also the effort of screening, imaging, monitoring,
following up on hits for optimization, etc.
Best regards,
Debanu
--
Debanu Das, Ph.D.
bio.site/debanu_das
On Sun, Dec 15, 2024 at 3:16 AM Saniya Dubey <
f97235562ca7-dmarc-requ...@jiscmail.ac.uk> wrote:
> Dear All,
>
>
g a micro focus beam) to get some
initial characterization of diffraction, and if lucky even get a unit
cell/space group to estimate/validate crystal components/composition,
verify protein crystals, and if very lucky, may even get an initial data
set and/or preliminary structure.
Regards,
Debanu
—
Deb
ology arsenal, *instead of
substituting workhorse solutions and approaches*, potentially *most useful
in cases only when experimental structures are not available or not
immediately possible to kick off the start of projects*.
Best regards,
Debanu
--
Debanu Das,
https://bio.site/debanu_das
On Fri, Dec
y/shipping process.
Best,
Debanu
On Fri, Jul 28, 2023 at 6:30 PM Jan Abendroth
wrote:
> Hi all,
>
> In addition to the statements above, our experience has shown that using
> the Customs broker as described on the CLS webpage has been helpful. Our
> weekly shipments from Seatt
Coot's lsq ligand;
CCP4MG Superpose equivalent ligand (might take some time to do manually or
few/many at a time but easy to execute and visualize); try with LSQKAB; or
CSD Ligand Overlay (used for ligand-based design when protein structures
are unknown).
Best,
Debanu
On Sat, Jul 15, 2023
Yes, zero occupancy would reflect that. But not the coordinates in any
proper way. Then what would be the point of associating occupancy and
B-factors with totally incorrect coordinates?
Debanu
On Fri, Mar 10, 2023 at 8:58 AM Jurgen Bosch wrote:
> Going back to RIP phasing methods :-)
&
,
Debanu
On Thu, Mar 9, 2023 at 3:57 PM Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
> Coot's ssm superposition does give the C-alpha rmsd, though, most easily
> seen if you run it from a terminal window? I guess it can't be miles
> different
-factors, which could lead to fairly incorrect biological
interpretations.
Best,
Debanu
On Thu, Mar 9, 2023 at 7:55 PM Debanu Das wrote:
> We dealt with this in-depth during structural genomics days when we
> deposited over 1500 novel, high-quality, experimentally-phased structures
> int
crystallographer/structural biologist can easily add in side
chain information if needed for modeling/computational chemistry reasons.
Best regards,
Debanu
On Thu, Mar 9, 2023 at 6:50 PM Jurgen Bosch wrote:
> I’d say no trimming to side chains for the following reason: There are
> non-structural biol
Consider merging with the Annual ACA meeting. The ACA meeting can also
benefit from more X-ray diffraction methods rigor and training and it will
help to elevate the continuity and history of the ACA and its previous and
current member participation and contributions in the field.
Best,
Debanu
On
Amen.
On Thu, Nov 3, 2022 at 5:19 AM Frank von Delft
wrote:
> Great, now we have two random number generators.
>
>
> On 03/11/2022 12:10, David J. Schuller wrote:
>
> https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2
>
> Evolutionary-scale prediction of atomic level protein structure w
ers and
so on.
It does not bypass, and is not related to the other aspects of the larger
quote I had or the entire set of rules in that link...:)
Cheers,
Debanu
On Tue, Jun 28, 2022 at 2:26 AM Tim Gruene wrote:
> Hi Debanu,
>
> the section of your quote of the NIH rules is introduc
rom a
violation of those rules. Participants and stakeholders include but are not
limited to"
Best regards,
Debanu
On Mon, Jun 27, 2022 at 1:13 PM James Holton wrote:
> Hey Debanu,
>
> Hmm. Last time I did it I didn't have to go through any IP lawyers to
> upload a pre-pr
would actually be no need for a new system to share
proposals. All funding agencies just have to open up a portal to access
submitted grants (and I'm quite sure the agencies already have massive
security around hacking attempts to access all this material).
Cheers,
Debanu
On Mon, Jun 27, 2022
or us as a community to
always have an eye on a larger and nobler purpose while working within
current practicalities and frameworks.
Thank you.
Best regards,
Debanu
On Mon, Jun 27, 2022 at 11:18 AM John R Helliwell
wrote:
> Dear Debanu,
> There is indeed much at stake here.
> Would I
initiatives. Transparency and openness in
publishing research is a different ball game, even though there too there
are lopsided effects at the end in many cases, but overall good for world
progress, hopefully.
Best,
Debanu
On Wed, Jun 22, 2022 at 6:09 PM James Holton wrote:
> Greetings all,
>
Hi Mike,
As an ex-JCSG team member, I can verify that the JCSG QC structure
validation server (as well as other ones we had), are unfortunately not
operational anymore. We are trying to rebuild (and reinvent along the way)
some more of the JCSG legacy stuff in our current efforts.
Best,
Debanu
On
the
experimental structure.
Best,
Debanu
--
Debanu Das
On Mon, Jun 7, 2021 at 1:11 PM Scott Horowitz wrote:
> For testing purposes, we want to solve structures of proteins that are not
> in the PDB and have no significant sequence homologues in the PDB (i.e. a
> blast of the pdb will get no sign
And to run it as a single command line option:
http://legacy.ccp4.ac.uk/html/pisa.html
On Tue, May 25, 2021 at 1:07 PM Debanu Das wrote:
> Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/
> or here: http://www.ccp4.ac.uk/pisa/
>
> Best,
> Debanu
>
> On Tue, Ma
Easy way to do it online: https://www.ebi.ac.uk/pdbe/pisa/
or here: http://www.ccp4.ac.uk/pisa/
Best,
Debanu
On Tue, May 25, 2021 at 1:04 PM Frank Von Delft
wrote:
> Yes I thought so too, but discovered I am too stupid to decode the highly
> parsimonious manual on the ccp4 pages.
>
Hi Frank,
PISA is your friend here.
Thanks,
Debanu
On Tue, May 25, 2021 at 12:44 PM Frank von Delft <
frank.vonde...@cmd.ox.ac.uk> wrote:
> Hello all - this presumably has a really simple solution:
>
> For a PDB file with a (correct) biomolecular assembly record (REMARK
> 350),
k at water
polygon structures): https://sourceforge.net/projects/pdbwaterpolygon/
Thanks,
Debanu
On Sun, Apr 4, 2021 at 10:27 AM Debanu wrote:
> Hi,
>
> This may be of interest in this discussion (the abstract is enlightening
> in itself):
>
> "Water polygons in high‐reso
k at water
polygon structures): https://sourceforge.net/projects/pdbwaterpolygon/
Thanks,
Debanu
On Tue, Mar 23, 2021 at 2:15 AM Barone, Matthias
wrote:
> can confirm jon´s comment. I find these in virtually every high-res
> structure. some of them wobble a bit given the AA close by, such
Hi All,
No more responses required, thank you.
Best,
Debanu
On Thu, Oct 8, 2020 at 8:54 AM Debanu Das wrote:
> Hello CCP4BB-ers,
> Posting this here as I have been unable to get a response yet from the
> CCP4 help desk:
> Can anyone point to how (specific download link for this ve
Hello CCP4BB-ers,
Posting this here as I have been unable to get a response yet from the CCP4
help desk:
Can anyone point to how (specific download link for this version) I can
download ccp4 7.0.72?
It appears challenging now to access legacy CCP4 versions.
Thanks,
Debanu
very well lived
with many important contributions to remember.
Best regards,
Debanu
--
Debanu Das,
Accelero Biostructures
On Sun, Jul 19, 2020 at 4:55 PM James Holton wrote:
> Ward was the Program Official for all my grants! My life will not be
> the same without him. He was always so sup
veals the N-terminal region with conserved amino acids
Debanu Das,* Qian Steven Xu,* Jonas Y. Lee, Irina Ankoudinova, Candice
Huang, Yun Lou, Andy DeGiovanni, Rosalind Kim, and Sung-Hou Kim"
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2023878/
I think there should also be examples of C-term
Hi,
Yes, SPASM works very nicely for doing a comparison like this. See Fig 3 in
this publication of ours where we performed a similar analysis:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116655/
Best,
Debanu
--
Debanu Das
On Wed, Jan 8, 2020 at 3:28 PM Rigden, Dan wrote:
> Dear Lei
>
&
are crystals that appear nice but do
not diffract well and there are crystals that do not appear nice but
lead to good/usable structures. So it's all about inner beauty. Never
give up on crystals/crystal optimization without testing them by
X-rays.
Best,
Debanu
On Thu, Jun 28, 2018 at 5:07 PM,
Hi,
I was going to suggest the same but since it has already been said, here’s a
cheeky suggestion: you could try determining the crystal structure of the
complex and get a direct sequence readout for the nuclei acid.
Best,
Debanu
> On Mar 5, 2018, at 9:34 PM, Philippe BE
above, you can then consider trying different DNA
lengths and blunt-end vs overhangs or different protein constructs.
Happy to discuss more about the specific case.
Best,
Debanu
Accelero Biostructures
> On Fri, Mar 2, 2018 at 5:34 PM, Natalia O wrote:
> Hello,
>
>
>
> I
Hi,
You can try the following using protein structures:
1) https://sbgrid.org/software/titles/quilt
2) Swiss PDBViewer, detect hydrophobic patches under Tool Surface
3) EBI PISA and look for negative delta G
4) look at protein-protein interaction and interface dbases
Best,
Debanu
> On Jul
e?
g) Lastly, more esoteric stuff like construct and vector optimization,
mutations, etc.
I am sure there may be a few other things you can try and there may be
more suggestions here.
Best,
Debanu
--
Debanu Das
On Thu, Jul 13, 2017 at 10:46 PM, Briggs, David C
wrote:
> Hi Chris,
>
&g
Yes, we have done this (addition of water to dilute screen reagents in the
well) and also try it now in some cases and in fact, this is also the rationale
behind Hampton's Crystal Screen Lite.
Best,
Debanu
--
Debanu Das
> On Jul 12, 2017, at 9:01 AM, Alun R Coker wrote:
>
> So
of work that may be useful for others now or in the future should be
reported since publications are also record keeping for the future.
Everything does not have to have high scientific impact today.
Best,
Debanu
--
Debanu Das
On Wed, Apr 5, 2017 at 4:46 AM, Stefan Arold wrote:
> Hi Mohamed,
solubility woes over other
factors, you can look into Hampton's (or other vendors) Solubility and
Stability Kit:
https://hamptonresearch.com/documents/product/hr008095_binder1.pdf
Or the pH Slice Kit:
https://hamptonresearch.com/product_detail.aspx?cid=30&sid=200&pid=616
Best,
Debanu
Structural Genomics resource to see if there is
anything on this target or related targets: http://www.webtb.org/
Best,
Debanu
On Wed, Mar 29, 2017 at 6:38 AM, Akilandeswari Gopalan
wrote:
> Dear all,
> I am a PhD student doing structural studies on a few proteins from
> Myco
Dear Xavier,
Great point and reminder!
Thanks,
Debanu
> On Feb 1, 2017, at 6:44 AM, Boaz Shaanan wrote:
>
> Hi,
> One possible (formal, I should say) way around this would be to use one of
> the homology modeling servers (my favourite recently is phyre2 but go for any
> serv
same metal and overall architecture was similar despite other
structure/dimer differences. Referee insisted we mutate our active
site residues and compare, which we did.
Hope this helps.
Best,
Debanu
--
Debanu Das,
Accelero Biostructures
On Tue, Jan 31, 2017 at 9:40 PM, Guillermo Montoya
wrote
beginning.
3) try reductive methylation on the incubated complex prior to setting up
screens if you have numerous exposed lysines.
Thanks,
Debanu
Accelero Biostructures
> On Jan 31, 2017, at 8:05 AM, sanjeev kumar wrote:
>
> Dear all,
>
> I am trying to stabilize a protein-prote
density
for the missing portion in addition to experimental phasing.
"Holographic methods in X-ray crystallography. IV. A fast algorithm
and its application to macromolecular crystallography"
http://scripts.iucr.org/cgi-bin/paper?S0108767395002315
Best,
Debanu
---
LinkedIn: www.linke
superimposing A/B on C/D and refinement with tight NCS then adjust
NCS restraints during model adjustments based on local differences or also see
if phenix autobuild helps.
Best,
Debanu
--
Debanu Das
Accelero Biostructures
> On Jan 24, 2017, at 8:42 PM, Pooja Kesari wrote:
>
>
,
Debanu Das.
> On Jan 10, 2017, at 3:30 AM, V F wrote:
>
> Dear all,
> I have a model with 4 molecules in asu. One of the domains is poorly
> ordered, weak density. Please see the screenshot with 2 panel (2
> chains side-by-side). My question: In the right panel:
> 1. Should
/nature/journal/v473/n7348/abs/nature09964.html
CNS DEN:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322598/
Best,
Debanu Das
> On Jan 2, 2017, at 12:32 PM, Eleanor Dodson wrote:
>
> I would try harder to get an MR solution from your best homologue.
>
> Things I would do..
Hi,
You can use 3DNA or NAB (Nucleic Acid Builder) or even try Coot and then use a
file converter to mrc.
Best,
Debanu
> On Dec 21, 2016, at 12:05 PM, Anindito Sen wrote:
>
> Dear All,
>
> I want to built a 3d model of DNA to be used to show the path of genome
> transfer
t low
conc under which you may reduce precipitation or even with partial
precipitation.
Best,
Debanu
> On Dec 25, 2016, at 6:43 PM, mesters wrote:
>
> Hi,
>
> although most widely used, Tris-NaCl buffers may be acceptable for many but
> unfortunately by far not all proteins.
storage/freezing.
Can try adding a little detergent/non-ionic detergent.
Consider different tag (N- vs C-term), construct optimization, engineer
mutations (happy to elaborate if desired).
Best,
Debanu
> On Dec 24, 2016, at 4:22 PM, Praveen Tripathi
> wrote:
>
> Dear all,
>
cryoprotection soak.
5) You should probably try some diffraction (maybe just 1-2 images) without any
additional cryo and/or capillary mount in mother liquor to see what your
resolution really is and see what is the impact from the cryoprotection step.
Best,
Debanu.
-Original Message
555 3555 1.61
LINK PDG C 209 O3' DT D 108 1555 3555 1.61
LINK O3' DT D 108 PDG C 209 1555 2555 1.61
Best,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Beh
Hi Vaheh,
I believe this is the list of products you are looking for from 08/21/13?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;aea5d439.1308
It has the Abs 280 nm of IMD from few different vendors.
Regards,
Debanu.
-Original Message-
From: CCP4 bulletin board
you have domainB placed correctly (and can also
obtain a reliable solution for domainA), your MR phases can be used later on to
locate heavy atom sites by difference Fourier methods and you can also combine
with experimental phases in non-optimal cases
Best,
Deb
dimer (protein dimer unit C) binds to another
already associated dimer (units A and B).
Also in DNA replication, transcription and mRNA splicing and translation
complexes where recruitment of third or more protein occurs only after initial
partners are already in complex.
Thanks,
Debanu
receptor tyrosine kinase, etc.
4) metallopeptidases with dimerization domain
Thanks,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Shiva
Bhowmik
Sent: Friday, August 09, 2013 10:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
2010 Jul 6.
Ligands in PSI structures.
Kumar A, Chiu HJ, Axelrod HL, Morse A, Elsliger MA, Wilson IA, Deacon A.
Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator
Laboratory, Menlo Park, CA, USA.
PMID: 20944227
http://www.ncbi.nlm.nih.gov/pubmed/20944227
Best,
Debanu
ege of London,
London WC1E6BT, UK. ben...@biochem.ucl.ac.uk
Hope this helps.
Thanks,
Debanu.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sandra
Quarantini [sandraquarant...@gmail.com]
Sent: Monday, October 15, 2012 3:53 AM
To: CCP4BB@
http://www.biotech.ou.edu/
Thanks,
Debanu
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tommi
Kajander
Sent: Friday, October 12, 2012 10:23 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] solubility estimates for domains/structures?
Hi all,
Does
be best to check out and screen several detergents, either by mini column
purification or by DLS.
Thanks,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Vitali
Stanevich
Sent: Friday, October 12, 2012 9:42 AM
To: CCP4BB@JISCMAIL.AC.
complicated.
And it is impressive in architecture too, forming a trimer with 12 TM in each
monomer, with 70A span in the periplasm and 50A in the inner membrane and very
little in the cytoplasm.
Thanks,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Adding to the popular suggestions..
Check out the PSI Protein Model Portal (http://www.proteinmodelportal.org/),
which allows submission to several servers including I-Tasser and Modeller as
well as some informative tutorials on modeling workflow, etc.
Also check out some other standalone serve
your target of interest is from a thermostable organism and expressed
in E. coli, you can try heating the sample to denature contaminating
proteins/proteases.
Best,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Theresa
Hsu
Sent: Tuesday
be worthwhile to screen a panel of
different detergents for extraction and purification for your particular target.
In 2005, we set up a fast protocol for screening a panel of 18 detergents in
48-72 hours,
http://smb.slac.stanford.edu/~debanu/posters/012605_PPCW2005_DDAS.pdf, which
includes
biocide sodium azide (~0.01%) might be tried.
The robot can be used to dispense in each crystallization drop or manually into
the stock solution.
Regards,
-Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of aaleshin
Sent: Tuesday, June 14, 2
ir innovations.
I hope he and his company will be remembered for all their achievements.
Regards,
-Debanu.
From: Dale Tronrud mailto:det...@uoxray.uoregon.edu>>
Date: Tue, Feb 8, 2011 at 11:47 PM
Subject: [ccp4bb] Ken Olsen, Founder of Digital Equipment Corporation, Died
Sunday
To: C
092-1098
Generating isomorphous heavy-atom derivatives by a quick-soak method. Part I:
test cases
P. D. Sun, S. Radaev and M. Kattah
In you r case, brominated DNA would also be a good option without doing
soaking. I think there is a paper also on phasing of the P in the DNA backbone.
Best,
-Deban
glycerol should help to improve
solubility
You can also check out Hampton's PCT Pre-Crystallization Test.
Thanks,
-Debanu.
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Matthew
Bratkowski
Sent: Thursday, August 12, 2010 11:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [c
large enough and you have many of them that you can
pick up and wash well, it would be best to try to get a mass spec on them or
run them on a gel to verify.
You may try the Rigaku FMS system if you have access to a synchrotron
beamline with such a setup.
Regards,
Debanu.
___
D
Aukhil, I., Joshi, P. & Hendrickson, W. A.
(1994). Proteins, 19, 48-54
Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). Comput. Appl. Biosci. 8,
275-282.
Good luck!
Debanu.
---
Debanu Das,
JCSG Structure Determination Core,
SSRL, SLAC National Accelerator Laborato
ay be able to tolerate better the exposure to
cryoprotectant or x-rays.
Although none of these answer your original question, it may help.
Best,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Artem Evdokimov
Sent: Friday, October 31, 2008 3:58
omit_box_pdb=target.pdb
composite_omit_type=sa_omit
For more details:
http://www.phenix-online.org/documentation/autobuild.htm#anch159
Regards,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of William G.
Scott
Sent: Saturday, July 26, 2008 11
up crystallization screens...while
also trying to explore binding partners or construct modifications and other
things.
Hope this is helpful.
Regards,
Debanu.
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Michael
Colaneri
S
If you have phenix installed, you may also try:
phenix.cns_as_mtz cns_file.cv
http://www.phenix-online.org/documentation/reflection_file_tools.htm
Regards,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Miller,
Mitchell D.
Sent: Thursday
even the lowest occupany ones ending up with something like
0.1-0.2 occ. In that case, what extra knowledge is gained by modeling 5 or more
ensembles other that possibly some lowering of R/Rf (which in itself may be
justifiable since lower R/Rf ==> higher model accuracy).
-Debanu.
-Origi
reveal the basis for structural polymorphism.
Nat Struct Biol. 1996 Dec;3(12):1002-9.
Also check tropomysin structure MR attempts from Carolyn Cohen's group.
Regards,
Debanu.
--
Debanu Das,
Structure Determination Core,
Joint Center for Structural Genomics.
Stanford Synchrotron Radi
.
Regards,
Debanu.
-Original Message-
From: CCP4 bulletin board on behalf of Lucas Bleicher
Sent: Fri 3/28/2008 8:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Model ensemble for x-ray crystallography
Some time ago I've heard about the idea of proposing
an ensemble of models (as i
-SG labs to ~$100K or below for SG structures (taking all
costs into account).
Regards,
Debanu.
--
Debanu Das,
JCSG, SSRL.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ramaswamy
Sent: Tuesday, March 18, 2008 4:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Su
Hi,
You can use dimethylamine borane (DMAB) for reductive methylation of the
surface exposed K's. You may also try NaBH4 or sodium cyanoborohydride but the
first may be best.
Don't know about D's and E's.
Best,
Debanu.
-Original Message-
From: CCP4 bulletin
, and competing with sypro orange binding) during the wide range of
the temperature cycling.
Regards,
Debanu.
--
Debanu Das,
Stanford Synchrotron Radiation Laboratory,
Menlo Park, CA.
--
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROT
contains a flowchart which can get you going. It can help to
screen a variety of detergents in about 72 hours. Let me know if you want a
copy, I'll have to look for it, but can send it to you.
Regards,
Debanu.
--
Debanu Das,
SSRL.
From: CCP4 bulletin
bp into it. And also consider
introducing Cys mutations into the protein to get a thiol cross-linked
protein-DNA complex.
Regards,
Debanu.
--
Debanu Das,
SSRL.
-Original Message-
From: CCP4 bulletin board on behalf of Melody Lin
Sent: Tue 11/6/2007 7:36 PM
To: CCP4BB@JISCMAIL.AC.UK
S
/
H. van den Bedem, I. Lotan, J.-C Latombe and A.M. Deacon. (2005). Real-Space
Protein-Model Completion: an Inverse-Kinematics Approach. Acta Cryst. D61:2-13
Regards,
Debanu.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of seglynn
Sent: Thursday
n
P3/R3 '' '' ''
P3121/p3221 '' '' ''
P61/P65 6n 6n 12n
Ref: CCP4 manual
Check both programs that you used. Hope this helps.
Thanks,
Debanu.
-Orig
tag
f) You could also try doing a denaturing prep and unfolding the protein. this
should probably make it bind but refolding may be a problem for your protein
size. however, if you have any assay set up and don't want to re-clone then you
could give this a shot.
Regar
rystals (without any
measurement) of a heavy atom compound into the drop with crystals, let is soak
for a bit and collected a successful MAD data set on it.
Regards,
Debanu.
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Derek Logan
Sent: Tuesday, Septemb
methods. The above techniques are quite well documented in literature.
The first 3 can be done in-house and so can FTIR. We were lucky enough to have
access to an FTIR setup at ALS.
Regards,
Debanu.
--
Debanu Das,
JCSG @ SSRL.
Forwarded message --
From: Savvas Savvides <[EM
be well worth spending say
$1000-$2000/structure to get it validated instead of just spending that on
printing fancy pictures. With the potential cost savings that labs are getting
with the advent on high-throughput methods for expression, purification,
crystallization, data collection, and struc
hould be around 22%)?
Check several different placements of the third molecule. Try simulated
annealing refinement.
What about twinning possibility? You can also use Phaser to try mr in both
P43212 and P43 groups just to make sure that the other space group just to make
sure your sg choice
protein-DNA complex system almost
equivalent to the lysozyme model.
Thanks,
Debanu.
--
Debanu Das,
JCSG,
SSRL.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Das, Debanu
Sent: Wednesday, August 15, 2007 11:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
mple using netropsin, Nucleic
Acids Res. 33, 4106-4116.
Regards,
Debanu.
--
Debanu Das,
JCSG,
SSRL.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Frank von Delft
Sent: Wednesday, August 15, 2007 11:14 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]
modeling.
Regards,
Debanu.
--
Debanu Das,
JCSG, SSRL.
-
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Stephen Graham
Sent: Tuesday, August 07, 2007 11:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] highly soluble proteins
to find heavy atoms sites using the partial MR
phases and then combine MR+experimental phases.
Regards,
Debanu.
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Eric Liu
Sent: Tuesday, July 31, 2007 2:24 PM
To: CCP4BB@JISCMAIL.AC.UK
Subj
er to:
Tan, S. , et. al JMB 2000,297(4), 947-59.
Thanks,
Debanu.
From: CCP4 bulletin board on behalf of bputcha
Sent: Mon 7/16/2007 9:01 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Protein-DNA complex for crystallization
Hi,
I am trying to crystallize a protei
tus to do this (look for
Corie Ralston). You can get more information from them or contact Robert Thorne
directly.
BTW, ALS beamline 12.3.1 has the FMS system if you want to try that out.
Regards,
Debanu.
---
Debanu Das,
Stanford Synchrotron Research Laboratory,
SLAC, Menlo Pa
I believe you can use lsqkab and DynDom. Get the direction cosines of the
rotation axis w.r.t. the centroid, etc. and also get a graphical representation
+ some more numbers for angular rotation, etc.
-Original Message-
From: CCP4 bulletin board on behalf of U Sam
Sent: Sat 7/7/2007 9:23
gers, Palm, Thumb,
Connection and RnaseH), the fingers and palm domains align quite nicely, but
there is a swing angle of approx. 70 degrees or so, between the connection
domains from the two proteins.
Thanks,
Debanu.
-Original Message-
From: Bernhard Rupp [mailto:[EMAIL PROTECTED]
Sent: Sa
Hi,
You can also use LSQKAB in CCP4 to get the angle between two similar domains.
-Debanu.
-Original Message-
From: CCP4 bulletin board on behalf of Kay Diederichs
Sent: Sat 7/7/2007 7:30 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to convert matrix to angle
Jiamu Du
ll be, but I think
you can try the above ratio or else try to get the pH between 8-9.
Thanks,
Debanu.
From: CCP4 bulletin board on behalf of Jacqueline Vitali
Sent: Thu 7/5/2007 6:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] L-alanosine
Dear colleagues,
atoms by difference Fourier methods using your partial model
phases in case you have not found all possible sites. Getting additional sites
may help your starting experimental phases together with combination of partial
model phases with exisiting phases.
Hope this help.
-Debanu.
--
Deba
ogram
that can make a color-coded picture automatically.
Regards,
Debanu.
--
Debanu Das,
Scientist, JCSG,
Stanford Synchrotron Radiation Lab,
California.
-Original Message-
From: CCP4 bulletin board on behalf of Aaron Oakley
Sent: Wed 6/13/2007 10:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [c
ubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%22Moravek+Z%22%5BAuthor%5D>
, Berman HM
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%22Berman+HM%22%5BAuthor%5D>
.
-Debanu.
Hi Ed,
I believe BEAST has been replaced by PHASER (which would allow you the
option of testing both space groups with only a single input reflection file).
I don't think there is any keyword in Beast which would allow you to do the
same.
Thanks,
D
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