Dear all, Thank you for the replies
I am using Coot 0.7. I went to "Extensions" then "Modelling" "Add other solvent molecules". There was no cacodylate under Solvent Ligands so I added a new residue type: CAC. This wouldn't stay where I put it. I also just tried Lothar's advice and generated CAC.cif and CAC.pdb using phenix.elbow. I used these as inputs in LigandFit and the cacodylate ions were fitted in 2 out of the 3 locations. However, after refinement the cacodylates fell apart again, i.e. As is not connected to any of the 4 components. I am trying the get monomer option as Herman suggests. Thank you very much for your help Best Regards, Oarabile M. Kgosisejo [email protected] ________________________________ From: CCP4 bulletin board [[email protected]] on behalf of [email protected] [[email protected]] Sent: October 27, 2014 2:29 AM To: [email protected] Subject: [ccp4bb] AW: Cacodylate won't stay in place Dear Oarabile, As Paul said, without any details it is hard to figure out what might be going on. Where did the cacodylate come from? Was it present in the starting pdb, did you create it yourself, or did you import it in Coot with the get monomer option? If you did not use the get monomer option, that would be the first thing to try. Delete the cacodylate present and use get monomer. That way you are sure that the nomenclature of the atoms is correct and that the cif file for cacodylate is loaded. Without cif file, the structure will explode, but in this case I would expect that Coot would not refine and produce an error message. Best, Herman Von: CCP4 bulletin board [mailto:[email protected]] Im Auftrag von Kgosisejo, Oarabile Gesendet: Samstag, 25. Oktober 2014 20:51 An: [email protected] Betreff: [ccp4bb] Cacodylate won't stay in place Hello all, I am trying to fit cacodylate ion in my model using Coot but it does not stay where I put it. The molecule breaks apart and some of its components attach to the peptide residues. Due to this, phenix.refine would not accept this as the input for refinement. Is there a way I can make cacodylate ion stay in its electron density and refine my structure with cacodylate ion? I appreciate your help! Best Regards, Oarabile M. Kgosisejo [email protected]<mailto:[email protected]>
