Hi Paul, Thank you for your response. After examined with density histogram, I realized they do not match. I did the map_to_structure in Phenix following the online tutorial to prepare the EM map before they build the model. Is it necessary to convert into structure factors before building the model? Or I can just use the original centered map? Best, Yangqi
Sent from Mail for Windows 10 From: Paul Emsley Sent: Wednesday, September 26, 2018 6:14 AM To: Yangqi Gu; COOT@JISCMAIL.AC.UK Subject: Re: mtz file not visible in Coot On 26/09/2018 03:59, Yangqi Gu wrote: > I am just beginning to learn Coot and model building. I have a very basic > question to ask. I used Phenix to convert my EM map into mtz file using > map_to_structure command, with h_min=3.4 A. And I tried to examine it in > Coot. However, no matter what I did, I could not see the density of the mtz > file. ( I tried zoom-in and zoom-out, change the map radius). I also tried to > open the original mrc file, I was able to see my density. I am just wondering > what I could do to visualize my map? It is not clear to me what is going wrong. I don't know about map_to_structure and what it produces - if it works like refmac does, it should produce an almost exact replica of the input map, so it is strange that if you can see the map that you can't see the map from the structure factors. Check the map histograms in Map Properties. Do they match? Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
