[phenixbb] Incorrect secondary structure assignment in a .pdb

Pavel Afonine pafonine at lbl.gov
Thu Jun 28 13:23:23 PDT 2018

> Nothing changes when I run phenix real space refinement with SS 
> restraints turned on. I can either input a .pdb file with correct SS 
> information in the header or a .pdb file with no SS information at all 
> and the end result (new refined .pdb) is the same file with the same 
> SS information in a new header. The information stays the same and 
> 'correct'.

Did you actually enable using SS restraints in refinement? Just 
providing HELIX/SHEET records in input PDB is NOT sufficient, you 
actually need to tell the program to use them!
If you did tell the program to use SS restraints (as it seems the case!) 
and still there is no effect, then please send us all files and we will 
Check the log file -- does it say anything about using SS restraints? It 
should be very verbose about it.

> The main problem in my original question is that when I (or the pdb 
> extract tool that converts a .pdb file to a .cif file for submission 
> to PDB) remove the header SS information altogether (why you would do 
> that for PDB deposition is unknown to me), that resulting .pdb file 
> still shows SS elements in different pdb viewers but SS info is no 
> longer correct. How can you have SS elements displayed if it 
> description is missing from the header?

You should not remove HELIX/SHEET records from PDB file yourself.
Phenix tools will not remove HELIX/SHEET records from PDB (if you find a 
tools that does it, please send us a bug report).
We can't control what other (non-Phenix) software do.


More information about the phenixbb mailing list