Re: [ccp4bb] Presence of negative density in Sim Omit map

lletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Friday, July 26, 2024 11:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map  | | You don't often get email from b45abf420e1f-dmarc-requ...@jis

Re: [ccp4bb] Presence of negative density in Sim Omit map

AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map You don't often get email from b45abf420e1f-dmarc-requ...@jiscmail.ac.uk. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi

Re: [ccp4bb] Presence of negative density in Sim Omit map

Green StreetUniversity of GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 bulletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, July 25, 2024 12:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in

Re: [ccp4bb] Presence of negative density in Sim Omit map

nt: 25 July 2024 07:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map External Sender: Use caution. Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level?As

Re: [ccp4bb] Presence of negative density in Sim Omit map

6a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: 25 July 2024 07:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map External Sender: Use caution. Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE c

Re: [ccp4bb] Presence of negative density in Sim Omit map

I also noticed one residue looks like a Phe and there is another that may be a Lys but not a very good view of it. When doing simulated annealing its not outside the realm of possibility that it will introduce errors in other parts of the model that could in theory explain the additional red d

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level? As Edward suggests - if you omit a well ordered feature the resultant difference maps often show high positive density and a surrounding complementary "sag

Re: [ccp4bb] Presence of negative density in Sim Omit map

Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps are constructed by Fourier transform without the 0 0 0 reflection, they have mean of zero (because the mean of a sinusoid over one period is zero). That means that any time you add positive (difference) density, which

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Renu, you may try using a Polder omit map for the region rather than a simulated annealing map. You may also check if the red density is due to a symmetry related molecule that is not modeled well. Hope it helps. JP On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj