[phenixbb] questions/problems with tls_as_xyz routines

David A Case david.case at rutgers.edu
Mon Apr 11 06:41:44 PDT 2016

I'm trying to use tls_as_xyz, but having some problems.

1. In the paper describing this, Urzhumtsev et al, Acta Cryst D71:1668, 2015,
there seems to be something wrong with Section 6.2, which describes results
on PDB entry "1dqv", syanptotagmin III.  The description says that there are
two copies of the molecule in the asymmetric unit, and the resolution is 2.5

However, the file with this code in the RCSB (which is indeed syanptotagmin
III) has one molecule per asymmetric unit, a single chain of 296 amino acids,
rather than two chains of 97 amino acids, as in Tables 2 and 3 of the paper
cited above; the resolution is 3.2 Ang.  And it doesn't look anything like
the picture of "1dqv" in Fig. 3a.

So something looks wrong; does anyone know what system Section 6.2 is using?

2. I'm asking the above because I'm having trouble with my own applications,
and was hoping to check that I could reproduce the results in the paper.
Apropos of that, is there a test case or example for tls_as_xyz in the phenix
distribution?  [I'm not all that familiar with phenix, so apologies if I've
missed the easy way to find this.]

3. Here is a summary of what is not working for me.  (I don't expect anyone to
debug this on such little information, but thought that someone on the list
might have done some similar calculation.)

    a. I took a small domain (residues 6-61 from GB3, PDB code 2IGD), and
       used Ethan Merrit's lsq_tls_fit to obtain a set of TLS tensors that
       best fit the deposited ADP's.  The statisitcs are pretty good,
       indicating (not surprisingly) that motions in this domain are well
       characterized as a rigid body--which is why I chose this system.
       I just used the CA atoms for this initial study.

    b. I used phenix.tls_as_xyz to compute an ensemble from the TLS matrices
       obtained in step a.

    c. I then computed ADP's from the ensemble, using tools from cpptraj
       in Amber, (or our own codes, which give the same results).  But
       the extracted isotropic B factors (and the anisotropic
       components) are much larger than the input ones.  So, the ensemble is
       giving me what I expected: a sampling of structures whose fluctuations
       arise from the input TLS matrices.

I've done a fair amount of due diligence in trying to track down errors on my
end, but I could be making a mistake on any one of the steps above.  Or, I
could be mis-interpreting what I should expect to get from the tls_as_xyz
procedure.  I'd be happy to share details off-line with any one who might
volunteer to help.

...thanks...dave case

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