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

Pavel Afonine PAfonine at lbl.gov
Wed Sep 30 17:46:52 PDT 2009

Hi Joe,

yes, I agree on this. It's on my list already and hopefully I do it soon.

Thanks for the feedback!


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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