Re: [ccp4bb]: averaging structures

[Jens Kaiser <kaiser@biochem.mpg.de>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

rams@poori.biochem.uiowa.edu wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Hello All,
>
> I remember this question being asked in a different context - but I did
> not find the answer so here I go again!
>
> I managed to solve a structure using an NMR ensamble and Beast.  I also
> manage to do the same with AMoRe (the Navaza version - the ccp4 version
> does not seem to do it).  I cannot seem to get the structure with one
> model - so thats fine.  I think the solution is correct as it is
> significantly higher in cc than the others.  Packs well.  The space group
> could be p4x2x2 and I get clear values for x - i.e., I can solve the
> structure only in p43212. So, I am happy :-)
>
> Trouble starts when I begin to refine.  I have tried refining with refmac
> and one model.  CNS with one model.  dm after rigid body refinement etc..
> and several starting models.  In every case, I end up producing maps that
> are good and bad (I can always see some side chains that show up clearly
> after throwing in a poly Ser model).  So, that gives me confidence.
>
> My data is good only to 2.2A resolution (crappy data to 1.8 available).  I
> have tried warp and resolve too.. Nothing seems to do well.  So, what I
> want to do is simply calculate phases from each one of the NMR models
> and average then "warp style" and calculate maps.  Is there a nice way to
> do it ?
>

most simple thing would be just to calculate Fc and Phi from your placed
model(s) using sfall.
to get rid of END-records wich perhaps are not liked by progs just use 'grep
-v'.
the following script should do what you want (but it is just typed in this
mail, not checked...)
it shows you only what to do.... if you have further questions, dont hesitate
to contact.

cheers

jens

PS.: if you're unsing MAIN, it's no prolem at all, just load everything (also
reflections :-), do an upd_segm) and calculate 2fofc and fofc, to make
comfortobale use of all the menues with an multi-model-file You have to do
some changes in the menues however ...



should be done somhow like this:

#!/bin/csh -f
#file: aver2fofc
#call: aver2fofc <replaced pdpfile> <truncated mtz-file> <name_of_measured_f>
<name_of_measured_sigF>>
#this is not checked! perhaps it works anyway... but the principal way should
be like this:

#produces pdb-file without ENDS..
\rm tmp.allmodel.pdb
grep -v END $1 > tmp.allmodel.pdb


#calc F for all models, will automatically scale them to
#fobs if you read them in ($2)
sfall xyzin tmp.allmodel.pdb hklin $2 hklout aversf.mtz << +
mode sfcalc hklin xyzin
labin FP=$3 SIGFP=$4
labo allin FC=FC PHIC=PHIC
+

#to calculate fofc or fobs-map, change scale F1 2. 0 to F1 1 0 or
additionally
# F2 1 0 to F2 0 0
fft hklin aversf.mtz mapout aver_2fofc_$1:r:t.map << +
labin F1=$3 SIG1=$4 F2=FC PHI=PHIC
scale F1 2 0 F2 1 0
exclude SIG1 2.0
+

mapmask mapin aver_2fofc_$1:r:t.map mapout aver_2fofc_$1:r:t.scal_unit.map <<
+
xyzl 0 1 0 1 0 1
scal sigm
+



>
> Thanks.
>
> Rams.
>
> --
> S. Ramaswamy
> Department of Biochemistry.
> University of Iowa.