There were some errors in the sugar dictionaries, at least some of which
have been fixed in the new release. Can you check whether the problem
persists with them..
Or send a fragment of your coordinates including the mannose and I will
try to idealise it here to see if that is the problem..
Eleanor
David W Borhani wrote:
Hi, I'm getting this error from Refmac (5.2.0005) with a N-linked
carbohydrate chain:
Number of atoms : 3558
Number of residues : 434
Number of chains : 22
I am reading library. Please wait.
mon_lib.cif
WARNING : CIS peptide bond is found, angle = 6.41
ch:AA res: 373 TYR --> 374 PRO
WARNING : CIS peptide bond is found, angle = 4.93
ch:BB res: 373 TYR --> 374 PRO
WARNING : link:SS is found dist = 2.034 ideal_dist= 2.031
ch:AA res: 261 CYS at:SG .->AA res: 321 CYS
at:SG .
WARNING : link:SS is found dist = 1.992 ideal_dist= 2.031
ch:AA res: 367 CYS at:SG .->AA res: 425 CYS
at:SG .
WARNING : link:SS is found dist = 2.001 ideal_dist= 2.031
ch:BB res: 261 CYS at:SG .->BB res: 321 CYS
at:SG .
WARNING : link:SS is found dist = 2.043 ideal_dist= 2.031
ch:BB res: 367 CYS at:SG .->BB res: 425 CYS
at:SG .
WARNING : link:NAG-ASN is found dist = 1.392 ideal_dist= 1.439
ch:BB res: 297 ASN at:ND2 .->DD res: 1 NAG
at:C1 .
WARNING : link:BETA1-4 is found dist = 1.390 ideal_dist= 1.439
ch:DD res: 1 NAG at:O4 .->Da res: 2 NAG
at:C1 .
WARNING : link:BETA1-4 is found dist = 1.399 ideal_dist= 1.439
ch:Da res: 2 NAG at:O4 .->Db res: 3 MAN
at:C1 .
WARNING : link:ALPHA1-6 is found dist = 1.405 ideal_dist= 1.439
ch:Db res: 3 MAN at:O6 .->Dc res: 4 MAN
at:C1 .
WARNING : link:ALPHA1-3 is found dist = 1.339 ideal_dist= 1.439
ch:Db res: 3 MAN at:O3 .->De res: 6 MAN
at:C1 .
WARNING : link:BETA1-2 is found dist = 1.465 ideal_dist= 1.439
ch:Dc res: 4 MAN at:O2 .->Dd res: 5 NAG
at:C1 .
ERROR: wrong tree structure .....
IERR = 1
There is error. See above
===> Error: Fatal error. Cannot continue
(The links reported above are correct.)
I see Prem got same error last year
(http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-01/msg00211.html),
but I could not find a reply/fix.
What is wrong (what does "wrong tree structure" mean?), and do I fix
it so that Refmac will run?
Thanks,
Dave
~~~~~~~~~~~~~~~~~~~~~~~~
David W. Borhani, Ph.D.
Structural Biology Group Leader
Chemistry Department
Abbott Bioresearch Center
Vox: 508-688-3944
Fax: 508-754-7784
Email: [EMAIL PROTECTED]
Smail: Abbott Bioresearch Center, Inc.
100 Research Drive
Worcester, MA 01605 U.S.A.
http://abbott.com
~~~~~~~~~~~~~~~~~~~~~~~~
begin:vcard
fn:Eleanor Dodson
n:Dodson;Eleanor
email;internet:[EMAIL PROTECTED]
tel;work:+44 (0) 1904 328259
tel;fax:+44 (0) 1904 328266
tel;home:+44 (0) 1904 424449
version:2.1
end:vcard
