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
