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
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
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 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
Hi Everyone
I have to calculate hydrophobic interactions in pdb files. Is any server
available for this type of calculation?
Thanks in advance
Amit
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
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
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
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
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
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
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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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..
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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)
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
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
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
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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
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