[buster-discuss] Several questions - BUSTER-TNT refinement

Jose Artur Brito jbrito at itqb.unl.pt
Fri Jul 19 15:01:12 CEST 2013

Dear Clemens,

I have a few questions regarding BUSTER-TNT refinement. I thought two times
before sending them to the buster-discuss forum because they are probably
too basic but in the end I decided to ask your help.

So, here's the thing:

- I solved the structure by SAD with the Fe anomalous signal with data
collected at 1.72A wavelength (the structure is to 1.98A and also has
two iodide atoms which were useful in phasing as extra sites);
during the refinement, I saw that there are two keywords in BUSTER that
I thought it could useful and used them: "wavelength=1.72" and
"AtomicFormFactorCorrection=yes"; was this OK, did I do the correct thing?

- now, I'm refining a second structure of the same protein but this time
reduced with dithionite; the resolution is 1.75A and the data was
collected at 1.23A wavelength; should I also use those two keywords?
This structure has the two Fe atoms and 1 iodide atom.

- is there any detrimental effect in using an "nmiss" higher that what
it is expected? I don't see ca. 20 residues at both termini and and a
loop of about 6 residues; I used "nmiss=1000" in the initial rounds of
refinement and reduced to "nmiss=300" in this last refinement;

- should I provide a sequence file to the program in order to tell it
which residues are actually missing? What is the keyword for this?

- the structure is a cytochrome and when refining the heme, BUSTER
corrects the format of COOT with "pad with spaces" and correct to
"nomenclature v2"; what is this? is there a conflict between the
libraries of both programs?

Sorry for the long e-mail... Wishing you all a nice weekend, best regards,

* José Artur Brito, PhD                        *
*                                              *
* Post-Doctoral Fellow                         *
* Membrane Protein Crystallography Lab         *
* Instituto de Tecnologia Química e Biológica  *
* Oeiras - Portugal                            *
*                                              *
* Tel.: +351.21.446.97.61                      *
* Fax:  +351.21.443.36.44                      *
*                                              *
* E-mail: jbrito at itqb.unl.pt                   *
* URL: http://mx.itqb.unl.pt                   *

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