Respected Mam,

The molecule is not along the C axis. I opened both these
molecules along with the pseudo-translation peak generated
by patterson function, it could be observed that the origin
of the one of the dimer corresponded to the 2nd peak (pseudo
translation) peak.

So I guess this is due to phaser recognising once the actual
origin and another time the pseudo-origin during MR. However
I am not sure whether it randomly selects one of the origin.

Thanking you
Respectfully
KAvya

> You knowe there are alternative indexing for H3 - you couldnt have solved
> one as h k l and the other as k h -l?
> And alternate origins - H3 is a polar spacegroup so if you redid the
> molecular replacement you may finish up anywhere along the c axis..
> Easiest is to do a superpose of both sets of coordinates and see what the
> transformation required is - it will almost certainly be a
> crystallographically acceptable fit
> Eleanor
>
>
> On 3 May 2013 10:02, Kavyashree Manjunath <[log in to unmask]> wrote:
>
>> Dear Sir,
>>
>>
>> > There used to be a chaos with H3 and R3 settings so you first thing
>> you
>> > might want to check that the same setting is used in both cases.
>> Easiest
>> > would be to check the CRYST1 record in your pdb files to make sure
>> that
>> > the same cell is used.
>>
>> I check it, the unit cell dimensions are identical as I did
>> not reprocess the data. I used the same processed data for both
>> with change only during scaling by adding the native Rfree set.
>>
>> > If you did not start for the second data set from the refined
>> coordinates
>> > from the first one but reran molrep instead, your molecule might have
>> > landed in a different asymmetric unit/unit cell/origin. In that case I
>> > would superimpose the coordinates from the second refinement on those
>> of
>> > the first refinement and maybe run one more cycle of refinement to get
>> rid
>> > of rounding errors. The should solve your problem.
>>
>> Ok.
>>
>> > Herman
>> >
>> > PS: I like the Effortless program, especially if they would add an
>> option
>> > to write the paper as well with some buttons to select the desired
>> journal
>> > e.g. Nature, Science, Cell etc. The cheat button should only be
>> available
>> > for experienced users though. ;-)
>>
>> That would probably be the ultimate aim of CCP4!!
>>
>> Thank you
>> Regards
>> Kavya
>>
>> >
>> > -----Original Message-----
>> > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
>> > Kavyashree Manjunath
>> > Sent: Friday, May 03, 2013 10:07 AM
>> > To: [log in to unmask]
>> > Subject: [ccp4bb] A small clarification
>> >
>>
>>
>> > Dear users,
>> >
>> > I wanted a small clarification, I was solving a ligand data in H3
>> space
>> > group with a dimer as the asymmetric unit.
>> >
>> > Initially, I had solved and refined this without using the same Rfree
>> > reflections as that of native data. So I resolved and refined the same
>> > data by considering the native Rfree reflections. In both the cases
>> after
>> > the final refinement, the R and Rfree had reasonably good values.
>> >
>> > The problem arose when I compared the maps of data -
>> > (1) solved without same Rfree as that of native and
>> > (2) solved with same Rfree as that of the native
>> >
>> > They did not superpose at all. How is this possible? Although it is
>> > originally the same data and in each case the map traced the molecule
>> very
>> > well, but when both maps are opened in coot they do not superpose at
>> all.
>> >
>> > I would like to mention that the data has a pseudo translation
>> symmetry
>> > with 17% peak. Is this responsible for the results I am getting?
>> >
>> > I hope one day there will be a program in CCP4 called "EFFORTLESS"
>> > which gives a structure from a given sequence!! :)
>> >
>> > Thanking you
>> > Regards
>> > Kavya
>> >
>> >
>> > --
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>>
>>
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