Hi Tom,

Thank you for your quick reply. Your solution worked to get "foreach" to work and I have notes below if others in the future run into my problem. I was able to solve the issue with a bash script that creates command run files on the fly but it's pretty messy so if you have another way to do this it'd be nice to have things a bit cleaner. Below is my solution/follow-up question, a clarification to the $file1 question you asked and some notes about updating. Major apologies if I repeat myself or grammatical errors, as I wrote this email I came up with several ideas on how to make things work and had to edit the post multiple times each time I tried something new.

Follow up question:

With your help I got this to work by typing these commands into the terminal directly:

$:chimerax --nogui

(waited to load chimerax)

$:open chimera-data-processing.cxc foreach S_0001_*-4-all-chain-A.pdb

Is there a way to run the command script with foreach while opening chimerax? for example:

$:chimerax --nogui chimera-data-processing.cxc foreach S_0001_*-4-all-chain-A.pdb

If I run this it give me a bunch of python errors and errors related to $file. The workaround I made was to have the master bash script write a new chimera script on the fly every time with the user inputted filenames saved in the master bash script.

masterscript.sh:

###run in terminal: "./masterscript.sh S_0001_ hsk2-template-with-metals.pdb

pdbstoalign=$1

pdbwithmetals=$2

###$1 and $2 are equal to the user input while starting the script

###pdb editing stuff happening

if ($x = 5) ###5th alignment

###create foreach running script

echo "open chimera-data-processing.cxc foreach $pdbstoalign-[1-1000]-all-chain-A.pdb" > chimeraxrun.cxc

echo "quit" >> chimeraxrun.cxc

###create data processing script

echo 'open $file.pdb' > chimera-data-processing.cxc ###print exactly this line not variable $file

echo "open $pdbwithmetals" >> chimera-data-processing.cxc
echo "info" >> chimera-data-processing.cxc
echo "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" >> chimera-data-processing.cxc
echo "save $file-sf-aligned.pdb #1 format pdb relModel #2; wait 30" >> chimera-data-processing.cxc

chimerax --nogui chimeraxrun.cxc

###pdb processing with output

chimeraxrun.cxc:

open foreach chimera-data-processing.cxc foreach S_0001_[1-1000]-4-all-chain-A.pdb ###pdb filename comes from bash script

chimera-data-processing:

open $file.pdb

open hsk2-template-with-metals.pdb ###filename from bash master script

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 $file-sf-aligned.pdb #1 format pdb relModel #2; wait 30

While this works it is very messy and I need to create multiple files on the fly. It would be much easier if I could pass variables into the chimerax scripts that I can use inside the script. Does this make any sense?

Clarification:

Hopefully the above example scripts clarifies why I asked about $file1 and $file2. I have 2 input files. a model with no metals and a template with models I need to align onto.

Updating issues:

I forgot to mention that I tried updating chimerax-daily with this command

sudo /usr/bin/chimerax-daily -m pip install --upgrade pip

which gave a success code. But when I checked the version via chimerax-daily --version I get this version.

UCSF ChimeraX version: 0.93 (2020-03-24)

Is there a way to update to the newest version without reinstalling? I found toolshed update documentation but this appears to be for packages not the entire build. As you can see it is not them most updated version. I downloaded bother chimerax and chimerax-daily again. chimerax installed and used foreach with no errors. However, chimerax-daily will not install unless I do a complete uninstall so I think I'll go forward with chimerax.

Another thing I noticed, while attempting ranges with chimerax-daily it only took single digit ranges. For example

S_0001-[1-10]-chain-A.pdb if only took pdbs with "1" in place of the range. if the range is 1-9 then it takes all files. If the range is 01-19 (trying to match number of digits) if only takes models 1 and 9. I get what it is doing here but I don't know the fix or if I'm doing it right. I'm just using a range for now to test 9 files instead of the full 1000. I'll replace the numbering with a '*' so it'll get them all. I won't have an issues going forward but thought this was significant for others in the future if I had typed it wrong.

Thank you again for your time and help,

Ryan

On Thu, May 5, 2022 at 12:01 AM Tom Goddard <goddard@sonic.net> wrote:

Hi Ryan,

The "foreach" option you tried is exactly intended for this use. The error message "Missing filename suffix foreach" suggests you are using an old version of ChimeraX (older than ChimeraX 1.3) that does not have the "foreach" option so it thinks that "foreach" is the name of a file. Your script only saves one file so I don't understand what you mean by saving two files $file1 and $file2. You would just use "save $file-sf-aligned.pdb ..." to save the aligned file.

Tom

On May 4, 2022, at 10:41 PM, Ryan Woltz via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

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

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
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