On 22/12/2017 16:51, Carter, Charlie wrote:
This is a strange question, even from me.
I’ve an undergraduate working on a project that requires superimposing large
numbers of pdb files. I would like to have him use lsqkab but he is rather
unsophisticated in a computational sense. He is already using various other
programs, e.g. Pymol, which he has had to download and install. I’d like to
avoid having him install and then learn to set up and use the entire ccp4 suite
if he will not need any of the programs except lsqkab. Further, I feel that
lsqkab brings functionality to the table that is superior to that in Pymol.
Is there any way to short cut the full CCP4 installation and provide him with a
functioning lsqkab module based on my ccp4 installation? In a bit more detail,
is there any way to load the necessary dynamic libraries so that lsqkab will
work with input pdb files?
Yes.
cd $CCP4_MASTER
tar cvzf ~/just-lsqkab-bits.tar.gz bin/lsqkab lib/libccpf* lib/libccp4*
lib/libmmdb2.* \
lib/data/syminfo.lib include/environ.def include/default.def
Then (having transferred just-lsqkab-bits.tar.gz as needed)
(just once)
cd some/where/for/extraction/on/student/machine
tar xf just-lsqkab-bits.tar.gz
(every time lsqkab is to be used)
setenv CCP4 /absolutify/some/where/for/extraction/on/student/machine
setenv CCP4_SCR ~/scratch # or wherever, create as needed
setenv CINCL $CCP4/include
setenv CLIBD $CCP4/lib/data
(tada!)
bin/lsqkab XYZIN .. (etc)
Your student can add /absolutify/some/where/for/extraction/on/student/machine/bin to your student's path, of
course.
Wishing you well,
Paul.
(I'd do superpositions in Coot (which also brings extra functionality to the
table), it goes without saying :-))
