-----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 <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 >> >> > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRK4KtUxlJ7aRr7hoRAmmHAJ98bjTECrsRsoksaeZku2BmEPF9WACeK1CE wyvRASnup1qIwPYjlbNeKDY= =7S0m -----END PGP SIGNATURE-----
