[phenixbb] chain and residue ID in phenix.erraser

Pavel Afonine pafonine at lbl.gov
Wed Nov 8 12:18:41 PST 2017


What would be really helpful is to make this tool to comply with all 
other Phenix tools that use Phenix atom selection syntax. It is 
confusing if different tools within the same software package use 
different languages to refer to atoms.

Pavel

On 11/8/17 11:34, Ursula Schulze-Gahmen wrote:
> Yes, chainID:residue number (N:32) is working. Thanks.
>
> It might be helpful for others to include this syntax in the error 
> message.
>
> In general, erraser is working great for RNA modelling at medium to 
> low resolution!
>
> On Mon, Nov 6, 2017 at 9:43 PM, Andy Watkins <andy.watkins2 at gmail.com 
> <mailto:andy.watkins2 at gmail.com>> wrote:
>
>     Try N:32, i.e., separate chain and residue number with a colon.
>     I'm not sure what other formats might be supported, but the
>     colon-including format definitely is.
>
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>     On Mon, Nov 6, 2017 at 8:30 PM, Ursula Schulze-Gahmen
>     <uschulze-gahmen at lbl.gov <mailto:uschulze-gahmen at lbl.gov>> wrote:
>
>         I am trying to run phenix.erraser, but I am not able to define
>         the single residue for rebuilding correctly. I am getting
>         error messaheg: Please make sure that you include both the
>         chain ID and residue number, for example 'A15'.
>         I want to rebuild nucleotide G32 in chain N, and defined the
>         residue as N32. That is not correct. What would be the correct
>         syntax for this case?
>
>         Ursula
>
>         -- 
>         Ursula Schulze-Gahmen, Ph.D.
>         Project Scientist
>         UC Berkeley, QB3
>         360 Stanley Hall #3220
>         Berkeley, CA 94720-3220
>         (510) 643 9491 <tel:%28510%29%20643-9491>
>
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>
> -- 
> Ursula Schulze-Gahmen, Ph.D.
> Project Scientist
> UC Berkeley, QB3
> 360 Stanley Hall #3220
> Berkeley, CA 94720-3220
> (510) 643 9491
>
>
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