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I am wondering whether the stuff in between the protein molecules in a crystal counts as a generic “liquid,” or perhaps something more interesting can be detected
if searched for? Maybe “alternate” conformations of the water networks can actually be found, given atomic resolution. I was going to try to do a quick job of this right now by picking waters at really extended distances from the model, but Coot keeps crashing
when I try to read in the sf files from the pdb. Not sure what’s wrong here.
JPK
From: Ed Pozharski [mailto:[log in to unmask]]
Sent: Saturday, November 14, 2015 11:06 PM
To: Keller, Jacob; [log in to unmask]
Subject: RE: [ccp4bb] proper modeling of residues into patchy electron density
Liquids have no long-range order no matter the resolution.
Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5
-------- 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
Well, I was wondering whether the uniform bulk solvent density assumption might break down given
sufficient data.
JPK
From: CCP4 bulletin board [mailto:[log in to unmask]]
On Behalf Of Ed Pozharski
Sent: Saturday, November 14, 2015 9:33 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] proper modeling of residues into patchy electron density
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.
Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5
-------- Original message --------
From: James Holton <[log in to unmask]>
Date: 11/14/2015 7:27 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
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?
-James Holton
MAD Scientist
On 11/14/2015 4:23 PM, Ed Pozharski wrote:
This is a bit confusing. Don't you already know the "location" from backbone coordinates?
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"?
Cheers,
Ed.
Happy Connecting. Sent from my Sprint Samsung Galaxy S® 5
-------- Original message --------
From: Quyen Hoang <[log in to unmask]>
Date: 11/14/2015 6:23 PM (GMT-05:00)
To: [log in to unmask]
Subject: Re: [ccp4bb] proper modeling of residues into patchy electron density
Let's see if we can settle this. Ed might remember where I stood, but my view had changed a bit.
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.
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.
Can we settle with this?
Cheers,
Quyen
On Nov 14, 2015, at 5:40 PM, Ed Pozharski <[log in to unmask]> wrote:
> On 11/14/2015 04:36 PM, Artem Evdokimov wrote:
>>
>> I would agree with both sides, since absence of evidence is not evidence of ansence.
>>
> Well, that's agnostic :)
>
> 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.
>
> Cheers,
>
> Ed