Dear all, dear Ian,
I am trying to run edstats from command line. I have read the previous
threads here and I was using the edstats.pl perl script. However I fail.
Here is what I type and what I get (same on a centos machine and my mac).
$ edstats.pl -hklin paefs_018_dimple_refmac.mtz -pdbin
Dear Peter,
the ccp4i2 EDSTATS task works differently to its ccp4i interface. There are
plenty of differences between ccp4i and ccp4i2 in terms of how interface
logic is handled, and using (internally generated) map coefficients is one
of them. Regrettably, due to a bug it used to be impossible to
On linux and windows there is a problem with EDSTATS in ccp4i2. I always get
error messages like cfft failed aso. I tried to read input maps in ccp4 format
and even mtz files with map coefficients, which is not in the original
description, but apparently required in the ccp4i2 versions (?). The
not win matches.
From: George Devaniranjan
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" f
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 lo
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
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 fi
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_ "f
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 check
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.
>
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
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 n
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 ref
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 witho
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