Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-17 Thread Robbie Joosten
or unknown hetero compounds.-UNX is for unknown solo atoms.-DN id for unknown deoxy nucleotide. Cheers,Robbie Date: Fri, 17 Jun 2011 12:22:50 +0100 From: twom...@globalphasing.com Subject: Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK On 16 Jun 2011

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-17 Thread Thomas Womack
On 16 Jun 2011, at 17:19, Pavel Afonine wrote: > Hi, > > On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote: > > Modeling more UNKNOWN atoms might be the future for these cases? > > one needs to specify chemical element type in 77-78 position, otherwise these > records are useless. But if

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-16 Thread Pavel Afonine
Hi, On Thu, Jun 16, 2011 at 7:49 AM, Jan Dohnalek wrote: > > Modeling more UNKNOWN atoms might be the future for these cases? > one needs to specify chemical element type in 77-78 position, otherwise these records are useless. Example: http://www.rcsb.org/pdb/files/3GR4.pdb HETATM15389 UNK U

Re: [ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-16 Thread Jan Dohnalek
We often fight these questions when "various ligands" bind to our proteins. Generally, even if we know it's not water but an unidentified ligand which cannot be properly modeled or we are not brave enough to place it in the density we leave majority of the density uninterpreted but DO model a few w

[ccp4bb] Follow-up: non-waters among structured solvent atoms

2011-06-15 Thread wtempel
Thank you everyone for your replies. The Nayal & Di Cera (1996) paper may be what I had in mind. I was looking for some estimate of how often water atoms are placed in protein models where they do not belong, and I expected a relatively high percentage. Simply extrapolating from the 0.01% water <->