Thanks for all the replies folks. Tom When using helices_strands_only=True, would that in Autobuild be different than the automatic helix finding at the end of autosol (with no sequence file) ? Thanks FR On Aug 4, 2008, at 12:03 PM, Thomas C. Terwilliger wrote:

Hi Francis,

I would say that a standard run of autobuild needs a decent map (after density modification) where you can see where a model would be built.

If you have a worse map than that, or low resolution (>3.5 A), then try this keyword:

helices_strands_only=True

in which case autobuild will run a lot faster and just try to build secondary structure in, skipping all the loops and skipping chain extension. It can build helices where you can hardly see them. If you are lucky then the map will get better after this..then you can try feeding the resulting overall_best_denmod_map_coeffs.mtz and overall_best.pdb in to a regular run of autobuild.

Best of luck, -Tom T

...

Hello all

Given a mediocre to bad experimental density map, what hopes does AutoBuild have of building a model? i.e. Should I be able to tell clear helicies and side chain density in the experimental density map before even attempting an autobuild?

Thanks

FR

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D