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RE: [ccp4bb]: molecular replacement woes!
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Hi Cheenu
Orthorhombic space groups that are NOT P212121 are really very rare, so
it is very likely that you have assigned the wrong spacegroup to your
data.
Here's the old wisdom, passed from supervisor to student through the
ages (or was there somebody that said it first? Anybody?):
"The spacegroup is a hypothesis, confirmed ONLY once the
structure has been fully refined."
(And sometimes not even then.)
So if you go round assigning spacegroups based only on the data, you're
setting yourself up for many months of futile hacking at some spacegroup
- particularly if you decide on something that's not P212121.
I assume you made your assignment based on the systematic absences
printed by scalepack (?). A non-obvious feature of the program (most
programs that do this, in fact) is that that if you never actually
recorded the relevant reflections to begin with, scalepack doesn't print
them either - and doesn't tell you that they're not measured. But in
P222 they're easy to find, so scale in P222 and then look for them in
the .sca file (using grep or something on unix). (Same applies for
mosflm/scala.)
That said, non-P212121 orthorhombics *do* happen, so, even if you did
measure all relevant reflections, they can still fool you, and it could
be worth trying out all the other combinations of screws as well.
No, the spacegroup that your model was in when it was solved has nothing
to do with your problem - that was a different crystal in a different
time.
How's the packing of your solution? Any clashes?
Also, there are at least 4 other programs you could try: amore, molrep,
epmr, beast.
Anyway, there are some tips.
phx.
> -----Original Message-----
> From: schakrav [mailto:schakrav@lamar.colostate.edu]
> Sent: Wednesday, June 26, 2002 4:19 PM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: molecular replacement woes!
>
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> hi,
> my name is srinivas chakravarthy (cheenu) and i am a graduate
> student in
> Dr.Karolin Luger's lab at Colorado State University. I am an
> absolute beginner
> in the field of crystallography and would deeply appreciate
> any input that
> comes my way pertaining to the problem i am now facing which is-
> I have synchrotron data from a nucleosome crystal which
> was indexed and
> scaled without any major problems in the space group p222(1).
> I get an overall
> completion of 96.7%. I run into problems at the molecular
> replacement stage
> (using CNS). the spacegroup of the model is p2(1)2(1)2(1).
> when i do a cross
> rotational search, going by the rotation function peak height
> values it seems
> to have worked. (highest values are .1591 and .1496 and the
> rest of the values
> are in the .06 range). this is on using "fastdirect". i
> havent tried "direct".
> when i do a translational search i do get a solution with a
> correlation
> coefficient (E2E2) which is significantly higher than the
> other solutions
> (monitor no. is .262) but on minimization refinement i get
> unreasonable r and
> free_r values. my final r is 0.5163 and the final free_r is
> 0.5231. the model
> and my molecule supposedly have a high degree of homology.
> my questions are 1.should i expect problems in molecular
> relacement on account
> of the model and my molecule being in different space groups
> (i've been told
> that i shouldnt)? if so what would be the nature of the
> problem? 2. what could
> be the possible reasons for the high r and free_r values?
> Do forgive the lack of precision in expressing my problem. My
> excuse is I am
> just beginning to use the terminology and the concepts.
> thanks for your patience,
> cheenu.
>
> Srinivas Chakravarthy
> Colorado State University
> Fort Collins
> CO-80521
>
>
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