Handling side chains, side_dock.sh

Given a reasonable main chain trace (the output file warpNtrace.brk from arp_warp.sh mode warpNtrace) and the sequence of the protein, the automated script side_dock.sh will match these main chain fragments to the sequence and build the side chains. The sequence information should be given in a so-called PIR file which can look like the following (all these lines are in a valid format, but your file does not necessarily have to be such a mess) :

>psp

VVRDVNWGALRIAVSTEDLTDPAYHCARVG
LIPQAVQLHT ERLKVQQVQG KWKVTDMVGD ICGDFKVPQA HITEGFSNTD FVMYVASVPS
E E G V L A W A T T CQTFSDGHPA

The only restriction is that the first line must start with the > symbol and the second line should be blank. The rest is worked out by the script.
Tricks and Tips

• In case you used the side option in arp_warp.sh you get already some side chains. The parameters used there, are a bit more conservative for the sequence docking than in this script. If all chains were docked anyhow, don't bother. Else try to run side_dock.sh on top.
• If you have a dimer or a higher multimer things get more complicated. It is not easy for side_dock.sh to understand which chain belongs to which monomer by itself. What you should do, is go briefly to the graphics, decide which chain belongs to which monomer and then run side_dock.sh with the chain names of the first monomer as command line arguments: (i.e. side_dock.sh test chains A B C) and then for the second monomer, (i.e. side_dock.sh test chains D E F G), etc. That will output several files in the files directory with rather obvious names.
• Take a look at the average confidence level. If its too low, below 10-15, it means that something might well be wrong. It basically means that the program can not decide for sure where to place some fragments into the sequence (there are good enough alternatives) and the side chain docking is not to be trusted too much! Examine the log file (logs/side_dock.log) and see if all the fragments or only a few cannot be placed accurately. Based on that you could decide what to trust and what not.