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From: George Devaniranjan devaniran...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, 11 June 2014, 19:22
Subject: Re: [ccp4bb] EDSTATS for an extracted fragment
Thank you Gerard for your suggestion.
I will look into the paper you suggested and MAPMAN too.
I am idealizing
Hi George
Yes you do. It's important to understand that you are not comparing the
MTZ file (the data) with the PDB file (the model): that's not possible,
at least not directly. So you can't simply change the PDB file, redo the
comparison and hope to get sensible results. EDSTATS is _not_
What you want is a test for how well each model agrees with its own map. It
is fair to argue that the model that is more self-consistent (agrees better
with its own map) is the better model. But you won't learn that by
comparing model A to map B.
However, conversely, if your modified model
On Wednesday, 11 June, 2014 20:01:45 Gerard DVD Kleywegt wrote:
What you want is a test for how well each model agrees with its own map. It
is fair to argue that the model that is more self-consistent (agrees better
with its own map) is the better model. But you won't learn that by
Thank you Gerard for your suggestion.
I will look into the paper you suggested and MAPMAN too.
I am idealizing fragments of PDB and while this would not agree when
compared with the well refined structure, my goal really is seeing if
these ideal fragments can still be identifiable when I look
HI,
I want to calculate real-space R factor/RSCC and such parameters using
EDSTATS in CCP4 but only for a selected fragment that has been
extracted and then modified (changed the Phi and Psi) from the native.
I have the original MTZ and MAP.
Is it even possible to calculate these values
Hi, I'm puzzled by what you are trying to do. You say you have the
original MTZ/MAP files. What have the original files got to do with it?
EDSTATS requires the MTZ/MAP file calculated for the supplied model. The
documentation states: ... the PDB file and the maps should all be from the
same
Hi, sorry small clarification.
The complete PDB file that you used to run the refinement job (i.e. the
input PDB file) will obviously only be suitable in the case that you did 0
cycles of refinement. If you did some refinement of the model then the
co-ordinates will have changed, and then you
Thank you Ian.
To clarify, I actually want to compare the new PDB file to the old MTZ
file to see how well the residues fit. This is why I mentioned that I have
the old MTZ file I generated from SF's which I got from the PDB.
I am not trying to improve the deposited structure, I am trying to get
On Tuesday, 10 June, 2014 19:13:57 George Devaniranjan wrote:
Thank you Ian.
To clarify, I actually want to compare the new PDB file to the old MTZ
file to see how well the residues fit. This is why I mentioned that I have
the old MTZ file I generated from SF's which I got from the PDB.
I
Thank you Ethan.
Supposing I want to compare with the experimental map, a small fragment of
the model (let's say residues 15-30 in a protein of 100 residues).
Supposing I start with one model but now extract from that model residues
15-30 (let's call it model 1) , modify it and now want to
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