UNL is for unknown ligand, while UNX is for unknown atom/ion.
And as Robbie said, UNK implies an amino acid of unknown identity.
http://www.wwpdb.org/documentation/format32/sect4.html
On 2/5/14, 1:38 PM, Robbie Joosten wrote:
Just to add to Matthew's good advice, UNK is the standard residue name
for unidentified amino acids. Using it for your compound may cause
conflicts in other programs such as COOT.
Cheers,
Robbie
Sent from my Windows Phone
------------------------------------------------------------------------
Van: Matthew Franklin
Verzonden: 5-2-2014 17:50
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: Re: [ccp4bb] no link_id
Hi Ronnie -
Refmac has done the job for you (or for your friend). The Refmac log
file says that Refmac has created a file called ????.cif (the exact
name varies). You should open up that file and inspect it; it will be
Refmac's best guess about the geometry of that link. I usually
specify only bond lengths and bond angles, leaving torsion angles
undefined (i.e. deleting those restraints) unless I know it should be
restrained to a certain angle.
The next time you run Refmac, use the "Library file" input line in
ccp4i to feed it this cif file; refinement should proceed OK after
this. You can also append the contents of the cif file that Refmac
made to your drug.cif file. Just cut and paste with a text editor.
Don't forget that you need to give your ligand a real 3-letter code,
not just "UNK", before depositing it. So you might as well do it
now. (Even if the structure will remain private, not deposited, I
would still change the code.)
- Matt
On 2/5/14 10:59 AM, Ronnie wrote:
I am asking this question on behalf of a friend: -Thanks!
Hi All - I am working at small biotech. We have minimal budget for
software, only CCP4 and Coot. We have a ligand that binds covalently
to cysteine. I define the parameter file using Prodrg in CCP4 to get
drug.cif file and then make a link in Coot between the Cys and the
Drug. The problem is Refmac keeps complaining that there is no
link_id for this bond:
I am reading library. Please wait.
mon_lib.cif
WARNING : link: CYS<-->UNK is without link_id
link will be created with covalent bond only. Bond= 1.610
WARNING : description of link:CYS-UNK is not in the dictionary
link will be created with bond_length = 1.610
Where do I specify this link_id, and where can I find an example for
the correct syntax? Is this done in mon_lib.cif or the drug.cif
file?? The bond length, if I'm not mistaken should be ~1.82 A for
distance between carbon and sulfur.
Thanks for any help.
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
