Dear Hailiang, While apparently no response came, here my 2 cents: Even if there would be an automatic utitility to generate links based on distances, I would never use it. Either the sugars have been properly refined and then the link cards are present in the pdb file, or the sugars have been fitted manually and may have been real space refined in coot or some other model-building program. In this case, the sugar positions are likely off, since sugars are very often rather disordered and have poor electron density. In this case distance-based link generators very likely will make wrong connections. I just cut and paste link cards from an other pdb file and manually edit them. I eagerly await the moment there will be a create link option in coot, where you just click on the two atoms to be linked and the link card gets generated.
Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hailiang Zhang Sent: Wednesday, March 09, 2011 1:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Automatic LINK generation Hi there, I am trying to build the LINK information in PDB header for sugar-containing protein, and I am wondering whether there is some utility in CCP4 (or any others) can do it automatically (eg by measuring inter-sugar distances). Thanks in advance! Best Regards, Hailiang
