If refmac left those residues alone I do not understand how planarity can
become distorted. And I would like to understand ...
As for the Wiki: I often find what I am looking for in a Wiki, but in this
email based BB I often find things which I was not looking for and am very
grateful for repetition of discussions.
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
On Tue, 16 Oct 2007, Anastassis Perrakis wrote:
> 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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