[phenixbb] Problem with Autobuild

Claudia Scotti claudiascotti at hotmail.com
Wed Mar 31 00:37:36 PDT 2010

Dear List,
Sorry fo r the easy question, but I have a problem with Autobuild. 


I'm trying to rebuild a scFv, composed of two domains linked by a linker. 


I've managed to find an MR solution with a polyalanine model deprived of the loops, which is my starting model for rebuilding.


I've given Autobuild three input files: the mtz, the model coordinates and the sequence of the scFv, asking to model only the beta strands and helices.


Problem is that in the final model Autobuild seems to guess incorrectly the density of two beta-strands, inserting the linker there instead of the expected side chains.


Any suggestions on how to correct this? Shall I manually rebuild this part to avoid problems? Or is it crucial to prevent errors, for example, that the model and the sequence are numbered so that they are in register?


Thanks in advance,




Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673

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