Re: [phenixbb] FEM mtz won't open in coot

8 May 2014

      Hi Parker,

can you please send me inputs so I can do comparisons myself and provide 
comments?

Usually, if FEM shows no density in places where there is density in the 
original map, that missing density is either noise or model bias. So it 
may not be a bad thing that you don't see it. This is all I can say 
without looking at actual data, model and maps.

Again, if you send me model and data, then I will provide detailed comments.

Pavel

On 5/8/14, 11:38 AM, de Waal, Parker wrote:
...
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
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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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