Hi Neshatul, as Takanori already pointed out, PyMOL will bond those atoms based on distance when loading the PDB file. So after unbonding and before writing the structure out as a PDB file, you should change the coordinates of the cysteine sulfur atoms. A neat way to accomplish this is to use PyMOL's sculpting feature, which involves a VDW terms and thus will move the sulfur atoms away from each other, because they clash after unbonding.
Example: fetch 4ins, async=0 as cartoon show sticks, resn CYS unbond name SG, name SG protect not name SG sculpt_activate * sculpt_iterate *, 1, 1000 Cheers, Thomas On 14 May 2014, at 07:25, T. Nakane <tn...@cam.ac.uk> wrote: > Hi, > > This is because PyMOL does not read SSBOND records > in PDB files. Actually, PyMOL determines if a bond > is present based on atomic distances and CONECT records. > http://www.pymolwiki.org/index.php/Connect_mode > > PyMOL does not write SSBOND records when saving a > PDB file. > > Best regards, > > Takanori Nakane > > On 2014-05-14 12:07, neshat haq wrote: >> Hello every one, >> I am not able save the pdb file, after I broke the disulfide bond. >> what I did was >> 1-loaded the pdb file >> 2-selected 3-button editing mode >> 3-selected the two atoms bonded by disulfide bond >> 4-unbond pk1,pk2 >> Now it shows the bond break, but when I was saving the file without >> disulfide bond, it was not working.----------all the time file was >> saved with disulfide bond. >> How can it be solved......................anyone suggest something. >> >> -- >> Best regards >> Neshatul Haque >> PhD, Dpt of Biotechnology >> university of hyderabad -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
