[phenixbb] FEM mtz won't open in coot

Pavel Afonine pafonine at lbl.gov
Thu May 8 09:28:17 PDT 2014


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) 355-9724Lab:(517) 353-9125/
>
> /FAX:(517) 353-9334Email:garavito at msu.edu <mailto:garavito at msu.edu>/
>
> /****************************************************************/
>
>
>
>
> On May 8, 2014, at 11:13 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto: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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>>
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