Re: [PyMOL] algorithm for alignment

Am Samstag, 26. Januar 2008 schrieb Lu Lin: Hi, Abhi, You mean save them separately? Is there some way to save them into one file? Thanks!! By default, the save command should save all (visible?) atoms. Should be in documentation of save. Any way you can also make a selection of your two

Re: [PyMOL] algorithm for alignment

Hi, 'save' will save all atoms by default, not only the visible ones. cat in Linux will surely be more efficient than loading in Pymol and saving, but the question related to alignment. cat doesn't do that for you. So the procedure would be: load A.pdb,A load B.pdb,B align A,B save

[PyMOL] algorithm for alignment

Hi all, Anyone know which algorithm PyMOL uses to align or super of two structures? Thanks a lot! Best, Linda

Re: [PyMOL] algorithm for alignment

...@delsci.info -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Lu Lin Sent: Friday, January 25, 2008 4:29 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] algorithm for alignment Hi all

Re: [PyMOL] algorithm for alignment

Hi Hally, Thank you for your reply! Could you tell me how to save the alignment result to a new .pdb file? Thanks again! Best, Linda Hally Shaffer wrote: Linda, To align two proteins, they have to have the same number of atoms. You can manipulate the pdb files to delete part of one protein

Re: [PyMOL] algorithm for alignment

there is something on the menu, file-save-molecule after the alignment, choose the molecule you want to save and just save. pymol saves the pdb with new coordinates. cheers, Abhi On Jan 25, 2008 10:29 PM, Lu Lin l...@cs.hku.hk wrote: Hi Hally, Thank you for your reply! Could you tell me how

Re: [PyMOL] algorithm for alignment

...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Lu Lin Sent: Friday, January 25, 2008 4:29 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] algorithm for alignment Hi all, Anyone know which algorithm PyMOL uses to align or super of two structures? Thanks

Re: [PyMOL] algorithm for alignment

Hi, Abhi, You mean save them separately? Is there some way to save them into one file? Thanks!! Best, Linda Abhinav Verma wrote: there is something on the menu, file-save-molecule after the alignment, choose the molecule you want to save and just save. pymol saves the pdb with new