Thanks. That's what I need. Qixu Cai
Email: caiq...@gmail.com 在 2013-2-25，下午9:38，Jon Agirre <jon.agi...@gmail.com> 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 <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
