Thanks, I should try it before I criticise ... Regards
-- Ian On Mon, Nov 22, 2010 at 10:01 AM, Eleanor Dodson <[email protected]> wrote: > It is a program Kevin Cowtan wrote - here is the info you get when you try > to run it.. > E > > > [c...@roo mariaH]$ csymmatch > <B><FONT COLOR='#FF0000'><!--SUMMARY_BEGIN--> > <html> <!-- CCP4 HTML LOGFILE --> > <hr> > <pre> > > ############################################################### > ############################################################### > ############################################################### > ### CCP4 6.1: csymmatch version 0.3 : 13/07/09## > ############################################################### > User: ccp4 Run date: 22/11/2010 Run time: 10:00:24 > > > Please reference: Collaborative Computational Project, Number 4. 1994. > "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, > 760-763. > as well as any specific reference in the program write-up. > > <!--SUMMARY_END--></FONT></B> > > Usage: csymmatch > -pdbin-ref <filename> > -pdbin <filename> > -pdbout <filename> > -connectivity-radius <radius/A> > -origin-hand > Apply symmetry and cell shifts to each chain in 'pdbin' to obtain the best > match to 'pdbin-ref'. > > > On 11/19/2010 12:34 PM, Ian Tickle wrote: >> >> 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<[email protected]> >> 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<[email protected]> >>>> 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:[email protected]] >>>>> Sent: Thursday, November 18, 2010 7:42 PM >>>>> To: [email protected] >>>>> Cc: [email protected] >>>>> 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<[email protected]> >>>>> 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 >>>>> >>>>> >>>>> >>> >>> > >
