Hi, Thomas, 

thanks for checking that and responding quickly. I also found out the meaning of the option myself. At the moment, I write some post-processing scripts to cope with that issue. 


On Tue, Aug 19, 2014 at 4:05 PM, Thomas Holder <thomas.holder@schrodinger.com> wrote:
Hi Hongbo,

you are right that the website and the implementation don't match, thanks for pointing that out. This was a feature request from a paying PyMOL sponsor, which often means that we put the feature only (or first) in Incentive PyMOL. But thinking about it, this is a rather small change and probably not worth to keep as a distinguishing feature. I'll port it to open-source today.

To clarify the issue with duplicated connect record. This is an unofficial PDB feature to store the bond order and is supported by several applications that read PDB files, but may break PDB file loading in other applications which don't support it. PyMOL always wrote duplicated connect records and the new setting allows you to switch that off.


On 18 Aug 2014, at 15:04, Hongbo Zhu 朱宏博 <hongbo.zhu.cn@gmail.com> wrote:
> Hi,
> I am using PyMOL 1.7 open source version in Ubuntu 14.04.
> I wanted to try a new setting  pdb_conect_nodup in pymol 1.7.
> It is listed as new features available for both "Open Source and Incentive" at:
> http://pymol.org/features#v1.7
> when I set it to on, I got:
> "Setting-Warning: not supported in open-source version of PyMOL"
> though the setting could be successfully set (get pdb_conect_nodup).
> After saving a test PDB files, I still see duplicate CONECT lines in the PDB file generated by PyMOL. So I guess the feature is indeed missing in open source version.
> Should the feature be made available to open source version users?
> cheers,
> Hongbo

Thomas Holder
PyMOL Developer
Schrödinger, Inc.