Am 22.11.10 10:49, schrieb Eleanor Dodson:
> On 11/18/2010 05:45 PM, Phil Evans wrote:
>> On 16 Nov 2010, at 13:22, Paul Emsley wrote:
>>
>>> Dear Phil,
>>>
>>> Sorry for the delay, I am only just back from somewhat extensive
>>> travels.
>>>
>>> On 01/11/10 12:26, Phil Evans wrote:
>>>> If I "colour by chain" (my preferred option), metal ions disappear
>>>
>>> Thanks for the notification of this bug. It is fixed now, rev 3245.
>>
>> thanks
>>
>>>
>>>> also is there any way of refining a zone around a metal ion without
>>>> the sidechains vanishing into the metal density? I know the
>>>> refine-by-sphere ("R") option works better, but then I have no
>>>> control over what I'm refining
>>>>
>>>
>>> Sphere refine is simply a thin layer around the refine-residues
>>> function which takes a list of residue specs - that gives you enough
>>> control, I hope. (You can also trivially change the "radius" in
>>> sphere refine.)
>>>
>>> Paul.
>>
>>
>> How do you change the radius?
>>
>> I had a long chat to Bernhard about this. My feeling is that in order
>> to avoid "user consternation" ((c) George Sheldrick), RS refinement
>> in Coot should _never_ move something into space already occupied by
>> another part of the same molecule (zero occupancy excepted). I
>> realise there are implementation difficulties, but I do think this is
>> a major problem.
>>
>> Phil
>>
>
>
> I absolutely agree with this. It is a disaster of curse when you have
> a metal - all nearby side chains rush to take up the density..
> Eleanor
This could be avoided by including geometrical restraints (VDW
distances, hydrogen bonds) with a shell of residues surrounding the
refined ones.
Hydrogen bonds would also stabilize secondary structure elements of the
refined part at low resolution.
Best regards,
Dirk.
--
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Dirk Kostrewa
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