[phenixbb] Parsing error

Nathaniel Echols nechols at lbl.gov
Thu Jul 14 10:29:29 PDT 2011

On Thu, Jul 14, 2011 at 10:22 AM, Yuri <yuri.pompeu at ufl.edu> wrote:
> I cannot figure out why I keep getting this error. I dont see anything wrong
> with my PDB.
> I realize I realize I have breaks in my chain, as there are regions of
> unclear density as of now I am building in what I can see...
> Heres what the log says:
> ========
> ================= Separating polymer chains into rigid bodies
> =================
>  (chain 'A' and segid '    ' and resseq 393:6)
>  (chain 'B' and segid 'B   ' and resseq 401:401)
> ================== Extract refinement strategy and selections
> =================
> The error is initial RESSEQ index > final RESSEQ index.
> I do not understand why it is picking them this way

Which version are you using?  I thought I already fixed this bug
recently, but on second thought, I may have forgotten an essential
step.  (Phil's suggestion is correct, but the current code is supposed
to do this for you.)

You can fix this by defining the rigid bodies yourself - the default
behavior is to automatically make each chain a rigid group, but since
we can't assume unique chain IDs, the code will use residue ranges as
well.  (This is new in the nightly builds; previously the entire
structure was treated as a single group.)


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