[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
>>>
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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