http://www.pymolwiki.org/index.php/Retain_order
see if this helps
João
On Fri, Aug 12, 2016 at 5:25 PM, windy <chxp_m...@163.com> wrote:
> Hi,
>
> Everyone.
>
> I always using pymol to prepare the pdb files for MD simulations.
> However, when I merge the extra small molecular (substrate optimized from
> the Gaussian09, mol2 formats) and the protein file (PDB formats) into the a
> single pdb, I found the atom order of substrate is not the same as the
> original mol2 files.
>
> It seems the pymol would put the the hydrogen atom after the heavy
> atom. It also rearrange the atom when convert the mol2 file to mol2 file
> when using the pymol. (The attachments, from the test1 to test2 by using
> pymol)
>
> However the rearrangement of the atom is not very convenient for the
> following actions. I wonder how to keep the original atom order when
> convert to other formats by using pymol. （I using PYMOL 1.7.0 in Ubuntu
> 14.04）
>
> Thanks very much.
>
> Chen
>
>
>
>
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--
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. http://sdm.link/zohodev2dev
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