Dear Pavel,
Is this density located on a symmetry axis?
There is quite often a lot of noise around these regions - and it may not, in
fact, be possible to model this satisfactorily.
Tony.
---
Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and
Dear Pavel,
you should also always consider your cryoprotectant molecules, so let's say
if you used PEG for cryoprotection, there's a very high probability you may
see it in your structure. It's very hard to say from the snapshots, but
for the patch of density depicted in fig.2 I would try PEG
Dear all,
I have an orthorhombic crystal (pointless suggests most likely space groups P 2 21 21 or P 2 21 2)
with two molecules expected in the asymmetric unit. Analyzing the native Patterson map I found the
following peaks (in fractional coordinates):
CELL 63.0400 117.2500 133.6500
Does anyone know how to access the 'Measure Cell' function in iMosflm? This
function in ipmosflm allowed you to click on a pair of spots, then input the
number of diffraction orders, to output a rough measure of the cell length.
Any help appreciated!
Thanks
Richard
The general rule is that a Patterson peak should be ~ 20% of the origin
before considering it significant so none of those would really need to be
considered.
Eleanor
On 25 February 2013 12:48, Michele Lunelli efu...@yahoo.it wrote:
Dear all,
I have an orthorhombic crystal (pointless
Hi Richard
I'm afraid it doesn't exist at the moment. It could be added if there's
sufficient demand for it.
On 25 Feb 2013, at 12:57, Bayliss, Richard (Dr.) wrote:
Does anyone know how to access the 'Measure Cell' function in iMosflm? This
function in ipmosflm allowed you to click on a
Dear all,
The matrix formats in different program always confuse me.
The matrix format of the REMARK 290 SMTRY section of pdb file is:
r11r12r13tx
r21r22r23ty
r31r32r33tz
What's the matrix format accepted by the transform file keywords of
the pdbset
Dear Qixu,
here's an excerpt from the pdbset manual:
TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz
I'm not sure what you mean by covert from the pdb file format to
the pdbset format. Please elaborate on this.
Jon
2013/2/25 Qixu Cai caiq...@gmail.com:
Dear all,
Imperial College London
Department of Life Sciences
Faculty of Natural Sciences
Research Associate
Salary: £32,100 - £35,620 per annum
We wish to recruit a Research Associate for up to 24 months in the first
instance with possible extension to up to five years to work in the research
group
Dear Jon,
Thanks for your reply.
The matrix format in the REMARK 290 section of the pdb file (download
from rcsb.org) is :
r11r12r13tx
r21r22r23ty
r31r32r33tz
And I want to extract the matrix information from the pdb file REMARK 290
section and use the matrix
Dear Harry,
It's a useful function. Could you please added it?
Thanks.
Qixu Cai
Email: caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China
2013/2/25 Harry Powell ha...@mrc-lmb.cam.ac.uk
Hi Richard
I'm afraid it doesn't exist at the moment. It could be added if
Hi,
Emacs, vi, any (text file) editor ? I wouldn't advise a word processing
program (Word and the likes).
Unless you want to do this on many pdb files in which case writing a
small program or shell script would be required.
Fred.
On 25/02/13 14:24, Qixu Cai wrote:
Dear Jon,
Thanks for
If you just want to generate symm mates from MTRIX records, you may
want to give GK's 'xpand' a go:
http://xray.bmc.uu.se/usf/xpand_man.html
Otherwise, I would follow Fred's advice.
Jon
2013/2/25 vellieux frederic.velli...@ibs.fr:
Hi,
Emacs, vi, any (text file) editor ? I wouldn't advise a
Nanobody-aided crystallization and structure determination of CFTR
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The following position may be of interest for individuals thinking of
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Hello Qixu Cai,
cut and paste is yet another option and probably quickest if it is
only for a few PDB files.
Best,
Tim
On 02/25/2013 02:30 PM, vellieux wrote:
Hi,
Emacs, vi, any (text file) editor ? I wouldn't advise a word
processing program
Hello everyone, I need your suggestion for slowing down crystallization for my
proteinmy protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9),
but it crystallize too fast. In 1 hr I can see tons of tiny needles. Can anyone
give me some suggestion on how to slow down the process? I
On Mon, Feb 25, 2013 at 8:02 AM, lei feng spartanfeng...@hotmail.com wrote:
I need your suggestion for slowing down crystallization for my protein
my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9), but
it crystallize too fast. In 1 hr I can see tons of tiny needles.
Can
Feng Lei,
I would personally recommend slowing down the process of nucleation either by
lowering the temperature of crystallization or by utilizing Al's oil. These are
two powerful ways to slow the overall kinetics of crystallization. Here is a
relevant reference for you:
Le 25/02/13 17:02, lei feng a écrit :
Hello everyone,
I need your suggestion for slowing down crystallization for my protein
my protein got hit in PEG/ION #5 ( 0.2 M MgCl2, 20% PEG 3350, pH 5.9),
but it crystallize too fast. In 1 hr I can see tons of tiny needles.
Can anyone give me some
a. Go with phase diagram gradually changing concentrations of protein,
precipitant, salt concentrations and pH. Find where you are going out of
crystallisation. Define region for streak seeding.
b. Screen for ratios of precipitant to protein from 1:9 to 9:1.
Dr Felix Frolow
Professor of
Hi Lei Fang,
I cannot tell what technique you are using for crystallization. Also, many
details like protein concentration, temperature of crystallization etc. are
missing in your email so it's hard to guess what's going on.
In any case, here are my thoughts. I used to get a shower of needles
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Dear Richard,
adxv has this functionality and you do not even need to put in the
diffraction orders, just drag the mouse pointer through two adjacent
reflections (or more and do the maths yourself).
Cheers,
Tim
On 02/25/2013 01:57 PM, Bayliss,
Try using dioxane as an additive. I'd suggest adding 5- 15% dioxane into your
well solution. This should inhibit nucleation resulting in fewer, larger
crystals.
On 25/02/13, Felix Frolow mbfro...@post.tau.ac.il wrote:
a. Go with phase diagram gradually changing concentrations of
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to compare mutants to a wild-type structure.
For example, structure2 has a higher B-factor for residue X but how can I
show that this is significant if the average B-factor is also higher?
Thank you for
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to compare mutants to a wild-type structure.
For example, structure2 has a higher B-factor for residue X but how can I
show that this is significant if the average B-factor is also higher?
Thank you for
Why not normalize each to its average b-factor? And...maybe they are not
significantly different in the first place?
JPK
On Mon, Feb 25, 2013 at 3:08 PM, Yarrow Madrona amadr...@uci.edu wrote:
Hello,
Does anyone know a good method to compare B-factors between structures? I
would like to
Thanks Nat,
I was planning on plotting B-factors vs. residue anyway, so maybe this
will save me time. I will take a look.
-Yarrow
Not a CCP4 solution, but the structure comparison program in the
Phenix GUI will plot B-factors for different structures of the same
protein. (I am happy to make
Thank you Manfred,
To be honest I have tried to understand the Pearson linear CC since
reading the nature crystallography methods paper by Karplus and
diederichs, but I am having trouble. I do not clearly understand what it
represents. Do you know any good resources that could help me out?
Hi Yarrow,
I'm sure other visualizing tools can do this, but I just wanted to share that
our free Discovery Studio
Visualizerhttp://accelrys.com/products/discovery-studio/visualization-download.php
can do this quite easily.
Contact me off the list and we can set up a time when I can show
Hi All,
I am sure that some of you have used AutoDock Vina so I thought I would give it
a go and ask two questions. I performed a round of docking and obtained an
output file containing 9 different models. The affinity (kcal/mol) ranged from
-4.5 to -3.0. My first question is what is
Dear All,
CCPBioSim are once again running a 1-day workshop covering the basics of
setting up Molecular Dynamics simulations for biological systems. The workshop
is on Wednesday 20th March 2013 at the Unilever Centre for Molecular
Informatics, University of Cambridge. The deadline for
Thanks. That's what I need.
Qixu Cai
Email: caiq...@gmail.com
在 2013-2-25，下午9:38，Jon Agirre jon.agi...@gmail.com 写道：
If you just want to generate symm mates from MTRIX records, you may
want to give GK's 'xpand' a go:
http://xray.bmc.uu.se/usf/xpand_man.html
Otherwise, I would follow
Dear all,
Thank you very much for help!
The problem was solved very easy (thanks Dominik A. Herbs). I just used another
program for refinement (Refmac5 instead Phenix.refine) and this noisy density
almost disappeared.
http://www.4sync.com/photo/--e2gHrG/Density-Refmac5.html
Thanks a lot for
Dear all,
currently, I have a data set scaled in P22121 which containing a PST of
(0.5,0.5,0.111). The structure were successfully solved by molecular
replacement. However, the R free factors remained as high as ~33% in the
refinement. I search the literature and found that it was common to
Dear Christine,
Your fist question is regarding range of energy in high affinity. In Autodock
Vina high affinity energy varies from -9 to -11 Kcal/mol. In my opinion -4.5
to -3.0 Kcal/mol is moderate affinity for ligand.
Second question is how to save individual orientation of Vina output
Hi Christine,
You can split outputs by this way (vina site) :
Separate models
All predicted binding modes, including the positions of the flexible
side chains are placed into one multimodel PDBQT file specified by the
out parameter or chosen by default, based on the ligand file name.
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