[phenixbb] Converting .mtz to xplor or having phenix output to xplor file

[Young-Jin Cho]

When I did phenix run, it made .map files that were not readable in my Pymol. I don't know this is the case for everybody. However, once I changed .map to .xplor, there was no problem.

Another follow up questions is how you can make difference map with positive and negative density maps showed up separately or together in Pymol as we see on the coot.

Thanks in advance,

YoungJin
 
----- Original Message -----
From: "Pavel Afonine" <PAfonine at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Tuesday, October 27, 2009 10:25:29 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Converting .mtz to xplor or having phenix output to xplor file


Hi Sam, 

two ways: 

- ask phenix.refine to output X-plor formatted map. For example, to run phenix.refine just to compute the map: 

phenix.refine model.pdb data.mtz main.number_of_mac=1 strategy=none write_maps=true 

- use "Create maps" option from main PHENIX GUI that will alow you to compute any map. 

Pavel. 



On 10/27/09 2:28 PM, Sam Stampfer wrote: 

Hi, 

This isn't exactly phenix-related but someone might know an easy solution. I'm trying to open an electron density map in pymol. It won't open .mtz files and the .xplor files I generated from ccp4i don't seem to work either. I need to have my density as a .xplor file in order for pymol to open it (I think). How would I generate a .xplor file from .mtz? Or, alternately, how can I set phenix to output a .xplor file? I've had it output to a cns file instead of .mtz but that didn't help me get it in .xplor format. 

Thanks! 
-Sam 

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