[ccp4bb] AW: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Herman . Schreuder
Deav Kavya, The acetate is probably conformationally disordered. I would examine the electron density maps to see if there might be an alternative orientation. If so, you could model this and with occupancies around 0.5 your validation problem would be solved and your model would probably be cl

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
On 05/27/2013 12:14 PM, Kavyashree Manjunath wrote: Later I tried with 0.8, 0.99 for which the map was normal and also validation did not report it as short contact. Is it ok if I give 0.99 occupancy? "Validation" most likely will not report any short contacts if occupancy is <1. If the distanc

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Kavyashree Manjunath
Sir, Ok yes. I tried with 0.5 occupancy, ended up getting positive density around acetate on both sides equally. Later I tried with 0.8, 0.99 for which the map was normal and also validation did not report it as short contact. Is it ok if I give 0.99 occupancy? Thank you Regards Kavya > > It doe

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
On 05/27/2013 11:27 AM, ka...@ssl.serc.iisc.in wrote: Sir, Ok. It is an acetate ion which interacts with its symmetry equivalent ion only one of its oxygen atoms is closer to its symmetry equivalent and not the entire ion. So do I need to give lower occupancy for this ion? Thank you Regards Kav

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Kavyashree Manjunath
Sir, Ok. It is an acetate ion which interacts with its symmetry equivalent ion only one of its oxygen atoms is closer to its symmetry equivalent and not the entire ion. So do I need to give lower occupancy for this ion? Thank you Regards Kavya > It is probably a wrong question to ask here. Pret

Re: [ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Ed Pozharski
It is probably a wrong question to ask here. Pretty much everything is "tolerated" by PDB during deposition, the report you get is an advice, not instruction. I wonder whether anyone has an example of the RCSB/PDBe/PDBj ever turning down submitted structure. The right question is whether the

[ccp4bb] Short contact between symmetry equivalents

2013-05-27 Thread Kavyashree Manjunath
Dear users, Is short contact (1.83Ang) between an atom and symmetry equivalent of itself tolerated during deposition? I am not able to get rid of this short contact appearing after refinement. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by Ma