If your DR_bind has failed for some reason you should get a webpage that looks like this below:
Our experience is that this is normally related to problems with the PDB file, often duplicated residues or residues that are missing backbone atoms. If you can please take the 'cleaned' PDB file and check it over and resubmit it via option A.
Often the problem residue is listed at the end of the last error file below. Also you can email (removed for this example) with this url so we can investigate the problem, Thanks.
The failed script was run1.pl so the error file to look at first should be run1.err.
The cleaned pdb file we're working with was: 1BGW.pdb
The original pdb file was: 1BGW.orig
The ConSurf file was: 1BGW.consurf
Log files:
leap.log,
Error files:
run0.err,
run1.err,
cluster 7 Number of triangles 35, average gap depth = 7.218 Cluster 8 Number of triangles 9, average gap depth = 7.668 Cluster 9 Number of triangles 14, average gap depth = 6.326 2 mark cleft 1077 Structure Sequence ALAWhich seems to indicate a problem with the Ala1077 reisdue. If we inspect the 1BGW.pdb file which is the 'cleaned' version of the original and look for the Ala1077 reisdue we see this:
ATOM 6073 CB ILE A1076 122.681 156.401 59.158 1.00137.50 ATOM 6074 H ILE A1076 121.598 158.903 60.075 1.00 0.00 ATOM 6075 N ALA A1077 123.158 158.258 62.279 1.00131.77 > ATOM 6076 N GLU A1108 123.717 151.061 59.017 1.00120.02 < ATOM 6077 CA GLU A1108 122.601 150.156 58.617 1.00120.05 < ATOM 6078 C GLU A1108 123.185 149.162 57.660 1.00119.32 < ATOM 6079 O GLU A1108 124.400 149.076 57.492 1.00119.90 <The obvious thing here is that there is only one atom listed for the Ala1077, the backbone N atom. Checking the original PDB file (1BGW.orig) for this residue:
ATOM 6073 CB ILE A1076 122.681 156.401 59.158 1.00137.50 C ATOM 6074 H ILE A1076 121.598 158.903 60.075 1.00 0.00 H ATOM 6075 N ALA A1077 123.158 158.258 62.279 1.00131.77 N ATOM 6076 N GLU A1108 123.717 151.061 59.017 1.00120.02 N ATOM 6077 CA GLU A1108 122.601 150.156 58.617 1.00120.05 C ATOM 6078 C GLU A1108 123.185 149.162 57.660 1.00119.32 C ATOM 6079 O GLU A1108 124.400 149.076 57.492 1.00119.90 OWe can see that the backbone atoms are not in the orignal PDB file either, infact in the MISSING record for 1BGW we see that there are known to be missing:
REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A1071 OG REMARK 470 PRO A1072 CG CD REMARK 470 ASN A1073 CG OD1 ND2 REMARK 470 ASP A1074 CG OD1 OD2 REMARK 470 GLU A1075 CG CD OE1 OE2 REMARK 470 ILE A1076 CG1 CG2 CD1 REMARK 470 ALA A1077 CA C O CBHowever if we check the 1BGW.ConSurf file we see that the ConSurf file includes the Ala1077:
667 I ILE1076:A 1.986 1 2.250, 2.250 1,1 17/74 Q,T, D,I,K,G,E,L,V 668 A ALA1077:A 1.534 1 0.969, 2.250 2,1 16/74 A,N,K,E,V,Q,D,I,L 669 E GLU1108:A 0.708 3 0.476, 0.969 3,2 74/74 S,A,F,N,P,E,Y,Q,D,C,I,LWe see that the Ala1077 residue is included in the ConSurf file, the most likely cause of the problem is that the missing backbone atoms are creating an issue.
We did indeed remove the Ala1077 N atom and the prediction continued.