Well, yes, a one-liner to move every atom to 1,1,1 would be:
awk '! /^ATOM|^HETAT/{print;next} {print substr($0,1,30) " 1.000
1.000 1.000" substr($0,55)}' whatever.pdb > ref.pdb
Which I suppose is a bit of a long one-liner, but still only one line.
The next line would be a call to
On 18/12/2017 13:15, Smith Liu wrote:
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?
Seeing as no-one else has
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>
签名由网易邮箱大师
<
On 12/18/2017 05:39 AM, Eleanor Dodson wrote:
I showed you pdbset ..
Find the centre of mass for your assembly.
Move it where you will
Thanks. What James was suggesting was somewhat different (if I understood
correctly): move EVERY ATOM to 1,1,1.
like:
awk -v FIELDWIDTHS="30 24 26" \
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
.
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
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
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
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"
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
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
lt;pems...@mrc-lmb.cam.ac.uk>
> Sent: Thursday, December 14, 2017 3:25:19 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] coordinate transformation
>
> On 13/12/2017 13:50, Kajander, Tommi A wrote:
> > Hello,
> >
> > If someone could point this out would be
nks to all who responded.
>>>
>>>
>>> Cheers,
>>>
>>> Tommi
>>>
>>>
>>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul
>>>Emsley
>>> <pems...@
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
;>> otherwise - but this solves my problem)
>>>
>>>
>>> Thanks to all who responded.
>>>
>>>
>>> Cheers,
>>>
>>> Tommi
>>>
>>>
>>> From: CCP4 bulletin board <CCP4
hanks to all who responded.
Cheers,
Tommi
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
<pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transfo
> >
> > Tommi
> >
> >
> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul
> Emsley
> > <pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, December 14, 2017 3:25:19 AM
> > To: CCP4BB@JISCMAIL.AC.UK
&
all who responded.
>
>
> Cheers,
>
> Tommi
>
>
> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
> <pems...@mrc-lmb.cam.ac.uk> Sent: Thursday, December 14, 2017 3:25:19 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp
.
Cheers,
Tommi
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley
<pems...@mrc-lmb.cam.ac.uk>
Sent: Thursday, December 14, 2017 3:25:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] coordinate transformation
On 13/1
On 13/12/2017 13:50, 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.
At the risk of not
Hi Tommy,
Try ACHESYM, it is very useful:
http://achesym.ibch.poznan.pl/
Here is the link to the publication:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257622/
Good luck,
Bartosz
Wouldn't the PISA server do something like this?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kajander,
Tommi A
Sent: Wednesday, December 13, 2017 8:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] coordinate transformation
Hello,
If someone could point this out
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
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