FC missing reference angles

google-code-export / nmrrestrntsgrid

Automatically exported from code.google.com/p/nmrrestrntsgrid

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FC missing reference angles #270

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago

I have recently updated ccpn and am still having a problem running these two 
entries. FC is not handling these particular dihedral angles: PPA, ALPHA, BETA, 
GAMMA, DELTA, EPSILN, ZETA, and CHI.

From the log file:
  Error: no reference angle found for name PPA...
...
Using CYANA library - courtesy of Peter Guentert.

CHI baffles me. I would expect that one to be there?

I'm attaching the log file for 2l8p.

Original issue reported on code.google.com by schulte....@gmail.com on 3 Mar 2011 at 4:38

Attachments:

linkNmrStarData.log

GoogleCodeExporter commented 9 years ago

Wim, do we need to update the residue name defs within these dihedrals defs.
Looks like a simple problem.

Original comment by jurge...@gmail.com on 4 Mar 2011 at 8:51

Changed state: Accepted

GoogleCodeExporter commented 9 years ago

Alas simpler than it looks - PPA is not a 'standard' CYANA residue as far as I 
know, so we'd have to manually add it to the CYANA reference library. This is 
something I never wanted to start messing around with though for various 
reasons... a more ad-hoc solution that can be dealt with in the presetDict is 
probably better.

Original comment by wfvran...@gmail.com on 30 Mar 2011 at 12:06

GoogleCodeExporter commented 9 years ago

PPA is meant to be a dihedral angle name and not the problem of the issue.

The issue here is with the other standard dihedral angles for the standard 
residues as given in the original data:

2  DG  ALPHA   -91   -31 

etc.

I think the problem is related with residue names being DG i.s.o. G. etc.

Original comment by jurge...@gmail.com on 30 Mar 2011 at 12:34

GoogleCodeExporter commented 9 years ago

Good point. I am a bit slow this week, not enough sleep. 

Anyway works now, though not for PPA and EPSILN, not in the CYANA library. 
Check out from SF CVS:

ccp/format/nmrStar/dihedralConstraintsIO.py

Original comment by wfvran...@gmail.com on 30 Mar 2011 at 1:07

GoogleCodeExporter commented 9 years ago

Chris can you reprocess these ones?

Original comment by jurge...@gmail.com on 30 Mar 2011 at 2:50

Changed state: Started

GoogleCodeExporter commented 9 years ago

After updating CCPN of course.

Original comment by jurge...@gmail.com on 30 Mar 2011 at 2:50

GoogleCodeExporter commented 9 years ago

I'll get to it as soon as I can.

Original comment by schulte....@gmail.com on 30 Mar 2011 at 3:30

GoogleCodeExporter commented 9 years ago

2l8p went from 240 converted to 368. 
2l8q went from 233 converted to 368.

Is this as done as it's going to get? At least for now?

Original comment by schulte....@gmail.com on 30 Mar 2011 at 4:15

GoogleCodeExporter commented 9 years ago

Yes, there were 414 and the ones missing could be the non-standard 
dihedrals/residues.
Great!

Original comment by jurge...@gmail.com on 30 Mar 2011 at 5:32

Changed state: Fixed