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]

****************************************************************

On May 8, 2014, at 11:13 AM, Pavel Afonine <[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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