Hello everyone, 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 It then halts at an error... Any Ideas?
It is really easy to fix I believe... The issue is I am running the GUI with several non-default options. It writes the scripts automatically, I do not understand why it is trying to pick them in a way that crashes it. Yuri On Thu, 14 Jul 2011 13:25:36 -0400, Phil Jeffrey wrote:
Unless I'm missing something really subtle, change:
(chain 'A' and segid ' ' and resseq 393:6) to (chain 'A' and segid ' ' and resseq 6:393) ^^^^^^^^^^^^
Phil Jeffrey Princeton
-- Yuri Pompeu
On Thu, Jul 14, 2011 at 10:35 AM, Yuri
It is really easy to fix I believe... The issue is I am running the GUI with several non-default options. It writes the scripts automatically, I do not understand why it is trying to pick them in a way that crashes it.
I forgot to convert the residue numbers to integers - as strings, "393" is less than "6", so the order ends up wrong. It'll be fixed in the next build, hopefully - if you are willing to send me the PDB file *OFF-LIST* (I don't need data, just the model) I will make sure what I'm doing works. thanks, Nat
On Thu, Jul 14, 2011 at 10:22 AM, Yuri
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.) -Nat
participants (3)
-
Nathaniel Echols -
Phil Jeffrey -
Yuri