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Subject:

Re: the matrix format

From:

Qixu Cai <[log in to unmask]>

Reply-To:

Qixu Cai <[log in to unmask]>

Date:

Tue, 26 Feb 2013 09:18:01 +0800

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (126 lines)

Thanks. That's what I need.

Qixu Cai

Email: [log in to unmask]

在 2013-2-25,下午9:38,Jon Agirre <[log in to unmask]> 写道:

> If you just want to generate symm mates from MTRIX records, you may
> want to give GK's 'xpand' a go:
> http://xray.bmc.uu.se/usf/xpand_man.html
> 
> Otherwise, I would follow Fred's advice.
> 
> Jon
> 
> 2013/2/25 vellieux <[log in to unmask]>:
>> 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) 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: [log in to unmask]
>> School of Life Sciences,
>> Xiamen University, Fujian, China
>> 
>> 
>> 2013/2/25 Jon Agirre <[log in to unmask]>
>>> 
>>> 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 <[log in to unmask]>:
>>>> 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
>> 41 rue Jules Horowitz
>> F-38027 Grenoble Cedex 01
>> Tel: +33 438789605
>> Fax: +33 438785494
> 
> 
> 
> -- 
> Jon Agirre, PhD
> Unit of Biophysics (CSIC-UPV/EHU)
> http://sourceforge.net/projects/projectrecon/
> +34656756888

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