<div dir="ltr">Thanks for clarifying its purpose! I guess I do still have one question, though: are ccp4 files computed via phenix.maps (from e.g., a .pdb and .mtz) unsuitable for real-space refinement (e.g., some kind of structural optimization with a scoring function that includes an electron density term) because such a ccp4 file is itself influenced by the starting model?</div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 25, 2016 at 1:57 PM, Dale Tronrud <span dir="ltr"><<a href="mailto:detBB@daletronrud.com" target="_blank">detBB@daletronrud.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
An mtz file is a generic container for information that is<br>
represented as Fourier coefficients - amplitudes and/or phases. The mtz<br>
you get from data reduction contains your observed diffraction pattern.<br>
There are quite a variety of things that might be in there, e.g.<br>
intensities, amplitudes, indications of anomalous scattering.<br>
<br>
The "map_coeffs" mtz probably echos all of those data and includes<br>
the amplitudes/phases which can be used to calculate several maps.<br>
These coefficients are derived from both your observations and the<br>
coordinates of your model that matches the "map_coeffs" file. The<br>
program could simply write a map file directly, but the Fourier<br>
representation takes less disk space and is quicker to read and write<br>
than a map.<br>
<br>
The "map_coeffs" file is a "throw away" file. You use it to look at<br>
your map, but when you continue refinement you should always use the<br>
original mtz. You don't want to refine your model against an mtz that<br>
contains data calculated from your model. While it might be okay, it is<br>
safer to stick with the original.<br>
<br>
Dale Tronrud<br>
<span class=""><br>
On 5/25/2016 10:38 AM, Andy Watkins wrote:<br>
> Thanks--that certainly makes sense. In that case, I suppose I have a<br>
> different question: what distinguishes the .mtz file suffixed<br>
> "map_coeffs," which is output by phenix.maps, from the input .mtz?<br>
><br>
> On Wed, May 25, 2016 at 1:28 PM, Christian Roth<br>
</span><div><div class="h5">> <<a href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a> <mailto:<a href="mailto:christianroth034@gmail.com">christianroth034@gmail.com</a>>> wrote:<br>
><br>
> You might look for the Real space correlation coefficient to see if<br>
> your model fit that particular map better than before, but thats<br>
> probably it.<br>
><br>
> There is no subset experimental data just influenced by one chain.<br>
> The whole complex contributes to each measurement and vice versa<br>
> your chain A model contribute to each measurement you made to<br>
> generate the maps. Sorry, but that's it<br>
><br>
> Christian<br>
><br>
> Am 25.05.2016 um 17:31 schrieb Andy Watkins:<br>
>> Perhaps necessary preface: I am largely learning as I go, and<br>
>> large parts of Phenix (and the details of refinement data file<br>
>> formats) are still black boxes for me.<br>
>><br>
>> Suppose I have a model of one chain of a complex and an .mtz<br>
>> describing the entire complex. I have performed some refinement<br>
>> procedure altering the model of that single chain.<br>
>><br>
>> My aim is to determine how this refinement procedure has affected<br>
>> the fit to the experimental data--or, really, the subset of the<br>
>> experimental data expected to be relevant for my model.<br>
>><br>
>> For obvious reasons,<br>
>><br>
>> phenix.model_vs_data chain_A.pdb whole_complex.mtz<br>
>> phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz<br>
>><br>
>> are undesirable: they evaluate the model of a single chain against<br>
>> the whole complex's data, and there's obviously a lot of<br>
</div></div>>> unsatisfied electron density. So, while this command /works/, it<br>
<span class="">>> reports an unrepresentative fit. (In theory, one solution to my<br>
>> problem would be to re-combine each chain's refined version, then<br>
>> run model_vs_data on the recombined, refined complex. I'm<br>
>> interested nonetheless in how it would work on the chains separately.<br>
>><br>
>> Now, during the refinement procedure, we of course generate .ccp4<br>
>> density maps for the individual chain models:<br>
>><br>
>> phenix.maps chain_A.pdb whole_complex.mtz<br>
>><br>
>> which produces the ccp4 file as well as, crucially,<br>
>> chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz<br>
>> file, i.e.<br>
>><br>
>> phenix.model_vs_data chain_A.pdb whole_complex.mtz<br>
>> phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz<br>
>><br>
>> leads to an evocative error: Sorry_No_array_of_the_required_type:<br>
>> No reflection arrays available.<br>
>><br>
>> My highest suspicion is that I need to alter maps.params in a<br>
>> particular way so that reflection arrays are also output to<br>
>> model_map_coeffs.mtz. I could also imagine that I need to be using<br>
>> another program entirely!<br>
>><br>
>> Thanks in advance for whatever help you can provide;<br>
>> unfortunately, I can't provide any input files.<br>
>><br>
>><br>
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