As I understood the problem, it is that automatic assignment comes out
differently for different structures of the same protein or proteins so close
that they should have the same secondary structure, due to differences in
quality of the structures. The question then is not how to determine secondary
structure more accurately, but how to override automatic secondary structure in
the graphics program and assign secondary structure from the best structure to
all the others.
And the answer may be in the wording of the question: "assign secondary structure to
the PDB file" (emphasis on FILE). If the PDB file has HELIX and SHEET records I
believe most applications will respect them rather than re-determining secondary
structure. So if you have a high resolution structure file that has helix and sheet
records, copy them to the other structures. If their is only one structure that is
getting assigned differently in different applications, check if it has HELIX and SHEET
records, and if not edit them in according to your best idea of the secondary structure.
On 01/30/2017 04:08 AM, Tim Gruene wrote:
Dear J. Vitali,
there are tools that have been mentioned by others, that assist with the
assignment. The final decision depends on you as researcher. You should
visually check the hydrogen bonding whether the boundaries are consistent with
the automated assignment.
People often seem to think that secondary structure is program driven, but
it's your structure that provides that data, and the researcher to make the
final decision.
Kind regards,
Tim
On Sunday 29 January 2017 11:41:49 AM chemocev marker wrote:
Hi
Is there any tool that can assign secondary structure to the PDB file. The
problem is if I used different modelling tools, there are regions in the
protein which does not remain consistent and looks different in different
application.
best
J. Vitali
