Hi Dipankar
you need to pit a unique identifier for each of your ligands,
eg
phenix.elbow --smiles=cyclopiazonic_acid.smi --id=CZA --output=cza --opt
best Preben
On 4/16/12 4:52 AM, Dipankar Manna wrote:
Dear Crystallographers,
After one round of refinement (restrained refinement) with
Dear all
I want to digest a tagged protein with TEV protease, it has disulfide bridges.
Is there any way of doing cleavage without DTT?
Thank you.
Theresa
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Dear Theresa,
I was not aware you need DTT for TEV protease activity. People do
on-column digestion, and as far as I remember, a Ni-column would turn
really uglily brown of you used DTT on those columns.
Have you tried to leave out DTT and the
I want to digest a tagged protein with TEV protease, it has disulfide
bridges. Is there any way of doing cleavage without DTT?
Yes, no problem. TEV is slowly inactivated oxidation of the active site
cysteine but that's about it. If you absolutely must have no reducer during
cleavage, simply
--- On Mon, 24/1/11, Eleanor Dodson c...@ysbl.york.ac.uk wrote:
From: Eleanor Dodson c...@ysbl.york.ac.uk
Subject: Re: [ccp4bb] Merging statistics and systematic absences
To: CCP4BB@JISCMAIL.AC.UK
Date: Monday, 24 Jan
Dear Allister
Could you please update refmac version. In the version you it seems that bulk
solvent mask calculation has some problems. New version (at the moment) can be
downloaded from this site:
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz
There is a
Oh dear - this is the version of Refmac in the latest ccp4 release - can
this be updated on the web site as soon as possible ?
Eleanor
On 16 April 2012 12:02, Garib N Murshudov ga...@mrc-lmb.cam.ac.uk wrote:
Dear Allister
Could you please update refmac version. In the version you it seems
Dear all
We are pleased to announce the public release of new versions of iMosflm and
Mosflm. We have addressed many bugs and performance issues, and also tidied
things up in some of the tasks.
If you are using a previous version we strongly recommend that you upgrade.
In brief -
I have used 5 mM beta-Mercaptoethanol, which is a weaker reducing agent than
DTT, and that keeps TEV happy as well.
Cheers
Florian
Am 16.04.2012 um 09:31 schrieb Theresa Hsu:
Dear all
I want to digest a tagged protein with TEV protease, it has disulfide
bridges. Is there any way of
On 16/04/12 03:52, Dipankar Manna wrote:
Dear Crystallographers,
After one round of refinement (restrained refinement) with ligand, I
inport the .cif file through '-Import CIF Dictionary' into Coot. But
when I am going for '-Real Space Refine Zone' for the ligand, its
showing Refinement set
Dear Garib,
Is there REFMAC option to output solvent mask information (e.g. Fmask
and PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL).
But I'm not sure that FC_ALL = FC + FMASK is correct or not.
Keitaro
2012/4/16 Garib N Murshudov
Yes there is. If you use command line (it is not available on the ccp4i yet).
If you run with command lines
refmac5 all others like hklin, xyzin etc mskout mask file name eof
all options you want
eof
Then there will be a map and you can visualise it using coot.
regards
Garib
On 16 Apr
A follow up:
In the new version there is FC_ALL_LS, PHIC_ALL_LS
That should be FC_ALL_LS = FC + FMASK.
I have not tried but if you can use vector difference map then it should be:
FMASK = FC_ALL_LS - FC
But it is after scaling. If you write out mask map then it is just 0 1 map (0
inside
Where can one find a discussion of the differences between Aimless and
Scala?
JPK
On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote:
Dear all
We are pleased to announce the public release of new versions of iMosflm
and Mosflm. We have addressed many bugs and
Hi there!
I think some of you have given my email for correspondence or CC, please I
do not have to do anything related to your conversation so please delete my
email address from your correspondence
I shall be grateful
THANKS REGARDS!
Tallat Hussain Ghazi
IT Manager / Head of Web
Dear Garib,
Thank you very much for your quick reply.
I tried mskout option and the output looked almost the same as the map
generated by FC_ALL - FC.
By the way, when mskout option is specified, refmac stops before CGMAT cycles.
Is there any way to do refinement with mskout option?
I have
Aimless is a complete rewrite of Scala, but does essentially the same task. I
haven't yet written it up properly, but there is a program document at
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/aimless.html
A rough flow of the program is as follows:-
Read file from eg POINTLESS, sort data if
Dear Ketaro
At the moment mskout option is a signal that the program should stop. Obviously
I can add an option to continue. However if you have mskout option it is likely
that you want to check what is going on with the mask. If you want to compare
starting and final mask then you could run
Dear Garib,
I think it is better if refmac outputs final solvent mask when mskout specified.
If one just wanted to calculate the mask, NCYC 0 should be specified.
I hope my suggestion would be accepted, but I'm not in a hurry.
FC_ALL is ML scaled FC+FMASK
Sometime it may be different from
Dear All,
Guillaume Ponchel referred me to ProOrigami (which can be installed
locally) to generate protein topology diagrams:
http://munk.csse.unimelb.edu.au/pro-origami/
Thanks again.
Best wishes,
Partha
On Mon, Apr 16, 2012 at 12:12 AM, Parthasarathy Sampathkumar
spart...@gmail.com
I've run into the same problem, and found David Waugh's FAQ to be a great
resource:
http://mcl1.ncifcrf.gov/waugh_tech.html
They use a 3mM buffer of 10:1 reduced:oxidized glutathione. I've tried that and
it cleaves my protein without reducing reducing the disulfide bridges.
I'll second someone
Hi guys:
Recently we need purchase some puck for Actor, unfortunately we can't find any
agency in China.
I really appreciate that if anyone can give us some suggestion about that? such
like brand, price, and necessary accessory?
Thanks for help
Best regards
Frank
Also keep in mind that many of the purchased TEVs are formulated with
some reducing agent (e.g. AcTEV comes in a buffer with 5mM DTT, if I
recall correctly). So unless the enzyme is buffer exchanged
beforehand, there will be some reducing agent introduced alongside it,
depending on the dilution.
Rigaku ACTOR robots can accept many different styles of pucks depending on the
LN2 dewar baseplate that the particular ACTOR is equipped with. Rigaku in
China will sell ACTOR pucks, but if you are looking for ALS-style pucks or
ESRF-style pucks or Unipucks or ???, then I am not sure where to
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