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[ccp4bb]: CNS: xtal_pdbsubmission.inp



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Hi Everyone:

I'm trying to use CNS's pdb submission (xtal_pdbsubmission.inp).

I can't seem to guess at the correct syntax for....
1) calling things ATOM as opposed to HETATM, and
2) adding chain names

If anyone has an example that works, I'd appreciate if you
could post the appropriate syntax to specify atom_protein 
and chain_1, chain_2, etc.

Some of what I've tried and typical errors are below.

Thanks in advance
diane


----------------------------------------------------------------
For #1 above (atom_protein), the example has 
{===>} atom_protein=(segid "" and not hydrogen);

but that doesn't work.

I've tried....
{===>} atom_protein=(known and not hydrogen);
{===>} atom_protein=(known and not (hydrogen or resname WAT));

Neither works.  No error, just all HETATM's with no ATOM's

----------------------------------------------------------------
For #2 above (chain_1, chain_2), the example has only one 
chain... so no example of syntax for multiple chains.

I have 2 chains with no chain name A or B.  But with residues 
numbered 1-999 and 1001-1999.

I've tried:
{* select atoms chain A *}
{===>} chain_1=(resnum 1 - 999);
{* select atoms chain B *}
{===>} chain_2=(resnum 1001 - 1999);

The error is.........
 %SELRPN-ERR: unbalanced parentheses.
 %SELRPN-ERR: selection has to end with a ")":
       ident (store9) ( ( resnum 1 - 999 
                                     ^^^
 %CNSsolve-ERR: unrecognized command:
       ident (store9) ( ( resnum 1 - 999 
                                     ^^^
I also tried 
{===>} chain_1=(resnum 1 resnum 999);
{===>} chain_1=(resnum 1 - resnum 999);
{===>} chain_1=(resnum 1 to resnum 999);
{===>} chain_1=(resnumber 1 - 999);
{===>} chain_1=(resnumber 1 resnumber 999);
{===>} chain_1=(resnumber 1 - resnumber 999);
{===>} chain_1=(resnumber 1 to resnumber 999);

I also tried removing the ";" because the error
says it should end with a ")", but that gave the
expected errors like these...

 %CNSsolve-ERR: unrecognized command:
 chain_2 
 ^^^^^^^


thanks again
diane

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diane h peapus, phd		dp72@cornell.edu
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