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Hi Fred,
this sentence of yours, "All pdb's are superposed by a common sequence
region, which also will be part of the tetramer interface." probably
hides the information which would be necessary for a reasonable answer
to your question.
If you still
Hi Tim,
Thanks for your replay. All pdb monomers have the same primary sequence
and a perfect matching long helix, which I have used to superpose the
coordinates. Such helix is almost straight so that, the idea would be to
create a vector along the helix main axis, shift this axis to a some
di
This sounds as though you will create a 4-helical rod?
There are lots of 4-helical bundles but they arenot completely rod like
- there is a twist in most I have seen.
Maybe you should do secondary structure matching to a suitable 4-helicl
bundle, match your helix in turn to each of the bundle h
Dear Fred,
In this case, I would take one monomer and edit the CRYST1 card of the
pdb to have a sufficiently large tetragonal unit cell.
Next I would manually align the helix of one monomer with the fourfold
axis, e.g. the Z-axis. If you display the unit cell, you will get e.g.
the 0,Z,0 axis to g
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Hello Fred,
as far as I understand your problem I am not aware of existing programs
to carry out the tasks. To automatise the process I would write a
program myself which takes the PDB-file and the reside numbers which
make that helix as input and:
1)
An old old trick for getting a straight helix along a crystal axis using
the GUI.
Run the Amore TABLING step - it is part of the GUI with the helix as
your "model". (See molecular replacement - amore suite.)
Amore calculates the ppl axes and will align it along the Z axis ..
Thank you Jorge..
I've done this sort of thing (but different) using the Clipper libraries in
C++. I found it easier to write short programs to do specific tasks rather than
try to write generic all-purpose tools
Phil
On 14 Dec 2011, at 15:07, Tim Gruene wrote:
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Jürgen,
Have you checked a simple selfrotation function in your currently favored
> space group ?
>
Yes, both selfrotation function and patterson map do not look suspicious in
I422.
> Do you have sufficient data collected to start out in P1 or C2 ? Then I
> would start there and systematically
Give XDS a try with your data or d*trek with 3d profile fitting.
Did you try iMosflm or the old Mosflm ? If old, then POSTREF WIDTH 15 might
help and POSTREF FIX BEAM
You saw the nice packing from Tjaard, if all your molecules have contact with
each other than that's fine I was just concerned ab
How about plotting the solvent content along with resolution limits of the
structures?
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
Afonine
Sent: Wednesday, December 14, 2011 12:02 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very strange lattice: high anisot
Hi Debasish,
On Wed, Dec 14, 2011 at 9:23 AM, Debasish Chattopadhyay wrote:
> How about plotting the solvent content along with resolution limits of the
> structures?
>
here it is:
Resolution Number of Solvent % (mean/min/max) Solvent % (mean/min/max)
range structures from remarks
On 13 December 2011 17:59, James Holton wrote:
> A small but potentially important correction:
>
> FC_ALL PHIC_ALL from REFMAC are indeed the calculated structure factor of
> the coordinates+bulk_solvent, but AFTER multiplying by the likelihood
> coefficient "D" (as in 2*m*Fo-D*Fc ). So, if you s
Dear CCP4ers,
We are currently fighting with our crystallization robot and would be happy
to find out if anyone else has experienced similar problems - and hopefully
found a solution.
To make a long and extremely frustrating story with our robot short:
We are running an ArtRobbins 4-Channel Phoe
Hi Everyone
I have to calculate hydrophobic interactions in pdb files. Is any server
available for this type of calculation?
Thanks in advance
Amit
Hi every,
I'm working with 2 crystal forms of a protein from 2 different
crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2
doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical
except in condition1, there is a clear positive density surrounded by a Glu
side
Dear Crystallographers,
is there a convention for denoting/measuring pore sizes in protein
structures? Maybe inter-atom distances minus van der Waals radii?
JPK
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email:
Hi Jacob,
There are a number of programs that can calculate the radius of a pore. The one
that comes to mind is called HOLE, and it can make a nice plot of the
y-coordinate along the pore vs. pore radius. I don't recall exactly how this
calculation is done, I think it is somehow related to the
google on "pisa pdbe" -- Eugene
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Luthra,Amit
[alut...@uchc.edu]
Sent: Wednesday, December 14, 2011 8:34 PM
To: ccp4bb
Subject: [ccp4bb] Hydrophobic interactions
Hi Everyone
I have to calculate hydroph
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