I dont think that isnt the correct format for a LINKR record.
LINKR C LEU A -1 N CYG A 0 LEU-CYG
LINKR C2 CYG A 0 N SER A 2
CYG-SER
It is like this - it points to a named LINK entry in your restraints
library eg LEU-CYGun refmac with "Review restraints" option from the GUI
it will create such an entry for you. You can then check whether you
agree with t he chemistry imposed.
Eleanor
If you r
On 12/02/2010 08:59 AM, Paul Emsley wrote:
> On 02/12/10 06:49, Dr. STEPHEN SIN-YIN, CHUI wrote:
>> Dear All,
>>
>> Please see the maps for the ASN residues of the protein, As suggested by
>> colleague, they are NAG which are connected to the N atom of ASN413& ASN611.
>> I put the NAG molecule to those density and try to use the following command
>> line in PDB,
>>
>> LINKR C1 NAG A1003 ND2 ASN A 611 1555 1555 1.45
>>
>> but after restrained refinement using REFMAC5 (quite latest version), the bond
>> distance between N of ASN and C1 of NAG seems to be off (1.28 A) from the value
>> I set for this restraint.
>>
>> My question is related to the true command of bond restraint for this
>> situation?
>> Also if I want to show a "link or line" between N atom of the ASN and C1 atom of
>> NAG in COOT, any idea how to do this?
>>
>
> The distance is controlled by the Refmac restraints library,
> specifically (in this case) the NAG-ASN bond (found in
> lib/data/monomers/list/mon_lib_list.cif). If you look at
> data_link_NAG-ASN you will see that the ideal distance is 1.439. You can
> tighten the restraint by adjusting the bond_value_dist_esd (although I
> would not recommend this).
>
> If you want to see it in Coot you should use a LINK line - careful with
> the formating. I believe that recent pre-release builds will display a
> (compatibly/correctly formatted) LINKR line too.
>
> Paul.
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