Have you tried
csymmatch -pdbin-ref one.pdb -pdbin two.pdb
That will move chains to match asfar as possible, using sym ops and
allowedorigin shifts to generate the best fit.
Eleanor
On 11/18/2010 12:26 PM, Ian Tickle wrote:
> OK now I understand. I couldn't find the script 'origin.com' you
> mentioned in the examples directory (at least from the filename I
> assume it's a script, not a MS-DOS program!), but it doesn't matter, I
> see the problem now. AFAIK there isn't a script in CCP4 that will do
> what you want entirely automatically, because it's actually quite a
> complicated problem in the completely general case of N molecules per
> a.u., though undoubtedly it could easily be scripted for the
> relatively simple case of 2 mols per a.u..
>
> I'm assuming you don't simply want to superpose the molecules just for
> structural comparison purposes, you want to superpose the entire
> *crystals*, so that the calculated structure factors and hence the R
> factors (values) remained unchanged for the transformed structure.
> This means you can't use just arbitrary rotation/translation operators
> as would be generated by superposition programs such as SSM, you have
> to restrict it to crystallographically-allowed origin shifts. There
> are various programs which will do this, I wrote one called
> 'reforigin' but there are others which will do the same thing, and
> which have been mentioned in previous postings.
>
> So what you have to do is superpose the two 'A' molecules using
> reforigin or whatever (remember, as long as it applies only
> crystallographically-allowed origin shifts). There is of course a
> problem here: the chain ID 'A' is only an arbitrary label, so there's
> a 50% chance that the molecule you called 'A' in structure 1 might be
> called 'B' in structure 2 (and vice versa). This means you have to
> try both possibilities! Now you see why it gets complicated in the
> general case with molecules 'A', 'B', 'C', 'D' ... you have to try all
> combinations! While you are superposing A/2 on A/1 (or B/2 on A/1)
> you must also transform the other chain B/2 (or A/2) using the *same*
> operator (I think the program does this for you, or at least it will
> print the matrix that was used for the 1st pair) - you must not
> superpose it independently.
>
> Finally you need to transform the other molecule B/2 (or A/2) in the
> example above. For this you can only use space-group symmetry
> operators - you get only one chance to use the allowed origin shifts
> with the first pair of molecules, after that the origin is completely
> determined for the entire structure, hence only space-group symmetry
> can be used to transform subsequent pairs. For this I find it easiest
> just to view the structure on the graphics, work out which is
> appropriate space-group operator and apply it just to the 2nd molecule
> using PDBSET.
>
> Hope this is all clear - there are many traps here for the unwary!
>
> Cheers
>
> -- Ian
>
> On Thu, Nov 18, 2010 at 10:55 AM, Rojan Shrestha<[log in to unmask]> wrote:
>> Hello Ian:
>>
>> I am afraid that whether my problem is not clear to you.
>>
>> Here is brief description of the problem.
>>
>> When I tried to superimpose two structures having two or more copies in ASU
>> for polar space group using symmetric operator, for one copies it used one
>> origin and for next, another origin is used. So there is origins shift
>> problem.
>>
>> Here is an example:
>> applying 0.50 0.50 -0.69 Y,-X,3/4+Z to chain A
>> applying 1.50 0.50 0.61 X,Y,Z to chain B
>> WARNING: ./input.pdb chain B is on a different origin!
>>
>> I used origin.com to superimpose two models.
>>
>> Now I hope you get the insight of my problem. Do you have any idea to solve
>> this problem?
>>
>>
>> Regards,
>>
>> Rojan
>>
>>
>> -----Original Message-----
>> From: Ian Tickle [mailto:[log in to unmask]]
>> Sent: Thursday, November 18, 2010 7:42 PM
>> To: [log in to unmask]
>> Cc: [log in to unmask]
>> Subject: Re: [ccp4bb] origin_shift in polar space group
>>
>> HI Rojan,
>>
>> I'm not entirely clear that there is a problem. After superposition
>> any origin shift that may have been present is removed: doesn't that
>> solve your problem?
>>
>> Cheers
>>
>> -- Ian
>>
>> On Thu, Nov 18, 2010 at 10:11 AM, Rojan Shrestha<[log in to unmask]> wrote:
>>> Hello:
>>>
>>>
>>>
>>> In polar space group when the two or more copies molecules are
>> superimposed,
>>> the origin is shifted.
>>>
>>> Does anybody have the solution to tackle this problem?
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>>
>>> Rojan
>>
>>
>>
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