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:[email protected] mailto:[email protected]/

/****************************************************************/

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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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

/****************************************************************/

/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] mailto:[email protected]/

/****************************************************************/

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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