gt;>> 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
t; 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, s
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
>>>>>&g
t;> 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,
>>>>&
27;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.
>>>
nix.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.
>&
gt;> 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.
&g
>
> 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"
: Friday, May 24, 2013 1:12 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Negative FoFc around ligand
>
> Sir,
>
> I used model without ligand for MR. This happens only for some atoms not
> for all. So should I reduce the occupancy for all atoms? I did use
> occupancy ref
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"
Sent: Friday, May 24, 2013 12:50 PM
To:
Subje
Manjunath
Sent: Friday, May 24, 2013 1:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Negative FoFc around ligand
Sir,
I used model without ligand for MR. This happens only for some atoms not for
all. So should I reduce the occupancy for all atoms? I did use occupancy refine
it showed
Sir,
I used model without ligand for MR. This happens
only for some atoms not for all. So should I reduce
the occupancy for all atoms? I did use occupancy refine
it showed different occupancy like 0.8, 0.6 for two
different atoms. I mean for the same ligand it shows
occupancy of 1 for one atom and
Sir,
I used model without ligand for MR. This happens
only for some atoms not for all. So should I reduce
the occupancy for all atoms? I did use occupancy refine
it showed different occupancy like 0.8, 0.6 for two
different atoms.
Thank you
Regards
Kavya
> -BEGIN PGP SIGNED MESSAGE-
> Ha
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Kavya,
I assume that you carried out molecular replacement without the ligand
in the search model (otherwise you are probably looking at model
bias). In that case the ligand most likely has reduced occupancy. You
can either manually set all atoms
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
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