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Re: [ccp4bb]: Error in Protin



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> The protein chain has a break with a few missing residues.  As I do
> protin (ccp4 v. 3.5), I get the following error:
> 
>         "PROTIN:  Check above for ***ERROR messages"
> 
> The error messages are
> 1)      "**** ERROR ****
>         Atom Name OT   Given for Residue No. 114 is not among those in the
>         standard table for the ALA  Group.  ATOM OMITTED."
>         - for both chains
> 
> 2)      "***ERROR: No atoms used for this Non-crystallographic symmetry"
>         - for the second chain.
> 
> The questions are:
> 
> 1) Why do I get the 1st error? I tried both OXT and OT1 card for the 114th
> (last residue).  But still the error.

You should include your protin command file so we can try to help your.
Anyway, if you use the latest ccp4 version, with the latest refmac5, you
will be able to skip the protin step... things will be much simpler !
This error most likely occur because of some problems with the
definition of the Cter residue. If your protein starts with residue Ser
15 and ends with residue Ala 114 (for example), with two copies in the
asu with chain ID A and B :
CHHNAM ID A CHNTYP 1
CHHNAM ID B CHNTYP 1
CHNTYP 1 NTER 15 SER 3 CTER 114 ALA 2

and then your NONX keywords.


> 
> 2) I gave the NONX card for NCS restraint but still I get error (2) as
> above.

I thinks this occurs because some atoms of chain A are related to
missing parts in chain B. eg residue 100 in chain A is built but not in
chain B, but your NONX keywords  tells protin that residue 100 A is
related to 100 B.

Again, including your command file would help !


hope this helps

laurent-- 


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Laurent Maveyraud               
Groupe de Cristallographie Biologique  -  IPBS-CNRS

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