Re: [ccp4bb] the matrix format

[Qixu Cai]

Thanks. That's what I need.

Qixu Cai

Email: caiq...@gmail.com

在 2013-2-25，下午9:38，Jon Agirre  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 :
>> 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 :
>> r11r12r13tx
>> r21r22r23ty
>> r31r32r33tz
>> 
>> 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
>> r11r12r13tx
>> r21r22r23ty
>> r31r32r33tz
>> 
>> 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
>> School of Life Sciences,
>> Xiamen University, Fujian, China
>> 
>> 
>> 2013/2/25 Jon Agirre 
>>> 
>>> 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 :
 Dear all,
 
 The matrix formats in different program always confuse me.
 
 The matrix format of the "REMARK 290 SMTRY" section of pdb file is:
 
 r11r12r13tx
 r21r22r23ty
 r31r32r33tz
 
 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

Re: [ccp4bb] the matrix format

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Qixu Cai,

cut and paste is yet another option and probably quickest if it is
only for a few PDB files.

Best,
Tim

On 02/25/2013 02:30 PM, vellieux wrote:
> 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 : r11r12r13
>> tx r21r22r23ty r31r32r33tz
>> 
>> 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 r11r12r13tx r21
>> r22r23ty r31r32r33tz
>> 
>> 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  
>> School of Life Sciences, Xiamen University, Fujian, China
>> 
>> 
>> 2013/2/25 Jon Agirre > >
>> 
>> 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 > >:
>>> Dear all,
>>> 
>>> The matrix formats in different program always confuse me.
>>> 
>>> The matrix format of the "REMARK 290 SMTRY" section of pdb file
>>> is:
>>> 
>>> r11r12r13tx r21r22r23ty r31r32
>>> r33tz
>>> 
>>> 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
>> 
>> 
> 
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] the matrix format

[Jon Agirre]

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 :
> 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 :
> r11r12r13tx
> r21r22r23ty
> r31r32r33tz
>
> 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
> r11r12r13tx
> r21r22r23ty
> r31r32r33tz
>
> 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
> School of Life Sciences,
> Xiamen University, Fujian, China
>
>
> 2013/2/25 Jon Agirre 
>>
>> 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 :
>> > Dear all,
>> >
>> > The matrix formats in different program always confuse me.
>> >
>> > The matrix format of the "REMARK 290 SMTRY" section of pdb file is:
>> >
>> > r11r12r13tx
>> > r21r22r23ty
>> > r31r32r33tz
>> >
>> > 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

Re: [ccp4bb] the matrix format

[vellieux]

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 :

r11r12r13tx
r21r22r23ty
r31r32r33tz

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
r11r12r13tx
r21r22r23ty
r31r32r33tz

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 
School of Life Sciences,
Xiamen University, Fujian, China


2013/2/25 Jon Agirre 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 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:
>
> r11r12r13tx
> r21r22r23ty
> r31r32r33tz
>
> 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

Re: [ccp4bb] the matrix format

[Qixu Cai]

Dear Jon,

Thanks for your reply.

The matrix format in the "REMARK 290" section of the pdb file (download
from rcsb.org) is :
r11r12r13tx
r21r22r23ty
r31r32r33tz

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
r11r12r13tx
r21r22r23ty
r31r32r33tz

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
School of Life Sciences,
Xiamen University, Fujian, China


2013/2/25 Jon Agirre 

> 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 :
> > Dear all,
> >
> > The matrix formats in different program always confuse me.
> >
> > The matrix format of the "REMARK 290 SMTRY" section of pdb file is:
> >
> > r11r12r13tx
> > r21r22r23ty
> > r31r32r33tz
> >
> > 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
>

Re: [ccp4bb] the matrix format

[Jon Agirre]

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 :
> Dear all,
>
> The matrix formats in different program always confuse me.
>
> The matrix format of the "REMARK 290 SMTRY" section of pdb file is:
>
> r11r12r13tx
> r21r22r23ty
> r31r32r33tz
>
> 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