Re: [PyMOL] bond connection file

2012-10-05 Thread Thomas Holder
Hi Vishwas, atom connectivity is the same for all states unless you have a discrete object. Try this: PyMOL set connect_mode, 1 PyMOL load file.pdb, discrete=1 Cheers, Thomas Vishwas Vasisht wrote, On 10/05/12 08:59: Hi Thomas, Thanks, it works for single frame. But when I use

Re: [PyMOL] bond connection file

2012-10-05 Thread Jordan Willis
Does every MODEL ENDMDL have a unique Connection list? Can you show me your PDB file? Jordan On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht vishwas.vasi...@gmail.com wrote: Hi Thomas, Thanks, it works for single frame. But when I use multiple frame (using MODEL and ENDMDL), the

Re: [PyMOL] bond connection file

2012-10-04 Thread Thomas Holder
Hi Vishwas, you can use PDB format with CONECT records. You need to set connect_mode=1 before loading the PDB file into PyMOL. http://pymolwiki.org/index.php/Connect_mode http://www.wwpdb.org/documentation/format33/sect10.html#CONECT Hope that helps. Cheers, Thomas Vishwas Vasisht wrote,