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 <[email protected]>
Sent: Sunday, August 23, 2020 7:31 PM
To: Reza Khayat
Cc: PHENIX user mailing list; Tom Terwilliger
Subject: [EXTERNAL] Re: [phenixbb] phenix.resolve_cryo_em
 
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 <[email protected]> wrote:

​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
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
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