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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 > > >