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Dear Jeorge,
the 'ghost' could be explained by a shift of an entire section, i.e.
you have to split several residues into A+B, not only the MET.
The cylR2 structure in 2XJ3 is one example where this was necessary.
Best,
Tim
On 11/12/2014 11:23 AM, Eleanor Dodson wrote:
> That looks really odd - the whole MET has a negative/positive
> ghost
>
>
> Second conformations usually branch at the CB, and dont look like
> that.
>
> Are you sure you havent somehow got two MET residues in the
> coordinate set ? Turn on cysmmetry display in coot and look for
> clashes around there.
>
> Does the rest of the map look OK?
>
> I would set the occupancies of the MET and nearby side chains to
> 0.00 (you can do that in coot) then refine and look at the maps
> again.
>
> This is very old fashioned but you can do this: distang xyzin
> coords.pdb dist inter end
>
> to get a list of close symmetry clashes & contacts Eleanor
>
>
> On 12 November 2014 09:17, Greg Costakes <[log in to unmask]>
> wrote:
>
>> Hi Jeorge,
>>
>> The simplest answer is that you have multiple positions for the
>> Methionine. So you can try adding in an alternate position for
>> it. However, you didn’t mention the sigma cutoff or e-/A^3 for
>> either of your density maps. Its quite possible that your fofc
>> map is just scaled way down and what you are seeing is an
>> exaggeration of what’s barely there. Hope this helps. Cheers!
>>
>> - Greg
>>
>>
>> -------------------------------------------------------------------------------
>>
>>
Greg Costakes, Ph.D.
>> Department of Biochemistry University of Cambridge 80 Tennis
>> Court Road Cambridge, CB2 1GA United Kingdom
>>
>> --------------------------------------------------------------------------------
>>
>>
>>
*From:* jeorgemarley thomas <[log in to unmask]>
>> *Sent:* Wednesday, November 12, 2014 8:16 AM *To:*
>> [log in to unmask] *Subject:* [ccp4bb] Refinement with
>> refmac05 and methionine density
>>
>> Dear All,
>>
>> I am refining the structure with refmac05, and after each
>> refinement the density around this methionine is flipping. and it
>> is difficult to say where this methionine actually have the
>> density. please suggest what I should I do. I am attaching the
>> snap here.
>>
>> Thanks in Advance for your kind suggestions
>>
>> Jeorge
>>
>>
>>
>>
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>
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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