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
