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 <frederic.velli...@ibs.fr>: > 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: caiq...@gmail.com > School of Life Sciences, > Xiamen University, Fujian, China > > > 2013/2/25 Jon Agirre <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>: >> > 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
