Thank you everyone for the input! Using the manual loading method I was able to view the new FEM map.
Unfortunately it appears that FEM map is slightly worse than my original map and is missing density in some areas. Has anyone encountered this before?
Best,
Parker
From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine
Sent: Thursday, May 08, 2014 12:28 PM
To: R.M. Garavito; [email protected]
Subject: Re: [phenixbb] FEM mtz won't open in coot
Thanks Michael,
correct, as discussed this morning, auto-open in Coot will not work for FEM maps, you need to load them manually. Thanks for feedback!
Pavel
On 5/8/14, 8:38 AM, R.M. Garavito wrote:
Pavel,
Just to let you know, the auto-open function works fine on the FEM mtz in the Mac version. Makes a nice looking map which I am looking at now in the context of earlier maps.
Michael
****************************************************************
R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office: (517) 355-9724 Lab: (517) 353-9125
FAX: (517) 353-9334 Email: [email protected]mailto:[email protected]
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On May 8, 2014, at 11:13 AM, Pavel Afonine mailto:[email protected]> wrote:
Hi Parker,
this requires loading map manually (not using auto-open, as Nat pointed out):
Start Coot ->
File ->
Open MTZ, mmCIF, fcf or phs ->
Choose file fem.mtz or whatever you called it, hit Open ->
In popped menu "Column Label Assignment" choose:
Amplitudes: FEM
Phases: PHIFEM
-> hit OK
Contouring at 1sigma is universally good. Going down to 0 should not change the appearance much.
Pavel
On 5/8/14, 8:01 AM, de Waal, Parker wrote:
Hello Everyone,
I'm having trouble opening the map file generated by phenix.fem in coot. Each time I try and load the .mtz file the follow error occurs 'Failed to find any suitable F/phi columns in the MTZ file'.
Dumping the mtz file I can see:
Col Sort Min Max Num % Mean Mean Resolution Type Column
num order Missing complete abs. Low High label
1 NONE 0 33 0 100.00 12.1 12.1 114.15 3.31 H H
2 NONE 0 33 0 100.00 12.8 12.8 114.15 3.31 H K
3 NONE 0 137 0 100.00 51.4 51.4 114.15 3.31 H L
4 NONE 0.0 10551.1 22963 71.24 406.13 406.13 39.60 3.31 F 2mFoDFc
5 NONE -180.0 180.0 22963 71.24 0.98 89.81 39.60 3.31 P PHI2mFoDFc
6 NONE 5.2 51589.8 0 100.00 1602.72 1602.72 114.15 3.31 F FEM
7 NONE -180.0 180.0 0 100.00 0.32 89.74 114.15 3.31 P PHIFEM
If someone could help me to rename these columns to a coot friendly format so that I would be greatly appreciative.
Best,
Parker
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