[Chimera-users] on beta strand assignmet by chimera

[Smith Liu]

Dear All,


I have a protein, which contains fragment aa 239-251. The protein has been fitted its map with 2 different (minor difference) resolution, and thus I have 2 PDB. For PDB 1 (the first resolution), the H-bonds inside aa 239-251 include:
#2 Gly 245.A N-Asn 242.A O 2.708A
#2 Asn 242.A N-Tyr 246.A O 3.120 A
#2 Val 248.A N-Val 240.A O 3.120 A
#2 GLN 251.A N-Ser 238.A 0 3.033 A


For PDB 2 (the second resolution), the H-bonds inside aa 239-251 include:
#0 Gly 245.A N-Asn 242.A O 2.715A
#0 Asn 242.A N-Tyr 246.A O 3.1206 A
#o Val 248.A N-Val 240.A O 2.858 A
#0 GLN 251.A N-Ser 238.A 0 3.074 A


Naked eye check found the H-bonds in PDB 1 were almost the same H-bonds in PDB 2.


However for PDB 2, aa23-242 and aa 247-251 form 2 strands, but for PDB 1, it was a un-disconnected loop for aa 239-251.


Will you please explain how chimer assign beta strand?


Best regards.


Smith
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