I prepared this on Sunday, here it is now:-
Well, I was 'shaken but not stirred' to see a program 'fake_Fobs'. However
James' posting on the Rfactor gap in MX is a more respectable, Sunday morning,
topic. I tried to find the previous threads on this via google and couldn't. So
apologies to all
Hi James,
I guess it depends on what you put in your simulated Fobs. With
phenix.fake_f_obs I can add lots of stuff including H, TLS, small random
rigid-body shifts averaged over ensemble of MD simulated models,
alternative conformations, libration motions of side chains around bonds,
etc.. etc...
Hi Alastair,
since you mentioned it... In our article "On the analysis of residual
density distribution on an absolute scale":
http://www.phenix-online.org/newsletter/CCN_2012_07.pdf
one of the conclusions was that we could not reproduce pronounced features
on the solvent/macromolecule border show
thanks for the reference to the script and additional discussion. I've
looked through the archives a bit but couldn't find an answer to a
question that's been on my mind for a while so my apologies if this
revisits well-trod ground. One of the potential sources of disagreement
contributing to
I feel like I should point out that there is about a 20% difference
between "Fcalc" and something I would call a "simulated Fobs". Fcalc is
something that refinement programs compute many times every second as
they apply 100 years worth of brilliant ideas to make your model (Fcalc)
match your
Below are some links to tools for simulating Fobs data:
phenix.fake_f_obs:
http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fake_f_obs.py
phenix.fmodel: http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fmodel.py
sftools (calc keyword): http://www.ccp4.ac.uk/html/sftools.html
diffraction
sftools is another option (for applying randomly distributed errors to Fc).
Depending on what you're simulating, it might be worth pointing out that
while it's relatively easy to simulate Fo, it's more difficult to
simulate sigFo realistically. This matters for any simulations using
sigma_a (
ay, September 04, 2013 5:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fo simulators?
Any pointers to open-source software for generating (for legitimate
purposes) simulated Fo data starting from Fc or pdb would be much
appreciated. I understand phenix.fmodel is an option - are there others?
thanks,
Alastair Fyfe
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Dear Alastair Fyfe,
sfall can generate amplitudes from coordinates, but I guess you know
this. Out of curiosity: What exactly to you mean to "simulate an
observation" as opposed to calculate amplitudes from a model? It
sounds nearly like an oxymoron t
Hi Alastair,
phenix.fake_f_obs might be of use depending on your goals. It's not a
fool-proof end-user tool (in terms of convenience of use, docs, etc etc
etc), and may require knowledgeable tweaking before you get a meaningful
outcome; if interested talk to me off list. I used it when some one
ch
Any pointers to open-source software for generating (for legitimate
purposes) simulated Fo data starting from Fc or pdb would be much
appreciated. I understand phenix.fmodel is an option - are there others?
thanks,
Alastair Fyfe
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