On Saturday, 14 November 2015 11:06:15 PM Ed Pozharski wrote:
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> Liquids have no long-range order no matter the resolution.
Tell that to the SAXS people who spend lots of beam time measuring
the water or buffer scattering in order to do background correction.
Ethan
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> Happy Connecting. Sent from my Sprint Samsung Galaxy SŪ 5
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> -------- Original message --------
> From: "Keller, Jacob" <[log in to unmask]>
> Date: 11/14/2015 10:45 PM (GMT-05:00)
> To: Ed Pozharski <[log in to unmask]>, [log in to unmask]
> Subject: RE: [ccp4bb] proper modeling of residues into patchy electron density
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> Well, I was wondering whether the uniform bulk solvent density assumption might break down given sufficient data.
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> JPK
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> From: CCP4 bulletin board [mailto:[log in to unmask]]
> On Behalf Of Ed Pozharski
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> Sent: Saturday, November 14, 2015 9:33 PM
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> To: [log in to unmask]
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> Subject: Re: [ccp4bb] proper modeling of residues into patchy electron density
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> No - a set of discrete water molecules would approach a uniform density as you elevate B-factors to infinity. But it would never be exactly identical to it, still having hills and valleys. Naturally, in practical terms such approach would
> be problematic because of potential model bias.
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> Happy Connecting. Sent from my Sprint Samsung Galaxy SŪ 5
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> -------- Original message --------
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> From: James Holton <[log in to unmask]>
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> Date: 11/14/2015 7:27 PM (GMT-05:00)
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> To: Ed Pozharski <[log in to unmask]>,
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> Subject: Re: [ccp4bb] proper modeling of residues into patchy electron density
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> Isn't that exactly what the bulk solvent correction is? Except that the B factor and occupancy of all the disordered water "atoms" are constrained to be the same?
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> -James Holton
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> MAD Scientist
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> On 11/14/2015 4:23 PM, Ed Pozharski wrote:
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> This is a bit confusing. Don't you already know the "location" from backbone coordinates?
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> I still would like to hear exactly how placing atoms to where no discernible density peak exists is improving a crystallographic model. I also know waters are there in large numbers, should I flood the bulk solvent area with discrete waters
> and state that B-factors will take care of "it"?
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> Cheers,
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> Ed.
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> Happy Connecting. Sent from my Sprint Samsung Galaxy SŪ 5
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> -------- Original message --------
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> From: Quyen Hoang <[log in to unmask]>
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> Date: 11/14/2015 6:23 PM (GMT-05:00)
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> To: [log in to unmask]
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> Subject: Re: [ccp4bb] proper modeling of residues into patchy electron density
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> Let's see if we can settle this. Ed might remember where I stood, but my view had changed a bit.
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> 1. Delete atoms of a side-chain for which no density is visible if one is using density to find out what the residue looks like.
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> 2. Model a complete residue even when density is missing for a side-chain atom if one is using the density to find the location of the residue.
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> Can we settle with this?
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> Cheers,
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> Quyen
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> On Nov 14, 2015, at 5:40 PM, Ed Pozharski
> <[log in to unmask]> wrote:
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> > On 11/14/2015 04:36 PM, Artem Evdokimov wrote:
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> >>
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> >> I would agree with both sides, since absence of evidence is not evidence of ansence.
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> > Well, that's agnostic :)
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> > Just a comment - omitting side chain atoms from the model does not assert that they are somehow missing from the chemical structure one is modeling. It means that their spatial distribution cannot be adequately approximated from experimental data via simple
> 3D gaussian. So when I am excluding atoms from disordered side chains, I am not saying that an X-ray fairy has cut off covalent bonds with a tiny magic chainsaw. I am just saying I don't have sufficient experimental evidence to locate these atoms.
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> > Cheers,
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> > Ed
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