Dear all,
I´m doing some comparissons of main chain conformations using LSQKAB
and I would like to know from you how can I quantify a delta atom
result.
For instance, when I compare two identicals main chains I have the
following result:
0.0011C A 1C A
0.0012N A
Well - I usually work in confunction with the graphics, so you can look
at the regions which differ.
I start with the rms difference. If that is > 2, I think there are
significant changes. So then you have to decide what Q you are asking,
and why. Is it that you want to use a model for Molecul
Hi,
we recently published a method that could be just what you need, and
easy to implement.
It detects covalent modifications of cysteines, and mercury, gold and
some platinums target cysteines...
have a look at this paper.
feel free to contact me if you want more information.
vincent
Fluor
Dear All,
Version 2.5.0 of the CCP4 Molecular Graphics Program
(CCP4MG) has just been placed on the downloads page:
http://www.ccp4.ac.uk/MG/download/
This version includes many bug fixes and improvements over 2.4.3, including:
### General bug fixes
* Fix very serious Vista/Windows 7 crash
On Sun, 2011-04-03 at 23:17 -0500, Jacob Keller wrote:
> While the b cutoff is still be tricky, I assume we could eventually
> come to consensus on some reasonable cutoff (2 sigma from the mean?)
Not likely - the distribution of ADPs is not normal, so you can't easily
convert Z-scores to probabil
This could be my last post ...
I am now leaving mercury
It's surface was safe and free
Meet a mystical gryphon and some alien mosquitos
They gave me some protein crystals
Which tried to shoot like 007
Missed them all but the heaven
Will try again with my new X8
Which 007 would surely hate
Now app
Hi Dale,
Set the occupancy of a marker atom to -99.99.
> This will unambiguously mark the atom as an imaginary one. This
> will, of course, break every program that reads PDB format files,
may be not every -:)
phenix.model_vs_data works just fine with
http://www.rcsb.org/pdb/files/1BQU.pdb
h
> Not likely - the distribution of ADPs is not normal, so you can't easily
> convert Z-scores to probabilities.
Could it be that they are not normal because of all of the outlier,
huge-b-factor sidechains? If every exposed sidechain without real
density gets a b-factor of 150, wouldn't that make a
Dear James,
You make a very good point. So far we only discussed the option of removing
alls side chain atoms except for CB. What if only a few side chain atoms are
outside the density? Should we just remove those? If we use the argument that
we should remove the atoms we cannot see, then sur
Nice one Pavel. PDB_REDO actually runs on these files but it's not pretty. I
updated my stripper program to remove all atoms with occ<0.00 instead of 0.00
Cheers,
Robbie
Date: Mon, 4 Apr 2011 07:26:23 -0700
From: pafon...@gmail.com
Subject: Re: [ccp4bb] what to do with disordered side chain
Hi Robbie,
I updated my stripper program to remove all atoms with occ<0.00 instead of
> 0.00
>
- I used to do it in the past in phenix.model_vs_data but then I found it
too boring since it was silently swallowing the problem cases -:) so I
reverted it back to the "naive mode" when it takes what'
On Mon, 2011-04-04 at 09:38 -0500, Jacob Keller wrote:
> Could it be that they are not normal because of all of the outlier,
> huge-b-factor sidechains?
That is part of it
> If every exposed sidechain without real
> density gets a b-factor of 150, wouldn't that make a sizeable and
> illegitimate
Dear Colleagues,
We hope that you are planning to join us in Toronto, Canada for the
International Conference on Structural Genomics 2011 which will be held on
May 10-14, 2011. We have an excellent scientific program prepared which
includes both oral and poster presentations (please see:
http://w
I like your IMGATM proposal, but wouldn't it also potentially break
some of the programs? Also--and this is a problem with deleting only
sidechain atoms in general--it seems that many, myself included, might
totally miss that an apparent "alanine" is really a trunco-lysine.
What I like is that it d
It's nice to see that this discussion pops up every two years or so with
exactly the same arguments :)
My vote (as always) is for leaving the atoms of disordered side chains
in with high B values, the B values are part of the models. Its up to
the popular Biologist's visualization software
hello all,
does anyone have the experience of Collecting Data from Long Unit Cell Axes ?
I have a crystal that diffracts to about 4 A. in some direction the spots
overlap. we can't use the data to index .we think it is because that there is a
long unit cell axes. so is there any method to sol
Deng,
You need a good synchrotron source with a low point spread detector, but not
least a careful consideration in crystal mounting so that your crystal rotates
apprx around the long axis during data collection to optimise the separation of
reflections on the detector
besides checking that
Hi Jacob,
The PDB header has a record for missing atoms. Coot has an option to find them
and any decent validation software will warn about incomplete residues. There
are PDBREPORT entries for every PDB file with a list of incomplete residues. If
a user makes a very small effort, he doesn't hav
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