RE: stepwise top

[Michael Buck <>]

This might help:  use this as a shell script replace $i with model
name.  This will find the best three models and move them into a
directory best3 and superimpose them.  It will also move the best
model into directory best1.  You will just need to replace the
impose section with loop modeling and add the 4th and 5th models.




>>>>

grep OBJECTIVE $i.B9999????|cut -d':'
-f1   > temp1      
grep OBJECTIVE $i.B9999????|cut -d' ' -f10  > temp2 

paste temp1 temp2 >temp3
sort -n +1 temp3 >temp4
sed -n '1,3w temp5' temp4 
cut -f1 temp5 >temp6
sed -n '1w temp6a' temp6
sed -n '2w temp6b' temp6
sed -n '3w temp6c' temp6
read SEQ1 < temp6a
read SEQ2 < temp6b
read SEQ3 < temp6c
echo $SEQ1
echo $SEQ2
echo $SEQ3
cp $SEQ1 best1/$i.pdb
echo "Finished"
rm temp1 temp2 temp3 temp4 temp5 temp6 temp6a temp6b temp6c
echo "#Superimpose models

SET ATOM_FILES = '$SEQ1' '$SEQ2' '$SEQ3' 

SET WRITE_FIT = ON
MALIGN3D" > impose$i.top
mod4 impose$i.top
cp $SEQ1 $SEQ2 $SEQ3 best3
cp $i.imposed impbest3
<<<<<<




At 09:19 AM 1/10/02 -0500, Andrej Sali wrote: 

> Yes,
> but it would require running a unix script out of the top file to do the
> sorting and file renaming.
>
>  
>
> Andrej
>
>  
>
> -----Original Message-----
> From: 
> [" eudora="autourl">mailto:]
> On Behalf Of Dan Thomas Major
> Sent: Thursday, January 10, 2002 6:53 AM
> To: modeller_usage
> Subject: stepwise top
>
>  
>
> Hi, 
> Is it possible in a modeller top file to calculate, let's say 100 models,
> and then tell modeller to refine the best 10 and then to add loops for
> the best 5 (all in one run). 
> Thanks, 
> Dan 
>
> --
>
> Dan Thomas Major (at Dr. B. Fischer's lab)
>
> Bar-Ilan University 
>
> Ramat-Gan, Israel
>
>

************************************************

Michael Buck

NCSU Genetics

Phone  (919)515-5759

Fax        (919)515-3355        

http://www4.ncsu.edu/~mjbuck

*************************************************