This is something you would normally not do in the course of refining a protein
structure, because the structure would no longer correspond to the observed
structure factors and no longer be consistent with the symops of the particular
space group.
There are applications for it in multi-crystal averaging, or to compare
directly the density map for structures from non-isomorphous crystals. For
doing this it is important to understand the difference between a MAP file
(.map, .ccp4) and a DATA file (.mtz). There are programs for
rotating/translating electron density (from a map file) given the
rotation-translation operator. I think ccp4 mapmask(?), also the uppsala RAVE
and MAVE packages.
So you could generate a map from your mtz (ccp4 prog fft), get the operator
relating new position to old
(coot or LSQAB? or LSQMAN), transform ("skew") the map to the new location in
a p1 cell, and calculate new p1 phased structure factors with SFALL (or use the map file
directly in coot). You need a mask for the skew operation, you can make it from your
coordinates using mapmask or RAVE mama.
On 12/18/2017 10:40 AM, Smith Liu wrote:
sorry, how i move the mtz into the transformed pdb for the question in my
previous email?
Smith Liu
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在2017年12月18日 23:37，Smith Liu <mailto:smith_liu...@163.com> 写道：
thanks. i may mean something other. for example, if i rotate the pdb by 30
degree (or 29.5 degree), or i shift the pdb along x-axis by something for
example 0.123*a, then how i move the mtz map correspondingly for the fitting of
mtz into the transformed map?
Smith Liu
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在2017年12月18日 21:58，herman.schreu...@sanofi.com
<mailto:herman.schreu...@sanofi.com> 写道：
Dear Smith,
The map extends through the whole crystal. What happens is that the map
is calculated around the atom you clicked on during centering. So by centering
on your transformed pdb, you will sample the same map at a different position.
Just load your transformed pdb and untransformed mtz and try.
If the transformed pdb does not fit the map, something went wrong
during the transformation of your pdb. If you have applied an origin shift (is
not equal to applying a crystallographic symmetry operation), you have to
recalculate the mtz, e.g. by running another round of refinement.
I hope this is clear so.
Herman
*Von:*Smith Liu [mailto:smith_liu...@163.com
<mailto:smith_liu...@163.com>]
*Gesendet:* Montag, 18. Dezember 2017 14:52
*An:*Schreuder, Herman /DE
*Betreff:* [EXTERNAL] Re: [ccp4bb] AW: Re: [ccp4bb] coordinate
transformation
you mean the mtz map will transform simutaneously?
*Smith Liu*
邮箱：smith_liu...@163.com <mailto:smith_liu...@163.com>
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在2017年12月18日 21:26，herman.schreu...@sanofi.com
<mailto:herman.schreu...@sanofi.com> 写道：
If you use coot with on the fly map calculation (e.g. you load an mtz
and not a map file), you do not need to transform the map. Otherwise I would
recommend to run one more round of refinement and produce a new map your usual
way. This will also get rid of any rounding errors due to the transformation.
Best,
Herman
*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>] *Im Auftrag von *Smith Liu
*Gesendet:* Montag, 18. Dezember 2017 14:16
*An:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Betreff:* [EXTERNAL] Re: [ccp4bb] coordinate transformation
Dear All,
If I have a set of PDB with the corresponding density map, after I
transform the PDB based on the suggestion of everybody, is any way to transform
the map so that the map will be fit with the transformed PDB?
Smith
At 2017-12-18 18:39:34, "Eleanor Dodson"
<0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk
<mailto:0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote:
I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will
pdbset xyzin mow.pdb
end
Find CoM 0.7 1.3 -0.2
Hmm - a little thought - centre at 1 -1 0 say
pdbset yzin now.pdb xyzout changed.pdb
symgen x , y-2, z
end
New CoM 0.7 -0.7 -0.2
Eleanor
On 18 December 2017 at 00:19, Edward A. Berry <ber...@upstate.edu
<mailto:ber...@upstate.edu>> wrote:
Neat idea!
And do you have a 1-line command for setting all the coordinates to
1,1,1? or 0.1,0.1,0.1 if I still want it near the origin but biased toward the
inside of the positive-going cell?
eab
On 12/14/2017 07:23 PM, James Holton wrote:
What I usually do for this is make a copy of the PDB file and change all the atom x-y-z positions to "1.000". Then I use
something like reforigin or my "origins.com
<https://urldefense.proofpoint.com/v2/url?u=http-3A__origins.com&d=DwMGbg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=kr4BAC6CGF8MkSeqVDxlDaQ3WprGVrjotZPIWrNrdts&s=RFDcNoPw6eYR8Aka4k3PWnf4_OIc98ZgWFd-LYwSoHo&e=>"
script to shift the original coordinates via allowed symmetry operations, origin shifts, or perhaps indexing ambiguities until it is as
close as possible to the "reference", which is at 1,1,1. I use 1,1,1 instead of 0,0,0 because there are generally at least two
symmetry-equivalent places that are equidistant from the origin. Declaring the reference to be a bit off-center breaks that ambiguity, and
also biases the result toward having all-positive x,y,z values.
In case it is interesting, my script is here:
http://bl831.als.lbl.gov/~jamesh/scripts/origins.com
<https://urldefense.proofpoint.com/v2/url?u=http-3A__bl831.als.lbl.gov_-7Ejamesh_scripts_origins.com&d=DwMGbg&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=kr4BAC6CGF8MkSeqVDxlDaQ3WprGVrjotZPIWrNrdts&s=9dlreI0nRWqq1Feor3gq_OOcpIxVPjpdRl2KTg9fMqg&e=>
You need to have the CCP4 suite set up for it to work. Run it with no
arguments to get instructions.
-James Holton
MAD Scientist
On 12/13/2017 5:50 AM, Kajander, Tommi A wrote:
Hello,
If someone could point this out would be very helpful... Wasnt there a
simple script somewhere that would transfer coordinates close to origin - if
they for some reason are not? Just cant find anything right away. Sure i have
done this before...
Thanks,
Tommi
