It makes an intelligent guess based on chain ID and proximity what is a
contiguous unit in the file, and moves on that basis. Separate chains
are always moved separately. Monomers within a chain which do not have
close contiguity to their neighbours - eg waters, broken chains - are
also moved separately. That's what -connectivity-radius does.
One limitation (which should be fixed but I haven't had time):
- without -origin-hand it doesn't try origin shifts
- with -origin-hand it tries all possible origin shifts, not just
those consistent with the spacegroup symmetry. Normally the symmetry of
the search target wins out and you get an exact answer, but with very
poor models it can occasionally give garbage.
There should be a gui - there isn't.
There should be documentation - there isn't.
Ian Tickle wrote:
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
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