[phenixbb] phenix.metal_coordination

YoungJin yjcho at brandeis.edu
Tue Jan 3 19:25:39 PST 2012

Thanks Ralf,
Actually that's what I did after several trials and errors. Once I 
deleted alternative conformers of waters (only metal), there was no 
problem. After that, I manually added B for the metal.

Thanks again.


On 1/3/12 4:06 PM, Ralf Grosse-Kunstleve wrote:
> Hi Young-Jin,
> Nigel who wrote the phenix.metal_coordination utility isn't back yet 
> from the holidays. You may be running into a limitation of the 
> utility. To work around it, I'd try with a temporary copy of the PDB 
> file with the alternative conformers removed. The resulting .edits 
> should be a good starting point.
> If this doesn't get you on the right track could you send me (not the 
> list) your pdb file?
> Ralf
> On Tue, Jan 3, 2012 at 10:19 AM, Young-Jin Cho <yjcho at brandeis.edu 
> <mailto:yjcho at brandeis.edu>> wrote:
>     Hi everyone and wish your happy new year.
>     I have a question regarding phenix.metal_coordination. when I typed my
>     pdb file that has two alternative conformations of different species
>     including metal such as a metal(B) and a water(A). It seems like, in
>     this case, phenix.metal_coordination doesn't read the metal.
>     Otherwise, is there other way I can let make .edits file for this pdb
>     file?
>     Thanks always in advance,
>     Young-Jin
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://phenix-online.org/mailman/listinfo/phenixbb
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120103/15404505/attachment.htm>

More information about the phenixbb mailing list