MRC map as molecular replacement model
Hi all, I want to use an MRC map obtained by low resolution EM reconstruction, as molecular replacement model in Phaser. I serached the phenixbb archives and learned that I should us phenix.map_to_structure_factors to convert the map file to mtz so it can be input into Phaser. When I do that I get an error "Sorry: Map must have origin at (0,0,0): recenter the map and try again". I have two questions? 1) What tool should I use to recenter the map and 2) Is there a better way to do this? Thanks in advance for your replies. Best regards, Priyamvada
Hi Priyamvada, We just changed map_to_structure_factors so that it no longer has this limitation. If you download a nightly build from today onward it should work. Let us know if not! All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Acharya, Priyamvada (NIH/VRC) [C] [[email protected]] Sent: Sunday, October 11, 2015 4:35 PM To: [email protected] Subject: [phenixbb] MRC map as molecular replacement model Hi all, I want to use an MRC map obtained by low resolution EM reconstruction, as molecular replacement model in Phaser. I serached the phenixbb archives and learned that I should us phenix.map_to_structure_factors to convert the map file to mtz so it can be input into Phaser. When I do that I get an error "Sorry: Map must have origin at (0,0,0): recenter the map and try again". I have two questions? 1) What tool should I use to recenter the map and 2) Is there a better way to do this? Thanks in advance for your replies. Best regards, Priyamvada
Dear Developers, I have two different questions. 1. I noticed the option main.ncs=True is no longer supported in the latest version (1.10.1-2155). Is it true that this option will be replaced by ncs_search.enabled=True from now on? 2. I noticed the phenix.ready_set can add hydrogens to waters. How are the hydrogens added to the O atoms? by the H-bonding direction? How accurate is it if the density is not observable? Thanks you so much in advance. Regards, Huanwang
Dear Huanwang, 1. I noticed the option main.ncs=True is no longer supported in the latest
version (1.10.1-2155). Is it true that this option will be replaced by ncs_search.enabled=True from now on?
Yes, this is just rearrangement of options. The underlying functionality is (almost) the same.
2. I noticed the phenix.ready_set can add hydrogens to waters. How are the hydrogens added to the O atoms? by the H-bonding direction? How accurate is it if the density is not observable?
Hopefully somebody else is more knowledgeable about this question. Best regards, Oleg Sobolev.
Thanks you so much in advance.
Regards, Huanwang _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
Hi Huanwan,
2. I noticed the phenix.ready_set can add hydrogens to waters. How are the hydrogens added to the O atoms? by the H-bonding direction? How accurate is it if the density is not observable?
positions of added H are optimized to have idealized h-o-h geometry and least clashes with surrounding atoms. It's purely geometric, no density involved. Pavel
participants (5)
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Acharya, Priyamvada (NIH/VRC) [C] -
Huanwang Yang -
Oleg Sobolev -
Pavel Afonine -
Terwilliger, Thomas Charles