Dear all,
I am looking for a program or webtool that can create canonical nucleic
acid helices (like B-form, A-form...) as well as a program that can
calculate helical parameters from a given helix.
Thanks in advance,
Florian.
--
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Hash: SHA1
Hi Florian,
You can use coot to create an ideal DNA! Simply:
Calculate -> Other Modelling tools -> Ideal DNA/RNA
Another possibility is 3DNA: (http://rutchem.rutgers.edu/~xiangjun/3DNA/)
For analysis you could use 3DNA or Curves
(http://www.ibpc.fr
Quanta (accelrys) had a feature for this.
J
Dear all,
I am looking for a program or webtool that can create canonical
nucleic acid helices (like B-form, A-form...) as well as a program
that can calculate helical parameters from a given helix.
Thanks in advance,
Florian.
--
Professor Ja
For the analysis of DNA molecules I would also recomend X3DNA
Another possibility is 3DNA: (http://rutchem.rutgers.edu/~xiangjun/3DNA/)
however if you would like to obtain a ideal model quicly try DNA tools
http://hydra.icgeb.trieste.it/~kristian/dna/model_it.html
Michal
--
Michal Jak
In which case is this new server the best place to host the list?
Simon
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Kjeldgaard Morten
Sent: 22 January 2007 07:30
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: ccp4bb on new site
Unfortunately, It appears
For a quick dna or rna: http://structure.usc.edu/make-na
Its super easy.
James
On Jan 22, 2007, at 12:11 AM, Florian Brückner wrote:
Dear all,
I am looking for a program or webtool that can create canonical
nucleic acid helices (like B-form, A-form...) as well as a program
that can calcu
I will be out of the office starting 01/22/2007 and will not return until
01/26/2007.
I will respond to your message when I return.
Dear all,
I'm sending a summary of useful advices which I received on
my email concerning the crystallization of a very acidic
protein. I would like to thank all the people who
responded!
Have a nice day!
Kornelius
There are an number (WT & mutants) of X-ray structures
published on xylose isom
Well, having got around to getting a password and exploring the
www.jiscmail.ac.uk website, I see that I can get a list title back,
using the subscription settings for the list. The option is
Mail Header Style, option 2:
LISTSERV-style, with list name in subject
gives me a [CCP4BB] added to t
Hi,
what is intended as a student? Phd student?
thanks
Francesco
2007/1/22, alberto podjarny <[EMAIL PROTECTED]>:
***Announcement*
The meeting "Biophysics of ligand binding to drug targets" will take place
at the Holiday Inn Hotel, Illkirch/Strasbourg, France, from May
On Sun, Jan 21, 2007 at 11:26:38PM -0800, Jan Abendroth wrote:
> Hi all,
> just realised that in the new ccp4bb setup (using various mail programs
> such as thunderbird, mail, webpine), the actual sender does not appear
> in the list of addressees, not even using "reply to all".
This is an issue
***Announcement*
The meeting "Biophysics of ligand binding to drug targets will take place
at the Holiday Inn Hotel, Illkirch/Strasbourg, France, from May 14 till May
16, 2007. There are still fellowships for students available. The deadline
is 1st February.
Detectio
I have a little movie of soaking dye
(methylene blue aka izit) into
lysozyme. can be useful for lectures.
http://www.ruppweb.org/level1/movies_list.htm
best, br
Bernhard Rupp
www.ruppweb.org
Will someone knowledgeable tell me what the present state of full 6
dimensional searches in molecular replacement?
With thanks,
Ed
Eaton E. Lattman, Ph.D.
Dean of Research and Graduate Education
Professor of Biophysics
Zanvyl Krieger School of Arts and Sciences
410.516.8215 (voice); 410.51
As far as the subject header line is concerned, ye olde ListServ command:
SET CCP4BB SUBJECTHDR
would probably work if one emailed it to the server (i.e.
[EMAIL PROTECTED] *not* CCP4BB@JISCMAIL.AC.UK)
or you can do it via the web interface. It appears that the mail/web
command interface will n
Hello All,
I am trying to soak some crystals with a small molecule that is quite
hydrophobic. I am having trouble with solubilty of the small molecule. It will
dissolve up to about 1 mM in 100 % DMSO, but precipitates at concentrations of
less than 15 micromolar when the DMSO concentration is b
Hi Todd,
DMF (Dimethyl Fluoride) is a good alternative to DMSO.
Sarathy
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Green, Todd
Sent: Monday, January 22, 2007 3:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: crystal friendly solvents that are
Do you mean N,N-dimethylformamide, aka dimethylformamide, aka DMF, or do I
need a chemistry lesson?
On Monday 22 January 2007 02:49 pm, Parthasarathy, Gopalakrishnan wrote:
> Hi Todd,
> DMF (Dimethyl Fluoride) is a good alternative to DMSO.
>
> Sarathy
--
Craig A. Bingman, Ph.D.
Center for
Sarathy (and Todd)
DMF is usually used for dimethyl formamide. From the name I have no idea what
"dimethyl fluoride" may be (methylene difluoride, though wrong, is used for
difluor methane,but that's not mixable with water, and only a liquid at low
temperature ;-) )
Todd,
If your protein has
Hi Todd,
You could try dissolving your compound directly into your PEG4000
precipitant. Alternatively, you could try other low molecular weight
PEGs.
Good luck,
Jeff
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Green, Todd
Sent: Mon
On Monday 22 January 2007 00:35, james whisstock wrote:
> Quanta (accelrys) had a feature for this.
Its so expensive, they don't even tell you the price.
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com
On Jan 22 2007, Eaton Lattman wrote:
Will someone knowledgeable tell me what the present state of full 6
dimensional searches in molecular replacement?
Presumably you're referring to systematic 6D searches, not stochastic ones
like in EPMR or QoS. Do you mean "can it be done on current hardw
So I've never actually tried this proposed extension to the idea, but:
I (and many others) have gotten small hydrophobics (toluene, iodobenzene etc.)
into proteins, and these things typically have very small partition
coefficients, and they aren't horribly volatile (that's why I am a little
pa
Toluenes and derivatized benzenes may absorp into your plastic tray? Or into
the tape covering your tray? Just few other destinations.
It would make sense that if the binding of the 'drug' to the protein is tight,
then you do not need much in immediate contact, it will get there. The method
On Monday 22 January 2007 04:57 pm, Maneesh Yadav wrote:
> I've noticed that the iodobenzene does largely disappear overnight (in
> hanging drop), I don't know if this is because of evaporation or the
> iodobenzene just "falls" into the reservoir. Maybe stick to sitting drop.
Or it partitions thro
A biochemist friend asked for examples of cases were a protein was
co-crystallized with or soaked in a ligand that bound in the wrong place -
say, because the ligand used wasn't quite the right one or because other
important ligands were absent.
I'm sure such examples are out there, especially w
Some felt that there was not enough going on
in the dye movie (well, soaking is not exactly
big action). I added a few frames before/after
to the end of the movie. This should make the
point nicely.
http://www.ruppweb.org/level1/movies_list.htm
br
Be
Hi Pheobe,
I remember an interesting paper that described how a structure revealed a
surprising role the buffer was playing in inhibition:
The 1.20 A resolution crystal structure of the aminopeptidase from Aeromonas
proteolytica complexed with tris: a tale of buffer inhibition.
* Desmarais
Sorry Guys,
I did mean Dimethyl Formamide and not flouride. I apologize, I was thinking of
the ATP anologs thread as I was typing the response.
Sarathy
--
Notice: This e-mail message, together with any attachments, con
Hi Phoebe,
We had a case were one ligand was bound in the active site (covalently bound)
and another in a pocket in the same crystal (PNAS, 102, 3599 (2005)).
Regards,
Mathews
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL
PROTECTED]
Sent:
Hi Phoebe,
Some of the info on Brian Shoichet's site might be of use. Worth a look
at least.
http://shoichetlab.compbio.ucsf.edu/
Anecdotally, I believe that gleevec was rationally designed from a
scaffold which bound one way, but after gleevec had been shown to be
effective, the X-ray struc
I'd like to add that the value of a molecular replacement solution tends
to be inversely correlated with the effort needed to find the solution.
In other words, the harder you have to work to find the MR solution the
less informative the phase information you tend to get. When you have
very hig
A follow up to this (for what it's worth) is that it's sometimes easier
to solve a structure by MR from a homologous structure determined by
experimental phases than it is to solve the initial structure by SeMet,
MIR, etc.
An example is the case of the structure determination of the second
isoform
But that isn't necessarily the case if the search is hard because your
search models individually constitute only a small part of the
asymmetric unit. Say that 80% of the AU consists of multiple
different proteins with known structure; the phase information would
be very high if you find the solu
Perhaps this will be of some use:
We've recently published a phosphatase paper showing two structures - one
was a soak, the other - a co-crystal. Same ligand and same protein in both,
and virtually the same crystallization conditions. The difference in ligand
binding was like night and day.
http:
Hi Filip,
You're right and the same applies if the MR is difficult because of
differing relative domain orientations in otherwise closely related to
proteins. As mentioned, my remark was aimed at distantly related search
models.
Bart
Filip Van Petegem wrote:
But that isn't necessarily the
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