Dear Sir,
Thank you all for your kind advice and clarifications.
I will keep the occupancy 1.0 for both the ligands and
refine without considering the negative density in this
case.
Thanking you
Regards
Kavya
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> Dear Kavya,
>
> I don't see much sense in having different occupancies within the same
> molecule (unless one atoms sits on a special position, but then refmac
> will take care of it).
>
> If positive density comes up it's a good sign the ligand really is
> there. At 2.2A I would not be too surprised some atoms show less
> density than others (but don't look too much at the map with a sigma
> level < 1: you are going to see what you want to see).
>
> It's difficult to judge without sitting next to you, so my advice is
> try to model it as good as your knowledge permits, and do take your
> chemical knowledge into account when doing so!
>
> Best,
> Tim
>
> On 05/25/2013 06:55 AM, Kavyashree Manjunath wrote:
>> Dear users,
>>
>> I tried giving occupancy of 0.65 and 0.6 respectively for all atoms
>> of the two ligands and refined. Now after refinement, the atoms of
>> ligand does not have negative density but those which did not have
>> negative density previously appear positive. So what do I need to
>> do? under what circumstances does a ligand have different
>> occupancies for different atoms or for a group of atoms. Any such
>> references are very much welcome.
>>
>> Thank you Regards Kavya
>>
>>> Sir,
>>>
>>> Yes it is around ligand. The average B-factor of one of the
>>> ligand is 36.78, of which one of the atom has occupancy B
>>> factor 0.58 39.37 0.56 38.77 0.87
>>> 37.00 Three atoms are of same type. The other ligand's overall
>>> Bfactor is 17.64. occupancy B factor 1.00 19.29
>>> 0.64 23.90 Two atoms are of same type.
>>>
>>> So in the present case should I put the occupancy of 0.56 for all
>>> atoms of ligand-1 and 0.64 for all atoms of ligand-2 and refine?
>>>
>>> I mean will it be wrong to put different occupancies for
>>> different atoms of same ligand?
>>>
>>> I could not see any alternate densities coming up for those
>>> atoms which did not have densities. But 2FoFc map would appear
>>> around these atoms at 0.7 sigma at the same position where the
>>> atoms are present.
>>>
>>> Thank you Regards Kavya
>>>
>>>> Hi Kavya,
>>>>
>>>> If I understand you correctly (from title and text), you meant
>>>> your negative FoFc was around your ligand, is that right? I
>>>> wonder if this is a case in which the ligand has an occupancy
>>>> below 1, but was modeled as 1, so the refinement program had to
>>>> give it a high B factor to compensate that, which results in
>>>> the electron density bleeding into nearby space where there
>>>> should not be so much of it. If you want to test this
>>>> hypothesis, one thing you can try is to set the occupancy to
>>>> 0.25, 0.5,0.75 and so on, and refine a few cycles to see what
>>>> happens to the maps. Also, what's the B factor of the ligand,
>>>> and what's the B of the nearby protein atoms? The difference
>>>> between them can also give you some hint for guessing the
>>>> ligand's occupancy. Some refinement programs(phenix.refine and
>>>> shelx) can also let you refine the ligand's occupancy.
>>>>
>>>> As to the "missing" atoms, that could be caused by alternative
>>>> conformations of the ligand - assuming you have already done a
>>>> thorough refinement.
>>>>
>>>> Zhijie
>>>>
>>>> -------------------------------------------------- From:
>>>> "Kavyashree Manjunath" <[log in to unmask]> Sent: Friday,
>>>> May 24, 2013 12:50 PM To: <[log in to unmask]> Subject:
>>>> [ccp4bb] Negative FoFc around ligand
>>>>
>>>>> Dear users,
>>>>>
>>>>> I am using refmac 5.7.0029 for refining a structure
>>>>> (resolution 2.2 Ang) bound to 2 ligands. After MR There is a
>>>>> very clear density of ligands but after refinement, I get
>>>>> negative fofc map near one of the ligand upto 5 sigma.
>>>>> However its 2fofc map covers the whole ligand. Also for the
>>>>> other ligand, I do not see any 2fofc density (at 3 sigma) for
>>>>> 2 atoms, without these atoms the ligand is unrealistic. But
>>>>> the density comes up around these at around 0.7 sigma.
>>>>> Overall completeness is 99.9% Rmerge 7.5%
>>>>>
>>>>> What else I need to check in the data. Kindly provide some
>>>>> suggestions.
>>>>>
>>>>> Thanking you Regards Kavya
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>
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>>>
>>>
>>>
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>>
>>
>>
>
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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