Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Edward A. Berry]

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
邮箱：smith_liu...@163.com

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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
邮箱：smith_liu...@163.com


<https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?iconUrl=https://nos.netease.com/mail-online/qiyelogo/defaultAvatar.png=Smith
 
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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" 
<176a9d5ebad7-dmarc-re

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Tristan Croll]

Assuming you have a good reason for doing that, I'd suggest the best 
approach would be to first generate a real-space map covering your 
original coordinates, and then apply the transform to that. To transform 
a volumetric map, all you're actually transforming is the (x,y,z) 
coordinate of its origin and the three vectors defining its axes - but I 
must confess I don't know off the top of my head any GUI tools to do 
that for you. Chimera can almost certainly do it, if you look through 
the manual.


On 2017-12-18 15:37, Smith Liu wrote:

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

邮箱：smith_liu...@163.com

签名由 网易邮箱大师 [4] 定制


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"
<176a9d5ebad7-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



Links:
--
[1]
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.163.com_dashi_dlpro.html-3Ffrom-3Dmail88d=DwMGbwc=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPor=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQm=VsiJhHbT-qp6n3QHdvilZeqY-0tA4mSqlVkx6nStzhMs=0Zu9ZB12d-Kh3exqmmGcW7PZIzCGKTXlXat7Qffx-lke=
[2]
https://urldefense.proofpoint.com/v2/url?u=http-3A__origins.comd=DwM

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Smith Liu]

sorry, how i move the mtz into the transformed pdb for the question in my 
previous email?




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月18日 23:37，Smith Liu 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
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




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 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" 
<176a9d5ebad7-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" 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


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

 

 

 

 

Re: [ccp4bb] AW: Re: [ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Smith Liu]

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
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




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 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" 
<176a9d5ebad7-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" 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


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

 

 

 

 

[ccp4bb] AW: Re: [ccp4bb] coordinate transformation

[Herman . Schreuder]

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" 
<176a9d5ebad7-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 
> 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"
 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


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