[phenixbb] Can PHENIX write the peak list to a PDB file?

[Morten Grøftehauge]

Dear Pavel,

Is this in? I wanted to do an anomalous peak search in a way that was faster
than the CCP4 route but it doesn't seem to be available.

Sincerely,
Morten Grøftehauge


On 1 October 2009 02:46, Pavel Afonine <PAfonine at lbl.gov> wrote:

>  Hi Joe,
>
> yes, I agree on this. It's on my list already and hopefully I do it soon.
>
> Thanks for the feedback!
>
> Pavel.
>
>
>
> On 9/30/09 4:41 PM, Joe Krahn wrote:
>
> A few more comments on writing peak coordinates, after going through
> peaks based on the current PHENIX log file:
>
> Having actual coordinates present as atoms makes it easy to measure
> distances to other atoms. Less importantly, if there are two peaks close
> to each other, it is not always obvious which peak matches the log.
>
> It may be sufficient to write the peak coordinates in the log file. That
> would avoid the need for adding another output file. It would not be
> that hard to parse into either a PDB file, or some sort of
> program-specific list or script.
>
> Thanks,
> Joe Krahn
>
> Krahn, Joe (NIH/NIEHS) [C] wrote:
>
>
>  Pavel Afonine wrote:
>
>
>  Hi Joe,
>
>
>
>  PHENIX has an option to find positive and negative peaks, but only lists
> them in the log file along with the residue they are closest to.
>
>
>  I have done it this way having the following in mind:
>
> - you load you refined model and maps in your favorite graphics program,
> Coot for example;
> - you take that +/- peaks list;
> - and you go residue-by-residue and check the flagged peaks.
>
>
>
>  Is it
> possible to write out the actual peak coordinates, such as to a PDB file?
>
>
>
>  It's possible of course, but I have a couple of questions:
>
> - why to do this?
> - what do I put as atom name, residue name, occupancy, B-factor, atom
> chemical type ?
>
> Thanks again for your feedback!
> Pavel.
>
>
>
>  Most of the time, I optimize a model by stepping through peaks, rather
> than walking through all residues. In most software, it is easy to step
> through residues in a PDB file, whereas converting the PHENIX log output
> into something that can automate this is likely program specific.
>
> My standard approach is to get a peak list in the form of a PDB file,
> sorted from the highest peak, and work through those peaks until they
> become too weak. I can fix model errors, or add a water at the peak
> position, or decide that it is something other than water. Having an
> atom at the peak makes it easy to add waters, which is good for
> lower-resolution or noisy maps, where I don't trust automated waters.
>
> Many programs write peaks as PDB files, usually with B-factor set from
> the difference-map sigma level. Some programs write them out as waters,
> which is probably safest to avoid problems with non-standard names. The
> occupancy is usually 1.0, but it could be set to zero to flag that they
> are not actual model coordinates.
>
> This approach used to be very common. Some new programs have built-in
> peak search utilities, so it may be getting less common for that reason.
>
> Thanks,
> Joe Krahn
>
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