Dear Badsha,
Is it possible to share the pdb such as by linking to it using dropbox, google
docs, etc..? It's hard to trouble shoot the issue without seeing the file.
Thanks,
Sean
P212121
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but
can be reduced with TCEP?
This could be due to the effective pH of TCEP HCl (~1.5-8.5) being wider than
DTT ~7.
Take Care,
Sean Seaver
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Take Care,
Sean Seaver
P212121
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I'd also recommend:
Learn Python The Hard Way By Zed A. Shaw
http://learnpythonthehardway.org/
Online Python Tutor
http://pythontutor.com/
Take Care,
Sean Seaver, PhD
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regulated.
Regards,
Sean Seaver, PhD
P212121
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that helps in getting you started, take care!
Sean Seaver
P212121
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How about having people just link to uploaded photos on flickr
(http://www.flickr.com/) or similar free service? If you upload the photos and
select 'all images' a link is produced that can be easily shared
(http://farm5.static.flickr.com/4134/4755503052_bc6835dcdc.jpg). CCP4 doesn't
have
Dear all,
We are working on protein-inhibitor complex crystal structures, although
we did get nice crystals and soaked them with inhibitor for several days,
all structures we obtained were empty!!There are nothing at the active site.
For several crystals. their color turned very clearly
Dear All,
I am trying to find out which molecules are frequently used by X-ray
crystallographers serving as cryoprotectants or as buffer molecules. The
idea behind this is to sort native ligands from molecules that appeared in
the electron density just because they were used in the
You may want to try the Heavy-atom Database System
http://hatodas.harima.riken.go.jp/
Version 2 (http://hatodas.harima.riken.go.jp/hatodas_v2/query/queryheavy.jsp)
allows for pH as a search option.
http://hatodas.harima.riken.go.jp/hatodas_v2/query/queryheavy.jsp
Hope that helps,
Sean
Dear D.L.,
I suspect the issue is in determining the correct space group. Sharing the
Rmerge and current space group would be useful.
Take Care,
Sean
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Hi Rojan,
This paper may be more on the intermediate level, but is certainly worth a read.
Koch MH, Vachette P, Svergun DI. Q Rev Biophys. Small-angle scattering: a view
on the properties, structures and structural changes of biological
macromolecules in solution. 2003 May; 36(2): 147-227.
Hi Chandan,
The closest sodium-sulfur interaction that I know of within a protein is in
entry 2BDG, Na (Atom 402, Chain A) to a CYS with a distance of 3.3 Angstroms.
A couple of examples exist of sodium-sulfur interactions that involve coenzyme
A (1FY7 and 1MJ9). I hope that helps.
Take
Hi Padmaja,
-Will it work on a Mac OS?
No
-Is there another program (free or cheaper) that will do everything DS does?
Currently, there is a free version that you can use of DS.
http://accelrys.com/products/discovery-studio/visualization-download.php
Hopefully that will give you a feeling if
I've been curious if there has been discussion about moving data processing and
refinement to a software as a service (SaaS) deployment. If programs were web
accessible then it may save researchers time and trouble (maintaining and
installing software). In turn, one could then process data
Dear Mark,
I put together a post about creating a movie using PyMOL, eMovie (free) and
Adobe ImageReady CS2 to generate a Quicktime movie.
http://www.p212121.com/2009/03/24/easily-make-movie-pymol/
I hope that helps.
Take Care,
Sean
P212121
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do not diffract to sufficiently high resolution so as to allow us to read off
the sequence from the map).
Since we have access to a lot of pure protein, I wonder if some clever mass
spec jock would be able to assemble enough overlapping sequenced fragments so
as to give complete coverage of
Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH?
I haven't checked the price.
Including shipping in the US
RbBr: 50 g 99% pure is ~$150.
RbOH: 25g 99+% pure in 50 % water runs about ~$120.
It would be interesting to see how the substitution would influence the
crystallization or
Dear Ivan,
If you take a look at the MPCD ( http://www.cinam.univ-mrs.fr/mpcd/ ) and
search for Fab it brings up 172 crystallization conditions. The names should
help you narrow down, which conditions are of a complex. Hopefully, you can
use those conditions to help you decide, which
Hi Christina,
The WASP server seems to working at this location (about half way down the
page):
http://www.jcsg.org/prod/scripts/validation/sv2.cgi
I hope that helps.
Take Care,
Sean
P212121
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Hi Jacob,
Darn that site doesn't seem to be working. I generated the files ion files and
thought it was good to go, but didn't view the outputs.
Apologies,
Sean Seaver
P212121
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screen real estate.
Take Care,
Sean Seaver
P212121
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nitrogen. I hope that helps.
Take Care,
Sean Seaver
P212121
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Hi Jacob,
A couple of years ago, I put together a list of papers that touch on radiation
damage:
http://www.p212121.com/2009/11/17/ultimate-list-on-cryocrystallography-radiation-damage/
To answer your question more directly - see pg. 40 of the following paper:
consider using google sites (
https://sites.google.com/ ) to roll your own solution.
I hope that helps.
Take Care,
Sean Seaver
P212121
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blends.
DMSO: http://www.bio.brandeis.edu/publications/bi035849h.pdf
Sodium malonate: http://journals.iucr.org/d/issues/2003/12/00/fw5004/fw5004.pdf
Take Care,
Sean Seaver
P212121
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,
Sean Seaver
P212121
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questions or comments you may have. I will follow up with results in about a
month.
http://www.p212121.com/2009/06/04/do-we-need-an-x-ray-diffraction-image-data-bank/
Thanks.
Sean Seaver
I say deposit it both ways, someone needs to start keeping those
computational chemists on their toes.
Hello Sylvia,
Two issues I would consider:
1) recheck the space group
2) make sure that I had selected a good model for my MR search
All the Best,
Sean
Hello Fred,
Thanks for bring this to attention and am sure that it will receive support
from those on the CCP4bb. I am huge a fan and supporter of science! I also
feel that virtually any effort to spread the word about science and research
should be taken. However, I am confident that the best
I like any attempt to set up a proper science channel, but I don't think
it will solve the problem of too few people choosing to do science.
Neither will any Internet thing.
The internet or tv will not solve the problem entirely, but I can say for
certain that not every scientist is going
Hello FX,
As already mentioned there a number of programs that can perform this task.
If you end up deciding to go with Coot, I put together a play by play that
should help.
http://bit.ly/oHqDW
Hope that helps.
Sean
Hello Fred,
Thanks for sharing! I have also been looking for ways to keep up on
literature. This weekend, I combined 17 structural journals into a single
RSS feed using yahoo pipes. I did a short post about it here:
http://tinyurl.com/yhp2xlm
I would be curious if others have any tips or
Hello Raju,
Welcome to crystallography! I don't have much information about predicting
structures, but have put together a list of resources about protein
crystallization:
http://tinyurl.com/ygmbpa3
Happy reading :)
Sean
I have a small complex, one component is 13 kDa with structure available
and the other is 7 kDa, which could not be able to grew crystals after lots
of efforts. It grew crystals after methylation and diffracted to 2.3 A,
however, I could not be able to solve the structure using the structure of
Thanks for bringing this article to our attention. I went ahead and created
a table of the PDBs in question including links to the structures, journals
and citations. My hope is that it will save others time trying to track
down this information.
http://bit.ly/5KqaRF
Hope it helps.
Sean
On Fri, 11 Dec 2009 15:30:53 -0500, Ibrahim Moustafa i.moust...@psu.edu wrote:
You are absolutely right, more information describing to what extents these
structures were falsified will be valuable to the community. Actually, it
will be more useful if the investigators can publish their report as
On Thu, 10 Dec 2009 13:06:36 -0600, Tanner, John J. tanne...@missouri.edu
wrote:
Some of you might be curious about the Ajees et al debacle that Jacob
mentioned in his message. Here are two links:
Nature Brief Communication that questioned the validity of one of Murthy's
structures:
I wanted to follow up on this 'older' thread and let people know that I have
updated the RSS feed to now include 26 resources. The feed now generates
about 1500 articles that are continuously updated, which is a bit much to read.
Therefore, over the next day or so I'm going to offer to create a
We are going to be a pretty unpopular bunch if this thread concludes that we
need to set off fire alarms in order to nucleate our crystals.
:)
Sean
You can build any 3D molecule easily in Discovery Studio Visualizer - It
is free but not for Mac OS
I have been pretty impressed with Discovery Studio Visualizer and feel that
it can serve as a nice compliment to Pymol.
I wrote up a brief overview and comparison between the two programs
I believe this is the article that you are looking for:
http://www.xtals.org/crystal_cryo.pdf
Cheers,
Sean
I am trying to create a homology model of a coiled-coil for use in
molecular replacement. I have a template poly-ala coiled coil that I like
to use, so that is fine. I want to thread my sequence onto the helix and am
trying to find a server/easy program that will do this.
As a starting point I
On Tue, 16 Mar 2010 20:11:29 -0400, Karthik S biokart...@gmail.com wrote:
Hi, I was looking around for programs that display space group symmetry
information and could not find any but perhaps i am lost for valuable or
relevant keywords.
I found two references TABLES and CRYST, but are there
I found the paper An Excel Spreadsheet for a One-Dimensional Fourier Map
in X-Ray Crystallography by William Clegg quite helpful. The paper
includes a supplemental spreadsheet in which you can adjust various
contributions of phase and amplitude. I wrote an outline of the first part
of the paper
Dear all,
I would like to know which is the more suitable method of using 2,3-Butanediol
as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both
can be tried?
Cheers
Gauri
--
I am sure both could be tried, but have found quite few papers mentioning brief
soaking with
Perhaps this is a case of a 'phantom crystal' that was discussed on the CCP4bb
awhile back:
http://bit.ly/b6Rgw7
All the Best,
Sean
to
supp...@p21221.com .
Take Care,
Sean Seaver, PhD
P212121
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Care,
Sean Seaver, PhD
P212121
http://store.p212121.com/
Hi Pius,
I just checked Monodihydrosterculin against our database of more than 1 million
antibodies and we aren't seeing anyone that normally offers this product for
sale.
Take Care,
Sean Seaver, PhD
P212121
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Hi Georg,
I haven't used the agarose method, but have sealed many capillaries using bees
wax without an issue.
Simply heat the wax until it melts, dip the capillary (rotate if it has a
larger diameter) then let cool.
I hope that helps, cheers!
Sean Seaver, PhD
P212121
http://store.p212121
Take Care,
Sean Seaver, PhD
P212121
http://store.p212121.com/
--
Dear All,
Alhough there are on-line explainations on the space group, I found it was
difficult to fully understand. Here we take P 1 21 1 as an exmaple, will you
please explain to me with easy language what each number
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