在2017年12月18日 21:58，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]
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
签名由 网易邮箱大师 [1] 定制
在2017年12月18日 21:26，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] IM AUFTRAG
VON Smith Liu
GESENDET: Montag, 18. Dezember 2017 14:16
AN: 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> 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>
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 [2]" 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 [3]
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
