Dear community,
I'm sorry if this is a repeated question, I've seen a few posts about taking in a file for the command line and doing some things then exiting. I got most of this down and I'm sure at this point it is just a matter or correcting a few lines of code.
I'm trying to automate a protein modeling protocol and I have 1000 decoys at this point. Now I need to insert the 5 metals into 5 different pockets into all my decoys for a final relax before selecting my top model. I have a template pdb with all the metals in place. For 4 of these metals I have used rosetta align mover to align a decoy onto the template around a single metal binding site, save the pdb, then add on the metal coordinates then repeat for the next binding site. So this method works because the chain is continuous around these metal binding sites. However the final metal binding site is in the center and coordinated by 4 chains coming together and the positioning needs to be very precise.
Chimera or chimerax solves this very well but I don't know how to put this into a script. I have a few solutions if someone can help me edit this to work. My script (chimera-data-processing.cxc) looks like this right now.
cd results/
open S_0001_X-4-all-chain-A.pdb ###X = 1-1000
open hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb
info
align #1:240-244,765-769,1290-1294,1815-1819@o to_atoms #2:240-244,765-769,1290-1294,1815-1819@o matchAtomNames true; wait 300
save S_0001_X-4-all-chain-A-sf-aligned.pdb #1 format pdb relModel #2; wait 30
cd ../
close
quit
This script is perfect if run for have a single model with the exact name written into the script after typing:
chimerax-daily --nogui chimera-data-processing.cxc
I have two main solutions
A) run a while loop that counts down and passes a filename to chimerax:
while ( X < 1000 )
chimerax-daily --nogui chimera-data-processing.cxc S_0001_X-4-all-chain-A.pdb hsk2-cam-homology-from-map-refined-6cno-alignment-template-1-all-chain-A.pdb
Where in the chimerax script I take the arg1 (S_0001*.pdb) and arg2 (hsk2*.pdb)(assuming chimera-data-processing.cxc is arg0) and modify to look like this:
open $arg1
open $arg2
...
save $arg1-sf-aligned.pdb #1 format pdb relModel #2; wait 30
open myscript.cxc foreach ~/data/*.cif
or
open chimera-data-processing.cxc foreach results/S_0001_*-4-all-chain-A.pdb
results in this error:
Missing filename suffix foreach
I also tried this:
chimerax-daily --nogui chimera-data-processing.cxc foreach results/S_0001_*-4-all-chain-A.pdb
But it just runs the command. this seems to ignore everything after the first filename. I also read that if I used foreach inside the script I could use $file to replace the filename it is currently working on, would there be a way to fave $file1 and $file2? to automate this I'd also like the change the name of the template file I'm aligning to. I also attempted the python method using sys.arg = arg[1] then running things but I couldn't get it to work because I have no experience in python. What is the suggested way to complete this task? Again this is in a much larger script with user inputs so ideally it would look like this in a script (very shorthanded just for the concepts). I can also run a python command script in my bash sctipt
pdb transformations
if (y = 5) ###alignment metal number)
while ( x < 1000)
###arg0 = command script arg1 = pdb to align arg2 = template pdb with metals
chimerax-daily --nogui chimera-command-script.cxc $filenamebase$x-$alignmentnumber-*.pdb $template.pdb ###strings for variables are provided when script is initialized.
###code to extract metal coords for S_0001_$x-4-*.pdb
done
fi
chimera-command-script.cxc:
open arg1
open arg2
align model #1 to model #2 on specific atoms
save arg1-new-filename.pdb
close
exit
if someone would like a follow-up email with my attempt at chimera python sctipt using runcommand I'm very happy to supply that as a foundation to help fix, I just thought this one is easier to fix since it is really close, the script works but only for 1 pdb at a time.
Apologies for bad scripting terminology and confusion with python, I've had to teach coding to myself so I might have misused terms.
Thanks for any help that can be given,
Ryan