Dear Sreetama,
I use an ancient superposition program which rejects all atom pairs deviating
more than 3 sigma and repeats this procedure until convergence. It then reports
the RMSD for all atoms and for the atoms deviating less than 3 sigma. I find
this an excellent method to separate the core
Sreetama,
See the following URL whether it is
useful to solve your issue
http://cluster.physics.iisc.ernet.in/3dss/
best,
Sekar
> Dear all,
> When calculating the RMSD between structures of homologous
> proteins, where there are large changes in the loop region(s), which RMSD
> sho
Dear all,
When calculating the RMSD between structures of homologous proteins,
where there are large changes in the loop region(s), which RMSD should be
reported - an overall value which may be inflated due to the deviations in the
loops, or separate values for the core and loop regio
Dear all,
Is there any software or web server available to calculate the volume of a
ligand if the ligand coordinates are provided?
Google seems to come up only with options to calculate protein cavity volume.
Thanks in advance,
Sreetama Das,
phd student,
Physics, IISc
Dear all
I have solved a structure of protein with ligand at 2.7 and 2.8 A. Both
have ligand bound in it as i soaked it.
For the first structure i soaked for lesser time and lesser concentration
of ligand and solved it at 2.7 A resolution. Although the ligand has good
density (2Fo-Fc at 0.9 sigma
A somewhat similar question, with a quick answer I hope: when programs output
CC's of 1/2 datasets, are several random halvings compared/averaged, and if
not, does this make a difference, or are the scores so similar there's no point?
JPK
-Original Message-
From: CCP4 bulletin board [ma
Hi all,
Related to the question I had a few days ago about how chains are displayed in
PyMol, some ideas below say it is ok to delete SegIDs that exist in columns
73-76 (and thanks for them).
For anyone who tried deleting SegIDs before, does it affect the pdb file? or is
it “safe” to do it?
I
Aimless can output scaled but unmerged data
OUTPUT UNMERGED
Or from ccp4i
Phil
Sent from my iPad
> On 12 Aug 2014, at 19:32, Kay Diederichs
> wrote:
>
> Hi Mike,
>
> this requires scaled but unmerged data, and there are few programs that
> support unmerged MTZ files. So it is probably nece
Hi Mike,
this requires scaled but unmerged data, and there are few programs that support
unmerged MTZ files. So it is probably necessary to write your own program(s),
that process XDS_ASCII.HKL or XSCALE.HKL. Or you start by extracting from
AIMLESS code.
HTH,
Kay
On Tue, 12 Aug 2014 13:52:30
Hello All,
I'm interested in doing some comparisons of random half data sets, inspired by
statistics like CC1/2, CC*, etc. Does CCP4 contain some tool to split unmerged
data into 2 random sets? Or is there some way to intercept this information
from something like XSCALE or Aimless, etc.? Thoug
Dear all,
I have a dataset of C2 symmetry and 2 molecules in the ASU. I am wondering
if I have to use thin shell Rfree set selection to avoid Rfree bias by NCS.
And which Rfree selection method is better?
Thanks in advance.
Xianchi
Thank you for all reply! You guys are really helpful! I appreciate it!
Bing
From: Oliver Clarke [oc2...@columbia.edu]
Sent: Monday, August 11, 2014 4:21 PM
To: CCP4BB@JISCMAIL.AC.UK; Wang, Bing
Subject: Re: Add water in the symmetry center?
Dear Bing,
My
I wrote a simple script following Prof. Jürgen's suggestion. I have
attached it to this email. It will only serve the purpose of generating
combinations based on specified positions and fragments.
regards,
harsh
On Mon, Aug 11, 2014 at 8:31 PM, Harshavardhan Khare
wrote:
> Hi Jürgen,
>
> Thank
Hello all,
I am trying to use DENZO (the command-line program) and XDISP for images coming
from Pilatus 2M (ESRF ID-23-2).
Does anyone know the detector’s definitions?
I tried “ccd unsupported-m225” but it doesnt fit.
Thanks
Meytal
---
Meytal Landau, Ph.D.
Assistant Pro
Dear all,
It seems that the last update of the ccp4 suite contains at least one bug in
aimless. Failed every time with the same error message (below) and worked again
when update was uninstalled. It is the update 6.4.0-020 that was the cause.
Did not know who to send to but hopefully at least
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