å)", ylab="counts", col="#c9dcff")
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# = 2 WORKED EXAMPLE: SUPERPOSITION =======================================
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# We superimpose the 1BM8 structure with the 1DUX crystal structure to be able
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# to explore possible DNA binding regions in 1BM8
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# The model for 1BM8 is already open as model 1 (#1)
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CX("hide #1 cartoons") # hide model 1 cartoon representation
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CX("open 1DUX") # assume this is opened as model #2
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CX("hide #2") # hide everything ...
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CX("select #2/C") # chain c (protein)
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CX("show sel cartoons") # ... and show cartoons of chain c (protein)
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CX("color sequential sel target c palette steelblue:darkmagenta")
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CX("view #2/C") # re-center the display
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CX("cofr #2/C:62@CA") # set pivot to an interface residue
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CX("select #2/A,B & nucleic-acid") # chains A, B are the cognate DNA
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CX("style sel stick")
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CX("show sel target ab") # show atoms/bonds
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CX("color sequential #2/A & nucleic-acid target ab palette teal:lightcyan")
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CX("color sequential #2/B & nucleic-acid target ab palette teal:lightcyan")
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CX("surface sel enclose sel") # compute joint accessible surface of both chains
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CX("transparency 50")
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CX("select clear")
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# Now superimpose the 1BM8 chain onto 1DUX chain C
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CX("show #1 cartoons")
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CX("matchmaker #1/A to #2/C pairing ss") # the actual superposition
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# study the general layout, and the position of the 1mb8 secondary structure
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# elements relative to 1DUX
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# Let's examine side chain orientations in more detail
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CX("hide #2/C cartoons") # hide the 1DUX protein
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# select all residues in 1BM8 that are within 3.5 A of the DNA chains (a, b)
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CX("select zone #2/A,B 3.5 #1 & protein residues true")
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CX("~select sel & H") # de-select H atoms
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CX("show sel target ab")
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CX("size stickRadius 0.4")
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CX("select clear")
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# The overall architecture of the Mbp1 APSES domain is a good match for the Elk
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# transcription factor binding mode; the detailed conformations of side chains
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# would need to change only to a minor degree. There is a very significant
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# degree of structural similarity; remarkable, given that the DNA is not the
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# target sequence of the Mbp1 transcription factor, AND the 1MB8 structure was
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# determined without a DNA ligand.
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CX("remotecontrol rest stop") # release the socket
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# Done.
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# [END]
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