[phenixbb] FEM mtz won't open in coot

Pavel Afonine pafonine at lbl.gov
Thu May 8 11:42:45 PDT 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:*phenixbb-bounces at phenix-online.org 
> [mailto:phenixbb-bounces at phenix-online.org] *On Behalf Of *Pavel Afonine
> *Sent:* Thursday, May 08, 2014 12:28 PM
> *To:* R.M. Garavito; phenixbb at phenix-online.org
> *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: ////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  <mailto:phenixbb at phenix-online.org>
>
>         http://phenix-online.org/mailman/listinfo/phenixbb  <http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb>
>
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
>     <http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb>
>
>
>
>
>     _______________________________________________
>
>     phenixbb mailing list
>
>     phenixbb at phenix-online.org  <mailto:phenixbb at phenix-online.org>
>
>     http://phenix-online.org/mailman/listinfo/phenixbb  <http://scanmail.trustwave.com/?c=129&d=t7Dr0wtxwUOeqd4xYqDpSfgkuCoj8ZQxnCe0qvjCOQ&u=http%3a%2f%2fphenix-online%2eorg%2fmailman%2flistinfo%2fphenixbb>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140508/cfdf0d8a/attachment.htm>


More information about the phenixbb mailing list