Where do I find documentation for csymmatch ? Google is normally good at finding program documentation (and sometimes code which is infinitely better) but not in this case - I even tried spelling it 'csymatch' just in case!
I was just interested to know whether csymmatch tries all combinations of matching A to A, A to B, A to C, B to C etc etc.? That's what people usually forget to do - i.e. they fail to observe the obvious that NCS-related molecules are not created identical! -- Ian On Fri, Nov 19, 2010 at 11:45 AM, Eleanor Dodson <c...@ysbl.york.ac.uk> wrote: > 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<ro...@riken.jp> 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:ianj...@gmail.com] >>> Sent: Thursday, November 18, 2010 7:42 PM >>> To: ro...@riken.jp >>> Cc: CCP4BB@jiscmail.ac.uk >>> 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<ro...@riken.jp> 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 >>> >>> >>> > >
