Hi,
I just installed coot version 0.3.3 using the universal binary provided by
Bill Scott. I have installed the coot directory to /usr/local/ and the
launcher is in my /Applications folder of my intel mac (2x2.66 GHz dual
core, version 10.4.9). I have 2 questions. Istall seemed to work just fine.
However, the 0-coot-history.py, 0-coot-history.scm, and 0-coot.state.scm
files are all getting written to my desktop. I didn't want to start messing
with paths, since everything else seems to run mostly fine. What do I need
to edit so that these files get stored in /Users/me? The second question
regards the planar peptide restraint patch. I tried to edit the file myself
and I am getting very strange results. This could be because a)I miffed up
the patch or b) my model stinks. (I am leaning towards b). The patch script
didn't work for me, so I just did a manual edit of mon_lib_list.cif.
Originally it read:
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
TRANS plane1 1 CA 0.020
TRANS plane1 1 C 0.020
TRANS plane1 1 O 0.020
TRANS plane1 2 N 0.020
TRANS plane2 1 C 0.020
TRANS plane2 2 N 0.020
TRANS plane2 2 CA 0.020
TRANS plane2 2 H 0.020
it now reads:
loop_
_chem_link_plane.link_id
_chem_link_plane.plane_id
_chem_link_plane.atom_comp_id
_chem_link_plane.atom_id
_chem_link_plane.dist_esd
TRANS plane1 1 CA 0.020
TRANS plane1 1 C 0.020
TRANS plane1 1 O 0.020
TRANS plane1 2 N 0.020
TRANS plane1 2 CA 0.020
TRANS plane2 1 C 0.020
TRANS plane2 2 N 0.020
TRANS plane2 2 CA 0.020
TRANS plane2 2 H 0.020
which seems to be ok, but the patch in the coot faq is missing the
TRANS plane1 1 CA 0.020
TRANS plane2 2 H 0.020
I just wanted to confirm that the patch was just pointing us to the correct
area to edit and not showing the entire loop, i.e., my edits are correct and
the extra 2 lines are indeed needed. Thank you :-)
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