Hi Sangita, This is trickier than it should be in PyMOL. The problem lies in the fact that when you cut one residue it makes two chemically separate entities that are stored internally as one object--so PyMOL tries to re-connect the bonds. One trick, that sometimes works is:
set connect_mode, 2 set connect_cutoff, 0 then load your file. Cheers, -- Jason On Mon, Jun 7, 2010 at 12:24 PM, Sangita Kachhap <[email protected]> wrote: > > > Hello all > > I have to cut phosphodiester bond in DNA.I am able to cut it by selecting pk1 > and pk2 and then deleting the bond. But I am not able to save the coordinate. > When I am saving by "save molecule" and aging loading the saved molecule > original molecule(Uncut DNA) is loaded. > > Can anybody suggest me how to save coordinate for cut DNA. > > With regard > Sangita Kachhap > JRF > BIC,IMTECH > CHANDIGARH > > ------------------------------------------------------------------------------ > ThinkGeek and WIRED's GeekDad team up for the Ultimate > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the > lucky parental unit. See the prize list and enter to win: > http://p.sf.net/sfu/thinkgeek-promo > _______________________________________________ > PyMOL-users mailing list ([email protected]) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/[email protected] > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) [email protected] (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ PyMOL-users mailing list ([email protected]) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/[email protected]
