Re: [ccp4bb] Bad sidechain geometry

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Bad sidechain geometry
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-10-16

Next message:
Subject: Re: Bad sidechain geometry
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-10-16

Subject: Re: Bad sidechain geometry
From: Anastassis Perrakis a {- dot -} perrakis {- at -} NKI {- dot -} NL
Date: 2007-10-16

On 16 Oct 2007, at 8:44, Tim Gruene wrote:

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> Hi Iain,
>
> I know there are (at least) two schools of thought and both have
> their justification, and my suggestion does not explain you
> phenomenon.
>
> However, instead of setting the occupancy to zero, I would rather
> delete the affected atoms/ residues.
>
> In my point of view this would make your submitted structure less
> error prone, especially to non-crystallographers, because they
> usually just look at the PDB file with a graphics viewer rather
> than the PDB file itself (and most viewers, unlike coot, do not
> highlight atoms with zero occupancy).

Oh - its been a year since we did not have "Episode 17: The return of
the Positionally Challenged" !

Although I am confident Garib will clear the landscape soon (0 occ
atoms are ignored for for everything, including restraints; it is an
old PROLSQ 'feature' that has been adopted by REFMACx as far as I know).

I personally btw like to leave the atoms there and let B's go high,
with similar arguments like Tim's, and with similar 'side-effects'.
Better be clear that a long side chains is there, rather than think
its Alanine. But, I am sure the archive has loads on that, including
all the arguments that counter the above.

Maybe I will set up a ballot in the (coming soon!) ARP/wARP blog ;-)

Tassos

>
> Omitting these residues should help correct interpretation of you
> data by others than you.
>
> As a side effect, it would solve your problem of bonds becoming
> distorted.
>
> Tim
>
>
> - --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> On Mon, 15 Oct 2007, Iain Kerr wrote:
>
>> Dear all,
>>
>> I'm refining a structure (with TLS, Hs in riding positions) to
>> 2.9A - Rfree ~29.9%/Rfac 26.5% in Refmac5 v5.2.0019. Rmsd bonds
>> 0.008A/1.1deg angles.
>>
>> In COOT (0.31) many of the residues whose side chains are (fully
>> or partially) set to 0.00 occupancy have really bad geometry...for
>> want of a better description, the side-chains literally look like
>> they have exploded...a few are intact but have distorted
>> planarity. This occurs in 25 residues out of 480 in the ASU.
>>
>> I have tried:
>>
>> 1. refining without TLS - no change
>> 2. no hydrogens - no change
>> 3. refining OVERall B-factors instead of ISOtropic - overall
>> geometry much worse (rmsd 0.088 bonds)
>> 4. DAMP 0.5 0.5 - no change
>> 5. BABINET scaling instead of SIMPLE - no change in geometry,
>> Rfree and Rfac increase ~3%
>> 6. relaxing geometry (rmsd 0.019A bonds/1.8deg angles)
>>
>> This occurs with two other structures at higher resolution
>> (~2.5A), although only a few violations..it seems to be much worse
>> at low resolution.
>>
>> Any ideas ?
>>
>> Thanks,
>> Iain
>>
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Bad sidechain geometry
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2007-10-16

Next message:
Subject: Re: Bad sidechain geometry
From: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DE
Date: 2007-10-16