Hi Seth,
we had similar experience with corina and it turns out that different corina versions handle _chem_comp_tor records differently. So it might be a good idea to try a newer version.
Older versions were writing _chem_comp_tor.id records as const_ per default, which are treated as constants in coot (i.e. those bonds are not rotateable). So simply changing e.g.
INH const_007 'C4' 'C5' 'N7' 'C8' -174.254 20.0000 2
to
INH tor_007 'C4' 'C5' 'N7' 'C8' -174.254 20.0000 2
or some such could be an easy solution. (Spacing, quotes, and chem_comp_tree seem irrelevant.)
As far as I understood, all this pain will vanish with coot's "torsion general", scheduled for 0.5. Fingers crossed...
HTH
JED
-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software [mailto:[log in to unmask]]On Behalf Of Seth Harris
Sent: 18 December 2007 06:20
To: [log in to unmask]
Subject: corina restraint libraries vs. libcheck format
Hi,
Can someone (e.g. Paul) tell me what part of the .cif restraints library COOT uses (and what format is expected) to recognize rotatable bonds in small molecules (i.e. Chi angles)?
I generally use libcheck and corina to generate .cif files of novel compounds in our structures semi-automatically, and while the latter produces more robust information, Coot feels that the ligand has no Chi angles once the library is read (though it does report X number of restraints successfully and the small molecule behaves appropriately during real space refinement). Monomer library sketcher also does not recognize which groups are planar groups but does show the structure. So at the moment I read in libcheck's library so I can spin various bonds, then read in corina's library again so I can snuggle the molecule into density without collapsing various ring systems inappropriately. Ugh.
Looking at the file contents they have similar loop structures and content with 3 notable differences. My corina examples lack H atom descriptors, have single quotes around many of the data fields, and the field columns are spaced differently. A few quick tests suggest that the last issue may be the crux of the matter. Are these files meant to be hard-wired to exact column spacings, like the lovely PDB format? I thought cif was supposed to get away from such punch-card ilke behavior, and I'm a bit confused since as mentioned the 'wrongly' spaced .cif restraints library is perfectly functional in real-space refinement (coot) or in refmac, just not so for edit chi angles (coot) or displaying planar groups (sketcher). Is there any way Coot (and ccp4, but perhaps all this should be posed on that list?) could be convinced to recognize these aspects? My last request on a different topic was scheduled for v0.9 disappointingly (or perhaps Paul will be skipping 5,6,7, and 8?? Obviously I'm too focused on the small stuff!) so if this one too I believe I'll have to get around to writing a paper, citing coot, and trying to time it to win a citation-based feature request award. Ha! Or I'd write a script to bring the corina file in line...I just need to know what the target actually is. I did make it most of the way through the ccp4 mmcif format web page, but I found my question wasn't going away.
Thanks as always for the great program, features, and rapid development.
Cheers,
Seth
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