Re: [ccp4bb] B-factors very high

2021-01-04 Thread Jon Cooper
--- > > Da: Eleanor Dodson > Inviato: lunedì 4 gennaio 2021 15:43:03 > A: Napolitano Silvia > Cc: CCP4BB@JISCMAIL.AC.UK > Oggetto: Re: [ccp4bb] B-factors very high > > Well - you dont give the resolution of your data or the "

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Paul Emsley
On 04/01/2021 14:38, Silvia Napolitano wrote: Dear CCP4 Community, I am currently working on the structure of a monomeric protein of 23KDa. The protein is generally quite "loopy" and I think I am mid-way refinement. At the moment I am struggling, among other things, with an extremely high B-fac

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Phoebe A. Rice
Dear Silvia, While high Bs can be a sign that parts of your model are incorrect (and therefore some careful manual rebuilding may be required), for things like poorly-ordered surface loops, they can simply be truth. A point worth remembering for newbies: your goal is to produce the model that

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Barone, Matthias
.AC.UK Subject: Re: [ccp4bb] B-factors very high Hmm - this is extracted from your log file: it looks more sensible.. 2899: b_iso_mean = 66.62 2907: b_iso_min= 63.50 (limit = 1.00) 2908: b_iso_max= 68.13 (limit = 80.00) 2909: b_iso_mean = 66.62 The average B

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
--- > *From:* CCP4 bulletin board on behalf of Eleanor > Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> > *Sent:* Monday, January 4, 2021 3:44:33 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] B-factors very high > > That polygon is no

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Alexandre Ourjoumtsev
Dear Eleanor, You are absolutely right. However, in Polygon, you could compare the models selected by resolution, by size, etc. I use this occasion to wish you and others a happy New Year ! Sacha Urzhumtsev - Le 4 Jan 21, à 15:44, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscma

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Pedro Matias
*Da:* Eleanor Dodson *Inviato:* lunedì 4 gennaio 2021 15:43:03 *A:* Napolitano Silvia *Cc:* CCP4BB@JISCMAIL.AC.UK *Oggetto:* Re: [ccp4bb] B-factors very high Well - you dont give the resolution of your data or the "wilson B" which will be recorded in the data processing log. If the res

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Barone, Matthias
iscmail.ac.uk> Sent: Monday, January 4, 2021 3:44:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] B-factors very high That polygon is not very useful I dont think. The statistics need to be given separately for structures solved at given resolutions. Eleanor On Mon, 4 Jan 2021 at 14:43

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
That polygon is not very useful I dont think. The statistics need to be given separately for structures solved at given resolutions. Eleanor On Mon, 4 Jan 2021 at 14:43, Eleanor Dodson wrote: > Well - you dont give the resolution of your data or the "wilson B" which > will be recorded in the dat

Re: [ccp4bb] B-factors very high

2021-01-04 Thread Eleanor Dodson
Well - you dont give the resolution of your data or the "wilson B" which will be recorded in the data processing log. If the resolution is 3A or less a) it is hard to refine a B value, and b) it certainly should be high.. So more information is needed. Eleanor On Mon, 4 Jan 2021 at 14:39, Silvia