[chimerax-users] Chimerax scripting error and passing user supplied arguments

[Ryan Woltz]

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 at o to_atoms
#2:240-244,765-769,1290-1294,1815-1819 at 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

      Option B is to use the foreach command described in the open command
documentation (
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html). However, a
copy and past of that command:

*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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20220504/8d8d0a49/attachment.html>