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Dear Antony,
I agree, modelling entirely separate entities with one occupancy for
all atoms inside make chemically much more sense and it has the
advantage that the refinement program can move e.g. ADP to a slightly
different position than ATP - it is unlikely that the common atoms
between the two molecules are exactly in the same position.
Best,
Tim
On 05/25/2013 12:34 PM, Antony Oliver wrote:
> Kavya,
>
> Presumably your enzyme is turning over the ATP? Driving it towards
> ADP?
>
> In that case I suspect that you may have a mixture of ATP and ADP
> (and possibly contaminating AMP). You could either model both ATP
> and ADP, and set relative occupancies of both (add up to 1). Or,
> you could assign different occupancies to the phosphate groups
> alone. I personally think the former is probably the correct
> method? Comments CCP4 community?
>
> Many regards, Antony.
>
>
> On 25 May 2013, at 11:29, <[log in to unmask]> wrote:
>
>> Dear Sir,
>>
>> That is true the ligand is ATP, the occupancy problem comes only
>> for the phosphates. This ATP tends to get cleaved to ADP and AMP
>> in other complexes I got. So in this case do you suggest keeping
>> different occupancies for nucleoside and phosphate groups? I am
>> not aware of any publication with this scenario so I am not sure
>> whether it is right.
>>
>>
>> Thank you Regards Kavya
>>
>>> Dear Kavyashree,
>>>
>>> It is possible that your bound ligand (for which you have
>>> strong electron density) is actually a break-down of the parent
>>> compound? We have seen this a couple of times now.
>>>
>>> Also - are the poorly refining areas (those with negative
>>> density) part of a pendant ring connected by a conformationally
>>> unrestricted bond? These quite often have poor density.
>>>
>>> Hard to judge without seeing the actual density - but
>>> understand why!
>>>
>>> Regards, Antony.
>>>
>>>
>>> Sent from my iPhone
>>>
>>> On 25 May 2013, at 10:40, "Kavyashree Manjunath"
>>> <[log in to unmask]> wrote:
>>>
>>>> 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
>>>>
>>>>
>>>>
> 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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- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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