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Dear Curt,
did I understand you correctly, that your molecule consists of ONE alanine,
only? This would explain your difficulties with BATON: it immediately comes to
the end of your molecule and tries to do 'lego_auto_mc' and 'lego_auto_sc'.
What you have to do is the following:
1). create an O-datablock containing the residue types of your sequence or
create a dummy-O-datablock with an arbitrary number of alanines (Fortran code
appended). Your mol name is, say, NEW1.
2). within O read this data block and make space for the atoms of your sequence
with the command 'sam_init_db NEW1'
3). now make an object for BATON with 'mol di ca ; end' and a CA-object for
your molecule NEW1 with 'mol new1 obj ca ca ; end'. Of course, at your very
start nothing will appear on the screen. It is a good idea to display your
whole molecule as well, to see your main chain and side chain atoms later, with
'mol new1 obj new1 z ; end'
4). for chain tracing with BATON pick a centre on your bones where you think
you want to start and invoke 'baton': the baton stick will appear with its red
end at your screen centre
5). go along your skeleton and accept your CAs with 'yes' as far as you dare,
then click 'no' and see what happens. (Your CA-trace will probably show long
connections to 'infinity' which could be removed by redrawing the CA-object.)
Good luck,
Dirk.
--
*****************************************************************
* Dirk Kostrewa | e-mail: dirk.kostrewa@roche.com *
* Hoffmann-La Roche Ltd. | tel: +41-61-688 7750 *
* PRPS-X B65/R312 | fax: +41-61-688 7408 *
* CH-4070 Basel, Switzerland | *
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X-Zm-Content-Name: poly_ala.f
c dk 10/92
c
c Program creates a poly-ala residue_type file, which can be read by "O" with
c the read_formatted command.
c
character filout*72,mol*5
write (6,'(a,$)') 'Enter number of alanines : '
read (5,*) num
write (6,'(a,$)') 'Enter mol name for O (a5): '
read (5,'(a)') mol
do i=1,5
if (mol(i:i).ne.' ') len=len+1
end do
write (6,'(a,$)') 'Enter output file name: '
read (5,'(a)') filout
open (1,file=filout,status='new',carriagecontrol='list')
write (1,'(2a,7x,i4,a)') mol(1:len),'_RESIDUE_TYPE C',
+ num,' (1x,5a)'
write (1,'(1x,5a)') ( 'ALA ', i=1,num)
stop
end
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