Hi all,
I answered/thanked Pavel privately for the more involving and expansive
learning advice on getting better acquainted with cctbx.
coot without the gui - scripting: I imagined that, after all, in
general, underlying gui commands are the modules with their
parameters/input data and then the resulting outputs.
Thanks James for indications/instructions and Paul later on
complementing them.
Now, I gotta do work/study.
Jorge
On 2/6/24 16:08, James Holton wrote:
Hey Jorge,
Did you know coot can be scripted and run without the gui? In general,
all you need is to record a session and then edit the session file. A
shell script for doing something similar to what you want would look
like this:
#! /bin/tcsh -f
#
#
set pdbfile = wrong.pdb
set mapmtz = refmacout.mtz
set chain = A
set resnum = 123
set TYP = LEU
cat << EOF >! mutate.py
imol_coords = handle_read_draw_molecule("$pdbfile")
imol_map = make_and_draw_map("$mapmtz","FWT","PHWT","",0,0)
set_go_to_atom_chain_residue_atom_name("${chain}",$resnum," CA ")
mutate_and_auto_fit(${resnum},"${chain}",imol_coords,imol_map,"${TYP}")
with_auto_accept([sphere_refine, 3.5])
save_coordinates(0,"coot.pdb")
coot_no_state_real_exit(0)
EOF
# run the program
coot --no-graphics --script mutate.py
A difference here is that instead of picking a particular rotamer, you
let coot do it for you based on the density.
This might sound like a heavyweight approach, but coot actually spins up
real fast when it doesn't need to build a graphics window.
I note you did ask for a way to specify a rotamer. I say try doing that
in coot and record the session. However, if that gets too complicated,
another way to do build-by-rotamer is with these awk programs that I
wrote long before coot was a thing. I still find them useful for
certain tasks. I have created a git repo for them here:
https://github.com/jmholton/build_pdb
HTH,
-James Holton
MAD Scientist
On 2/6/2024 8:24 AM, Jorge Iulek wrote:
Dear all,
As I cannot find by myself, maybe someone can indicate here.
I would like a program, command line - not gui, that I would
simply indicate residues and the desired rotamer, and so it will
change the coordinate file to complete/change side chains accordingly,
say, somehow like I say for Glu251 make it rotamer tp10, and so on.
Less desirable would be to indicate a reference structure for the
specific rotamer. But I would really prefer that I indicate the
specific residue and the rotamer I want.
Is there such a program or any ideas for a combination of programs?
Thanks,
Jorge
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