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
Hi Jan, Kevin,
Our experience shipping from San Francisco to CLS has ranged from arrival
on 2nd day to 10th day (both extreme), most commonly on 3rd or 4th day,
irrespective of using the CLS recommended customs broker or FedEx as the
international broker. The main parameter is likely if the packag
Hi Rams,
You could consider using LigPlot+, generate LigPlots for all 'n' PDB files,
and then also superimpose all the plots to see the variations in the
protein-ligand interactions of the same ligand bound to different proteins.
Alternatively, you could try to write a program using Coot's lsq li
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 :-)
> So Harry
Try POSA and FATCAT from Godzik group for structural clusters/trees and
multiple/flexible structure alignments:
https://academic.oup.com/nar/article/48/W1/W60/5848494
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086100/
https://posa.godziklab.org/
https://fatcat.godziklab.org/
Best regards,
De
-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
We dealt with this in-depth during structural genomics days when we
deposited over 1500 novel, high-quality, experimentally-phased structures
into the PDB. Think it’s prudent to trim/truncate side chains without
reliable density.
Non-structural biologists using PDB structures without expert help c
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
gt; Tim
>
>
> On Mon, 27 Jun 2022 13:31:35
> -0700 Debanu Das wrote:
>
> > Hi James,
> >
> > I think it is quite different for publications/open publications
> > (investigator initiated submissions on outcomes of grant-funded
> > research, which are meant
ewers on how to revise your application. I know I always try to get all
> the help I can get.
>
> Might even be able to use biorxiv to do it? Or am I missing something?
>
> -James Holton
> MAD Scientist
>
>
> On 6/27/2022 12:16 PM, Debanu Das wrote:
>
> Thinking
at 11:58 AM Debanu Das wrote:
> Dear John,
>
> For sure it is an aspiration as a society and as a civilization: to think
> beyond individual nations. And for that we have some examples as you
> mentioned at the scientific (IUCr, PDB) and political level (UN). We also
> have t
can: the UN, International Council for Science, IUCr……
> So, it probably isn’t a one size fits all idea that James has put forward…
> Best wishes,
> John
>
>
>
> Emeritus Professor John R Helliwell DSc
>
>
>
>
> On 27 Jun 2022, at 19:03, Debanu Das wrote:
>
>
>So, 2nd question is: would you do it? Would you upload your application
>into the public domain for all to see? What about the reviewer comments?
>If not, why not? Afraid people will steal your ideas? Well, once
>something is public, its pretty clear who got the idea first.
I do not think this (
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
> What I need is a command line that always works. Presumably that's a well
> defined problem...?
>
>
>
> Sent from tiny silly touch screen <http://www.9folders.com/>
> ------
> *From:* Debanu Das
> *Sent:* Tuesday, 25 May 20
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), what program do I
Hi,
This may be of interest in this discussion (the abstract is enlightening in
itself):
"Water polygons in high‐resolution protein crystal structures"
Jonas Lee, Sung‐Hou Kim
https://pubmed.ncbi.nlm.nih.gov/19551896/
Download software here (you can analyze input pdb file to look at water
polygo
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
>
&
Hi Anirban,
At JCSG, we subjected ~180,000 crystals from ~3500 unique/novel
proteins/complexes to X-ray diffraction screening, resulting in >1500
novel structures in the PDB at an average resolution ~2.0A. In theory,
if we had the bandwidth now to sort through all that data to pull out
images of t
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 BENAS
> <0d88e888355
Hi Natalia,
One rule of thumb in crystallography: anything is possible!
We have seen many cases of individual proteins (or their complexes with small
molecules, proteins or nucleic acids) where we ended up with structures
starting from low resolution initial crystals. So before taking a decisio
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 26, 20
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
Hi Akila,
In addition to what others have asked about the dialysis buffer, a few
more comments that might help to decide next steps because the
precipitation (note precipitation and aggregation are related but not
synonymous) may be due to several different or related reasons:
1) At what stage ar
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
Dear Bill,
So sorry to hear this news and the passing of another wonderful
scientist and contributor in our field. It was very interesting
reading your obituary. May his soul rest in peace.
I first heard about John and Abraham as a graduate student and later
on when I joined Sung-Hou for postdoc
Hi,
If you have density for the protein and the DNA and the density for
the protein is correct and you see left-handed DNA density, then I
suppose you are seeing Z-DNA?
Doesn't seem like a problem of incorrect enantiomorph if your protein
density is fine. You can pull out a Z-DNA structure
Hello Balaji,
You may try the following:
1) Try different detergents
2) Use a 100 kDa concentrator after protein purification if possible, to
eliminate as much of empty detergent micelles as possible. You probably
have a lot of these since the CMC value of LDAO is ~0.023% and mol. wt.
of
Hi Peter,
After you have finished checking the data again for twinning, etc.
as suggested by Eleanor,
you might try the following:
1) Refine using the simulated annealing refinement protocols in CNS and
then check R-values and map quality. If you try that, you can also test
a few different
Hi,
Do you have any biochemical evidence that points to oligomeric nature
of your protein? Does SEC indicate monomer/dimer/trimer/tetramer?
If not or even if so, what does the crystal packing with your MR
solution with 4 molecules suggest about monomer interactions? Does that
correlate with S
Hi,
You can use the make-na server http://structure.usc.edu/make-na/
which uses the Nucleic Acid Builder molecular manipulation language
http://www.scripps.edu/mb/case/casegr-sh-3.2.html.
Output will be a pdb file or a mmCIF if you want. Or you could also
download the program from the secon
Hi Shankar,
I believe it is better to use CNS make_cv_twin.inp to define the
reflections related by the twin operator and then use this cv file to
carry out refinement using the twin_lsq refinement target in CNS than to
actually try to detwin the data and then carry out refinement with the
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