Hi Rohit,
You should make sure that the LLP has the correct chainID and residue number in COOT. When that is sorted, COOT will treat it correctly. You may need to save and reload your model. You should not need to add any LINK records to your PDB file because the CCP4 dictionary correctly defines LLP as 'peptide'. This also means that Refmac will treat your residue correctly.
If this doesn't work, you may need to open the PDB file in a text editor to move the LLP atoms between the atoms of the previous and next residue.
Cheers,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> rohit kumar
> Sent: Thursday, February 11, 2016 15:45
> To: [log in to unmask]
> Subject: [ccp4bb] PLP to LLP
>
> Dear all,
>
> I want to convert my PLP into LLP.
>
> When I replace PLP to LLP in coot it does not fit well after single round of
> refinement and also I am unable to joint LLP to the main chain.
>
> However, in coot PLP and Lys are interacting is clearly seen.
>
> Can the PDB depositor do this?
>
> Thanks in advance
>
>
>
>
>
>
>
>
> --
>
> WITH REGARDS
> Rohit Kumar Singh
> Lab. no. 430,
> P.I. Dr. S. Gourinath,
> School of Life Sciences,
> Jawaharlal Nehru University
> New Delhi -110067
|