Re: [ccp4bb] Short contact between symmetry equivalents
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 distance between atoms is still ~1.8A, you have a problem. Perhaps it is not an acetate. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Short contact between symmetry equivalents
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 does not interact - you cannot have 1.8A distance between atoms. > Assuming that it is indeed acetate it must be partially occupied, 0.5 or > less. Keep in mind that when you lower occupancy you may see additional > density for whatever occupies the space on the other side of the > symmetry element (e.g. water) which you may need to model. > > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Short contact between symmetry equivalents
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 Kavya It does not interact - you cannot have 1.8A distance between atoms. Assuming that it is indeed acetate it must be partially occupied, 0.5 or less. Keep in mind that when you lower occupancy you may see additional density for whatever occupies the space on the other side of the symmetry element (e.g. water) which you may need to model. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Short contact between symmetry equivalents
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. 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 short contact you mention is tolerated > by laws of nature. It's fairly common to have, say, a water molecule > split in two positions near symmetry axis - as long as you have it at > occupancy<1.0, it's ok. > > On 05/27/2013 05:21 AM, Kavyashree Manjunath wrote: >> 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 >> >> > > > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Short contact between symmetry equivalents
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 short contact you mention is tolerated by laws of nature. It's fairly common to have, say, a water molecule split in two positions near symmetry axis - as long as you have it at occupancy<1.0, it's ok. On 05/27/2013 05:21 AM, Kavyashree Manjunath wrote: 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 -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
