Re: [ccp4bb] NCS and manual building
MAIN does that for ages (n_molecules->generate_others). Also, the new COOT can
do that (look in the - rather cluttered - treasure
chest 'Extensions'->'NCS'->'Copy NCS chain')
HTH
-j.
On Wednesday 26 November 2008 00:25:12 Prakash Rucktooa wrote:
> Dear Olga,
>
> I have also encountered the same problem. Find below a script which will
> automate the superposition of one protomer onto the others.
>
> Best wishes
>
> Prakash
>
>
> Superposition script :-
>
> #!/usr/bin/tcsh -f
>
> grep -v -E '^END' Aorig.pdb > new.pdb
>
> rm mat1.mat
>
> foreach chain_name ( B C D E F G H I J )
>
> # Superposition of A on chain_name
> superpose Aorig.pdb tot.pdb -s ${chain_name} Aon${chain_name}.pdb | grep
> -A 4 Rx >> mat1.mat
>
> # Changing chain name to ${chain_name}
> pdbset xyzin Aon${chain_name}.pdb xyzout ${chain_name}.pdb < CHAIN $chain_name
> END
> eof
>
> grep -E "^ATOM " ${chain_name}.pdb >> new.pdb
>
> rm Aon${chain_name}.pdb
>
> end
>
> Olga Boudker wrote:
> > Dear all,
> > I am working with a relatively low res. crystal structure with
> > multiple protomers in the asymmetric unit related by NCS. I am
> > currently running rounds manual model building in Coot and refinement
> > using Refmac5. Could anybody suggest a shortcut for the following
> > procedure: I start with an initial model containing all protomers;
> > generate NCS operators for A to B, A to C et c.; rebuild protomer A;
> > use the operators and the rebuilt A to generate all other protomers;
> > and combine them all in a single pdb file. Currently I do all that
> > manually using lsqkab and text edit and it is really painful. Is
> > there an available routine to do this? For various reasons I would
> > like to stick with Refmac5 rather then CNS, in which of course the
> > symmetry would have been easier to implement.
> > Many thanks,
> > Olga
Re: [ccp4bb] NCS and manual building
Olga Boudker wrote: Dear all, I am working with a relatively low res. crystal structure with multiple protomers in the asymmetric unit related by NCS. I am currently running rounds manual model building in Coot and refinement using Refmac5. Could anybody suggest a shortcut for the following procedure: I start with an initial model containing all protomers; generate NCS operators for A to B, A to C et c.; rebuild protomer A; use the operators and the rebuilt A to generate all other protomers; and combine them all in a single pdb file. Currently I do all that manually using lsqkab and text edit and it is really painful. Is there an available routine to do this? For various reasons I would like to stick with Refmac5 rather then CNS, in which of course the symmetry would have been easier to implement. Many thanks, Olga Coot has tools to do this.. Fit your rebuilt A chain back over B C etc, change the chain ID appropriately and write it out. You need to reassemble the whole agin but it does the standard superpositions.. Eleanor
Re: [ccp4bb] NCS and manual building
Dear Olga,
I have also encountered the same problem. Find below a script which will
automate the superposition of one protomer onto the others.
Best wishes
Prakash
Superposition script :-
#!/usr/bin/tcsh -f
grep -v -E '^END' Aorig.pdb > new.pdb
rm mat1.mat
foreach chain_name ( B C D E F G H I J )
# Superposition of A on chain_name
superpose Aorig.pdb tot.pdb -s ${chain_name} Aon${chain_name}.pdb | grep
-A 4 Rx >> mat1.mat
# Changing chain name to ${chain_name}
pdbset xyzin Aon${chain_name}.pdb xyzout ${chain_name}.pdb <> new.pdb
rm Aon${chain_name}.pdb
end
Olga Boudker wrote:
Dear all,
I am working with a relatively low res. crystal structure with
multiple protomers in the asymmetric unit related by NCS. I am
currently running rounds manual model building in Coot and refinement
using Refmac5. Could anybody suggest a shortcut for the following
procedure: I start with an initial model containing all protomers;
generate NCS operators for A to B, A to C et c.; rebuild protomer A;
use the operators and the rebuilt A to generate all other protomers;
and combine them all in a single pdb file. Currently I do all that
manually using lsqkab and text edit and it is really painful. Is
there an available routine to do this? For various reasons I would
like to stick with Refmac5 rather then CNS, in which of course the
symmetry would have been easier to implement.
Many thanks,
Olga
--
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Netherlands Cancer Institute
Plesmanlaan 121
1066CX Amsterdam
The Netherlands
Office : +31(0)205121957
Mobile : +31(0)634454024
e-mail : [EMAIL PROTECTED]
_
Re: [ccp4bb] NCS and manual building
Use Coot option 1) rebuild your chain A and superimpose manually with Coot A to the other chains, then write out a new merged PDB file option 2) use the Coot command which allows you to copy whatever you have modeled in one chain to the other chains. for more info check out the link: http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC136 option3) since your NCS operators won't change by much you can generate a script using Moleman - but option 1+2 are easier Jürgen On 25 Nov 2008, at 11:18, Olga Boudker wrote: Dear all, I am working with a relatively low res. crystal structure with multiple protomers in the asymmetric unit related by NCS. I am currently running rounds manual model building in Coot and refinement using Refmac5. Could anybody suggest a shortcut for the following procedure: I start with an initial model containing all protomers; generate NCS operators for A to B, A to C et c.; rebuild protomer A; use the operators and the rebuilt A to generate all other protomers; and combine them all in a single pdb file. Currently I do all that manually using lsqkab and text edit and it is really painful. Is there an available routine to do this? For various reasons I would like to stick with Refmac5 rather then CNS, in which of course the symmetry would have been easier to implement. Many thanks, Olga -- - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
[ccp4bb] NCS and manual building
Dear all, I am working with a relatively low res. crystal structure with multiple protomers in the asymmetric unit related by NCS. I am currently running rounds manual model building in Coot and refinement using Refmac5. Could anybody suggest a shortcut for the following procedure: I start with an initial model containing all protomers; generate NCS operators for A to B, A to C et c.; rebuild protomer A; use the operators and the rebuilt A to generate all other protomers; and combine them all in a single pdb file. Currently I do all that manually using lsqkab and text edit and it is really painful. Is there an available routine to do this? For various reasons I would like to stick with Refmac5 rather then CNS, in which of course the symmetry would have been easier to implement. Many thanks, Olga --
