?Hi, I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be appreciated. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031
Hi Reza,
Yes, I'm sorry about that. The current nightly build fixes one clipping
issue (wrong boxing done by default). If that doesn't work, please let me
know and I'll try to help.
Another option is to box your map before running resolve_cryo_em and then
specify "box_before_analysis=False" and then you can control the clipping
yourself. (You can use map_box to do this)
All the best,
Tom T
On Sun, Aug 23, 2020 at 4:13 PM Reza Khayat
Hi,
I'm running into a clipping issue with phenix.resolve_cryo_em. The program seems to be improving the map; however, portions of the map get clipped. Any suggestion would be appreciated.
Best wishes, Reza
Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010
Hi Tom,
Thanks for the help. I fixed the problem by assigning model_1= to a structure that was refined into the original cryo-EM map.
The nightly build (Aug 24th dev-3965) does not read the sequence file. It errors with sequence file not found.
Best wishes,
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and Biochemistry
New York, NY 10031
________________________________
From: Tom Terwilliger
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