[phenixbb] Getting Residual Bs

Pavel Afonine pafonine at lbl.gov
Sun Mar 30 01:07:30 PDT 2008

Hi Frank,

> What *is* the tool in phenix to from total to partial?  I suspect it's 
> one of the phenix.pdbtools adp commands, but the documentation is a bit 
> sparse on that program.

There is currently no such tool simply because no-one ever asked for 
this. It is trivial to add and I will implement it as an option in 
phenix.pdbtools as soon as I get to it (hopefully, really soon). It will 
be documented as well.

> Hi, here's what triggered my earlier rant:
> I took a pdb from phenix.refine back into refmac, with same TLS 
> definitions, but leaving the ANISOU cards in (accident).  I ran this 
> through TLSANL, asking for total B.
> Refmac has left the ANISOU cards, but all zero except the first 
> element.  ATOM B is much lower.

As I said previously, working on phenix.refine I do not expect people 
jumping between the programs. I assume if phenix.refine is missing an 
option and someone run into a need of it, he or she will write us and 
ask for that feature rather than switching to another software. We 
usually try to address such requests quickly. Having this in mind, I do 
not spend much effort on making this jumping easy.

With some minor exceptions (which are working on currently) 
phenix.refine covers the functionalities of most popular software 
packages and has a whole lot of unique features.

Frankly, I do not know what Refmac will do with phenix.refine PDB files 
containing TLS.


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