Hi,
Emacs, vi, any (text file) editor ? I wouldn't advise a word processing
program (Word and the likes).
Unless you want to do this on many pdb files in which case writing a
small program or shell script would be required.
Fred.
On 25/02/13 14:24, Qixu Cai wrote:
Dear Jon,
Thanks for your reply.
The matrix format in the "REMARK 290" section of the pdb file
(download from rcsb.org <http://rcsb.org>) is :
r11 r12 r13 tx
r21 r22 r23 ty
r31 r32 r33 tz
And I want to extract the matrix information from the pdb file "REMARK
290" section and use the matrix in the pdbset.
so I have to convert the matrix from
r11 r12 r13 tx
r21 r22 r23 ty
r31 r32 r33 tz
to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz.
How can I do it?
Thanks.
Qixu Cai
Qixu Cai
Email: caiq...@gmail.com <mailto:caiq...@gmail.com>
School of Life Sciences,
Xiamen University, Fujian, China
2013/2/25 Jon Agirre <jon.agi...@gmail.com <mailto:jon.agi...@gmail.com>>
Dear Qixu,
here's an excerpt from the pdbset manual:
TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32
r33 tx ty tz
I'm not sure what you mean by "covert from the "pdb file format" to
the "pdbset format"". Please elaborate on this.
Jon
2013/2/25 Qixu Cai <caiq...@gmail.com <mailto:caiq...@gmail.com>>:
> Dear all,
>
> The matrix formats in different program always confuse me.
>
> The matrix format of the "REMARK 290 SMTRY" section of pdb file is:
>
> r11 r12 r13 tx
> r21 r22 r23 ty
> r31 r32 r33 tz
>
> What's the matrix format accepted by the "transform file"
keywords of the
> pdbset program?
> is it "r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz"?
> And how to covert from the "pdb file format" to the "pdbset format"?
>
> What's the matrix format of "apply NCS operators" in phenix GUI?
>
> Thanks a lot!
>
> Qixu Cai
--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888
--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
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