That would seem to violate rule #1 of macromolecular depiction: Never change the coordinates! But then I can't imagine why one would want to not draw a disulfide bond in a real protein structure, so maybe this is some kind of exercise where it is not important to adhere to the experimental results, like generating a peptide that spells out your name with its sequence. If it is a real protein and you want to present your result as that protein's structure, i would prefer breaking the bond every time, perhaps with a script.
eab On 05/14/2014 11:23 AM, Thomas Holder wrote: > 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 > ------------------------------------------------------------------------------ "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
