where are the optimized wxc_scale and wxu_scale when optimize_wxc_scale and optimize_wxu_scale = True?
Hi all I went through the time to optimize_wxc and optimize_wxu to help pull out some density for ligands (i.e. all sequence assigned residues are built). However, it would be nice if the resulting .def was updated with the optimized wxc and wxu. Where are those values? I didn't think for wxc it was scale=XX in the following lines.. r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles= 0.70 scale= 7.00 r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles= 0.96 scale= 8.00 ... etc Refining with the scale= value that phenix ultimately chose didn't work form me (resulted in awful geometry and high r/rfree). 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
HI Francis, currently these values are not preserved - they are re-determined at each macro-cycle. The reason for this is that they can be very different from run to run, however I think I will make it possible to preserve them in the .def file - it's on my list now, so will be available in the future. The fact that the values that you picked up from "scale" did not work may well reflect what I said above: the values may change (sometimes) significantly between the macro-cycles. Pavel. On 8/7/09 8:56 AM, Francis E Reyes wrote:
Hi all
I went through the time to optimize_wxc and optimize_wxu to help pull out some density for ligands (i.e. all sequence assigned residues are built). However, it would be nice if the resulting .def was updated with the optimized wxc and wxu. Where are those values? I didn't think for wxc it was scale=XX in the following lines..
r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles= 0.70 scale= 7.00 r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles= 0.96 scale= 8.00 ... etc
Refining with the scale= value that phenix ultimately chose didn't work form me (resulted in awful geometry and high r/rfree).
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
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participants (2)
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Francis E Reyes -
Pavel Afonine