Re: [ccp4bb] negative density in difference map

2011-11-23 Thread Ian Tickle
I assumed that since this topic came up fairly recently, in fact 3 weeks ago (see thread starting from http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg23628.html), it wasn't just a re-run of the same question. Perhaps the original poster could clarify whether we are talking about unexplained

Re: [ccp4bb] negative density in difference map

2011-11-23 Thread Garib N Murshudov
There may be several reasons. 1) Artefacts (some of them) a) effect of mask: if there are large holes inside molecule and there should be no electron density (for example hydrophobic holes) then in older versions masks would put a constant density there and as a result difference map would

Re: [ccp4bb] negative density in difference map

2011-11-23 Thread James Holton
Sounds like rad dam to me. See Burmeister, W. (2000)."Structural changes in a cryo-cooled protein crystal owing to radiation damage", Acta Cryst. D 56, 328-341. The first sign of a Met loosing its S-CH3 group will be a negative difference peak on the S. -James Holton MAD Scientist On 11/2

Re: [ccp4bb] negative density in difference map

2011-11-23 Thread Nat Echols
On Wed, Nov 23, 2011 at 7:57 AM, Ian Tickle wrote: > On 23 November 2011 07:54, Careina Edgooms wrote: >> I have a question about a 2F0-Fc difference map that I calculated with >> Refmac. > > On 23 November 2011 15:40, Nat Echols wrote: >> The negative density around Met S could be radiation da

Re: [ccp4bb] negative density in difference map

2011-11-23 Thread Ian Tickle
On 23 November 2011 07:54, Careina Edgooms wrote: > I have a question about a 2F0-Fc difference map that I calculated with Refmac. On 23 November 2011 15:40, Nat Echols wrote: > The negative density around Met S could be radiation damage. But you wouldn't expect to see -ve density in the 2Fo-Fc

Re: [ccp4bb] negative density in difference map

2011-11-23 Thread Nat Echols
On Tue, Nov 22, 2011 at 11:54 PM, Careina Edgooms wrote: > I have a question about a 2F0-Fc difference map that I calculated with > Refmac. In some instances it gives me negative (red) density around part of > a side chain and no positive density in sight. Furthermore the entire > residue fits wel

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

2011-11-23 Thread Ian Tickle
or alternate confonformers against the >> density for CA. >> >> >> >> Alternatively, your side chain B-factor restaints might be too tight. >> >> >> >> Anthony >> >> >> >> >> >> ________________ >> From: CCP4 bulletin board [CCP4BB@JISCM

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

2011-11-23 Thread Eleanor Dodson
restaints might be too tight. Anthony From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Careina Edgooms [careinaedgo...@yahoo.com] Sent: Wednesday, 23 November 2011 6:54 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] negative density in difference map

Re: [ccp4bb] negative density in difference map [SEC=UNCLASSIFIED]

2011-11-23 Thread DUFF, Anthony
Subject: [ccp4bb] negative density in difference map Good morning CCP4 members I have a question about a 2F0-Fc difference map that I calculated with Refmac. In some instances it gives me negative (red) density around part of a side chain and no positive density in sight. Furthermore the entire

[ccp4bb] negative density in difference map

2011-11-22 Thread Careina Edgooms
Good morning CCP4 members I have a question about a 2F0-Fc difference map that I calculated with Refmac. In some instances it gives me negative (red) density around part of a side chain and no positive density in sight. Furthermore the entire residue fits well into the blue density of the compl