[phenixbb] FEM mtz won't open in coot

R.M. Garavito garavito at msu.edu
Thu May 8 08:38:51 PDT 2014


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:  garavito at msu.edu
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On May 8, 2014, at 11:13 AM, Pavel Afonine <pafonine at lbl.gov> 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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