Re: [ccp4bb] SeMet data

[Nukri Sanishvili]

Hi Lindsey,
As I mentioned to you in the separate email, 180 degrees for each half is
too little.

Here I'll try to explain some more about SAD vs. MAD:
What I have observed at our beamlines is that the majority of those who
collect MAD data, do it as as an afterthought of SAD. Priority in these
experiments is given to SAD and after it is done, some folks decide to
collect more data at a different wavelength "just in case". There are two
big mistakes in this approach, also explaining why SAD so often "works
better than MAD":
1. Unless one collects the second wavelength from a fresh part of the
crystal, or from a different crystal, there is too much radiation damage in
the second data set. Therefore, the differences in the intensities are
mostly caused by radiation damage and not by anomalous or dispersive
signal. This, of course, kills phasing. This is how SAD can be "better"
than MAD.
In a proper experiment, both wavelengths must be given equal priority. I.e.
distribute the crystal life time equally between the two.
2. Another mistake also stems from the fact that the 2nd wavelength is
treated as "addition" to SAD. Whether it is optimal or not is a different
discussion but typically, the SAD data are collected at the absorption
peak. Then, for 2-wavelength, one collects inflection point. What is lost
in this approach is the whole purpose of a MAD experiment, which is to use
the dispersive signal along with the anomalous one. Dispersive signal
between the inflection point and the peak wavelengths is not so great. In a
good experiment, one of the wavelengths is at the inflection point (as a
must). One could argue that the other is not at the absorption peak but
above the peak (in energy) in order to increase the dispersive signal. How
much above, will depend on particular f' and f" plots. Further the better
for the dispersive signal, but you also want to retain good anomalous one.
So, some compromise needs to be made here.
Bottom line is that SAD and MAD are two different experiments and one is
not a simple expansion of the other. You need to make a decision which one
you are doing and collect data accordingly.

Cheers,
Nukri

On Tue, Aug 27, 2019 at 11:30 AM Doyle, Lindsey A 
wrote:

> Hi Nukri,
>
> Thanks so much for your response. I appreciate the advice.
> 1. Yes, I verified that the anomalous option is turned on during data
> processing. Always a good question to ask
> 2. I collected 180° for each half. I have not tried phasing just one half.
> I’ll give a try but with my space group being P 21 the completeness and
> redundancy might be pretty low. I have a couple inverse beam data sets with
> wedges of 5° but they were about the same as the ones with 1°
> 3. I’ve been collecting 0.5 sec exposures but without reducing the flux.
> This seems to be one of the most recommended things and will be definitely
> doing it on my next run.
> 4. I’ve tried both SAD and MAD with peak 12661 (0.9793 Å) and inflection
> 12658 (0.9795 Å)
>
> Thanks again,
> Lindsey
>
>
> On Aug 26, 2019, at 6:54 PM, Nukri Sanishvili  wrote:
>
> Hi Lindsey,
> Obviously, one would need a lot more information to properly diagnose the
> problem and I am sure much smarter people them me will ask you for that.
> But just to move the task by couple of steps, I want to point out couple of
> things.
> 1. Trivial question: did you have the anomalous option turned on during
> data processing? (Just like from the IT help - is your computer turned on?)
> 2. How much data did you collect for each half of the inverse beam
> geometry? If you have enough, try phasing with only one half. When done
> properly, inverse beam experiment is great but it can easily get tricky
> introducing systematic errors and thus swamping anomalous signal.  If you
> redo the inverse beam, use little wider wedges, say, 5-10 degrees.
> 3. I thought an example of diffraction image would not give any useful
> information but... Judging by how smooth the background is on your Pilatus
> image, I am guessing you have used a lot of exposure. Can you calculate how
> much dose did you put in your crystal? If you are going to re-do the
> experiment, I would suggest reducing the exposure level and collecting more
> data.
> 4. Because you are not showing f' and f" plots, I am guessing that you are
> doing SAD. If it fails and you end up redoing your experiment and you have
> crystals for it, you might want to try 2-wavelength MAD but for that you
> would need to know exactly where is inflection point and collect one of the
> datasets there.
>
> Good luck!
> Nukri
>
> On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:
>
>> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
>> acids, incorporation verified by Mass Spec). I've already collected several
>> datasets (ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of
>> anomalous signal during data processing. I'm most familiar with HKL2000,
>> but I have tried XDS and DIALS auto-processing. Here is a scan:
>> http

Re: [ccp4bb] SeMet data

[Ivan Shabalin]

Hi Lindsey,

My couple cents:

1) Make sure to use "Auto-corrections" option for scaling with HKL. This 
option is great for extracting the anomalous signal.


2) Im also with Andreas and Nukri on collecting 360 at lower dose and 
leaving the inverse beam for later.


Best,

Ivan


With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/

On 8/27/19 03:21, Andreas Förster wrote:

Dear Lindsey,

I'm all with Nukri on this one.  12 Se atoms (whose incorporation you've 
shown) should be plenty to give you enough anomalous signal to phase the 
data and solve the structure.  That's why I would do the simplest 
experiment first.  Collect 360° of data at the peak energy, maybe a bit 
finer sliced than you have now (0.1° per image) and with fewer X-rays.  
Reduce exposure fivefold (just a guess, but most people tend to 
overexpose - see Winter et al., Acta D 75:242, 2019) and see what you 
can get from this one dataset after processing with FRIEDEL'S_LAW= FALSE.


Look at the table "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS 
FUNCTION OF RESOLUTION" in CORRECT.LP and see how far the anomalous 
signal extends (Anomal Corr values above 15 to 20, highlighted by XDS 
with an asterisk) and how strong it is (SigAno values, above 3 gives you 
confidence, though I have solved structures with much less signal).


If the anomalous signal isn't enough for structure solution, collect 
more data from the same crystal.  This is one reason why you reduced the 
exposure in the first place.  Move the detector in or out depending on 
the processing of the first 360° (How far does diffraction extend?) and 
collect another 360°.  Or change chi/kappa.  (See Basu et al., Acta D 
75:262, 2019 for inspiration.)  Or - and this is the best but unlikely 
to be necessary with your crystals - do two-wavelength MAD.  This 
shouldn't be an afterthought to the SAD experiment, though, but properly 
planned as one comprehensive experiment.  Using the inflection and 
remote energies might be a good idea because it maximizes the 
differences between the two datasets.


Inverse beam can be powerful but also poses challenges.  I use this 
technique only if I fail otherwise.


All best.


Andreas





On Tue, Aug 27, 2019 at 3:55 AM Nukri Sanishvili > wrote:


Hi Lindsey,
Obviously, one would need a lot more information to properly
diagnose the problem and I am sure much smarter people them me will
ask you for that. But just to move the task by couple of steps, I
want to point out couple of things.
1. Trivial question: did you have the anomalous option turned on
during data processing? (Just like from the IT help - is your
computer turned on?)
2. How much data did you collect for each half of the inverse beam
geometry? If you have enough, try phasing with only one half. When
done properly, inverse beam experiment is great but it can easily
get tricky introducing systematic errors and thus swamping anomalous
signal.  If you redo the inverse beam, use little wider wedges, say,
5-10 degrees.
3. I thought an example of diffraction image would not give any
useful information but... Judging by how smooth the background is on
your Pilatus image, I am guessing you have used a lot of exposure.
Can you calculate how much dose did you put in your crystal? If you
are going to re-do the experiment, I would suggest reducing the
exposure level and collecting more data.
4. Because you are not showing f' and f" plots, I am guessing that
you are doing SAD. If it fails and you end up redoing your
experiment and you have crystals for it, you might want to try
2-wavelength MAD but for that you would need to know exactly where
is inflection point and collect one of the datasets there.

Good luck!
Nukri

On Mon, Aug 26, 2019 at 5:45 PM L. Doyle mailto:ldo...@fhcrc.org>> wrote:

I have some Seleno-Methionine protein crystals (12 SeMet of 211
amino acids, incorporation verified by Mass Spec). I've already
collected several datasets (ALS BL5.0.2) but I seem to be losing
(rejecting?) a lot of anomalous signal during data processing.
I'm most familiar with HKL2000, but I have tried XDS and DIALS
auto-processing. Here is a scan: https://ibb.co/LZqm33p and here
is an example of a frame: https://ibb.co/gR3ZR47. Each frame is
0.25° and I'm using inverse beam with wedge size 1°. Maybe I
need to adjust my collection strategy? All previous datasets
have been in space group P 21 with dimensions of approx. 24.5Å,
85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional things
I can be doing in HKL but I've run out

[ccp4bb] Student/postdoc fellowships for Understanding Biology through Structure, March 16-20, 2020

[Tom Terwilliger]

Hi Structural biologists, particularly students and postdocs!

Student/postdoc fellowships still available for Understanding Biology
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Fe,NM). The fellowships cover registration and hotel (you still have to get
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Speakers at the symposium will be encouraged to present sufficient
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After the main conference there will be an optional Phenix workshop with
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Best regards,
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Thomas C Terwilliger
Laboratory Fellow, Los Alamos National Laboratory
Senior Scientist, New Mexico Consortium
100 Entrada Dr, Los Alamos, NM 87544
Email: tterwilli...@newmexicoconsortium.org
Tel: 505-431-0010



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Re: [ccp4bb] SEC and MALS

[Kushol Gupta]

Hi everyone – 

 

I highly recommend Vladimir Uversky’s publications on the quantitative analysis 
of intrinsically disordered and flexible proteins by SEC. 

>From my experiences across many projects using SEC-MALS, what is described 
>here is a very common occurrence (and very commonly misunderstood).

 

Kushol

 

Kushol Gupta, Ph.D.

Research Assistant Professor,   
Department of Biochemistry and Biophysics

Director,   Johnson Foundation 
Structural Biology and Biophysics Core

  Perelman School of Medicine at  
 The University of Pennsylvania

  kgu...@upenn.edu / 267.259.0082 /  
 www.stwing.upenn.edu/~kgupta

 

From: CCP4 bulletin board  On Behalf Of arjen jakobi
Sent: Tuesday, August 27, 2019 4:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SEC and MALS

 

Dear Natesh,

 

as Petri pointed out this is a common behavior for proteins/protein complexes 
that deviate substantially from a "globular" shape. It is very typical for 
elongated proteins/protein complexes containing e.g. extended coiled-coil 
regions. These samples will elute much earlier from a SEC column than expected 
from their molecular weight, seemingly suggesting oligomerisation is some form. 
MALS will allow you to unambigously characterize their molecular weight 
independent of their hydrodynamic radius.

 

See e.g. https://elifesciences.org/articles/42129 for a recent example. You 
will find many if you search for coiled-coil structures or other motifs that 
impose elongated shapes.

 

Best,

Arjen

 

On Tue, 27 Aug 2019 at 07:57, Natesh Ramanathan mailto:nat...@iisertvm.ac.in> > wrote:

Dear  Friends,

 

Can you share your experience with examples of MALS giving lower 
molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
Dimer),  for the same protein sample?

 

  If you have/know any published paper, can you please point me to that 
reference paper or send me the paper?

 

Many thanks.
Best regards,

Natesh  




 

-- 

--
"Live Simply and do Serious Things .. "
- Dorothy Mary Crowfoot Hodgkin OM, FRS

"In Science truth always wins"
- Max Ferdinand Perutz OM FRS
--
Dr. Ramanathan Natesh
Assistant Professor, 

School of Biology,

Indian Institute of Science Education and Research Thiruvananthapuram 
(IISER-TVM),

Maruthamala P.O., Vithura,

Thiruvananthapuram,  695551, Kerala, India

nat...@iisertvm.ac.in  
http://www.researcherid.com/rid/C-4488-2008

ORCID:   
http://orcid.org/-0002-1145-5962

https://publons.com/author/1520837/ramanathan-natesh#profile

http://faculty.iisertvm.ac.in/natesh


Office Ph. 0091- 471-2778087

 

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[ccp4bb] Announcement: 11th International Workshop on Radiation Damage to Biological Samples

[Dworkowski Florian (PSI)]

The 11th International Workshop on Radiation Damage to Biological Samples will 
be held at the PSI, Switzerland from lunchtime 25th to lunchtime 27th of March, 
2020.

The Workshop will address essential questions and challenges of radiation 
damage to biological samples during their examination with ionizing radiation. 
The workshop will cover various X-ray and electron scattering techniques, from 
crystallography to imaging, and offers ample opportunities for information 
exchange and discussion among researchers from around the globe.
Please go to https://indico.psi.ch/e/rd11 for first information on the event.
Registration will open in October 2019. Further details will be available 
shortly.

** If you have suggestions for speakers please send them to 
elspeth.gar...@bioch.ox.ac.uk or 
martin.w...@ibs.fr or submit an abstract on the 
website. **






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Re: [ccp4bb] SEC and MALS

[arjen jakobi]

Dear Natesh,

as Petri pointed out this is a common behavior for proteins/protein
complexes that deviate substantially from a "globular" shape. It is very
typical for elongated proteins/protein complexes containing e.g. extended
coiled-coil regions. These samples will elute much earlier from a SEC
column than expected from their molecular weight, seemingly suggesting
oligomerisation is some form. MALS will allow you to unambigously
characterize their molecular weight independent of their hydrodynamic
radius.

See e.g. https://elifesciences.org/articles/42129 for a recent example. You
will find many if you search for coiled-coil structures or other motifs
that impose elongated shapes.

Best,
Arjen

On Tue, 27 Aug 2019 at 07:57, Natesh Ramanathan 
wrote:

> Dear  Friends,
>
> Can you share your experience with examples of MALS giving lower
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
> Dimer),  for the same protein sample?
>
>   If you have/know any published paper, can you please point me to
> that reference paper or send me the paper?
>
> Many thanks.
> Best regards,
> Natesh
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] SEC and MALS

[Rajiv gandhi.s]

Because MALS can capture distinct migrant form of the same protein,
sometimes  protein with disorder and elongated structure behave differently
in  SEC. In SEC we can't distinguish them.  Whereas MALS have scattering at
three different angles,  by that we can captures those multiple forms of
the same protein.
Please provide the image for more information.

On Tue, Aug 27, 2019, 12:30 PM Petri Kursula 
wrote:

> Hi,
> that's typical behaviour for an elongated/disordered molecule, given that
> SEC separates based on hydrodynamic radius, not MW.
> Petri
>
> Petri Kursula
> --
> Professor
> --
> Department of Biomedicine
> University of Bergen, Norway
> http://www.uib.no/en/rg/petrikursula
> 
> petri.kurs...@uib.no 
> --
> Faculty of Biochemistry and Molecular Medicine
> University of Oulu, Finland
> --
>
>
>
>
>
>
> On 27 Aug 2019, at 07:57, Natesh Ramanathan  > wrote:
>
> Dear  Friends,
>
> Can you share your experience with examples of MALS giving lower
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg.
> Dimer),  for the same protein sample?
>
>   If you have/know any published paper, can you please point me to
> that reference paper or send me the paper?
>
> Many thanks.
> Best regards,
> Natesh
>
>
> --
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
>
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor,
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
>
> nat...@iisertvm.ac.in
> http://www.researcherid.com/rid/C-4488-2008
> ORCID: http://orcid.org/-0002-1145-5962
> https://publons.com/author/1520837/ramanathan-natesh#profile
> http://faculty.iisertvm.ac.in/natesh
>
> Office Ph. 0091- 471-2778087
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
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Re: [ccp4bb] SeMet data

[Andreas Förster]

Dear Lindsey,

I'm all with Nukri on this one.  12 Se atoms (whose incorporation you've
shown) should be plenty to give you enough anomalous signal to phase the
data and solve the structure.  That's why I would do the simplest
experiment first.  Collect 360° of data at the peak energy, maybe a bit
finer sliced than you have now (0.1° per image) and with fewer X-rays.
Reduce exposure fivefold (just a guess, but most people tend to overexpose
- see Winter et al., Acta D 75:242, 2019) and see what you can get from
this one dataset after processing with FRIEDEL'S_LAW= FALSE.

Look at the table "SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS
FUNCTION OF RESOLUTION" in CORRECT.LP and see how far the anomalous signal
extends (Anomal Corr values above 15 to 20, highlighted by XDS with an
asterisk) and how strong it is (SigAno values, above 3 gives you
confidence, though I have solved structures with much less signal).

If the anomalous signal isn't enough for structure solution, collect more
data from the same crystal.  This is one reason why you reduced the
exposure in the first place.  Move the detector in or out depending on the
processing of the first 360° (How far does diffraction extend?) and collect
another 360°.  Or change chi/kappa.  (See Basu et al., Acta D 75:262, 2019
for inspiration.)  Or - and this is the best but unlikely to be necessary
with your crystals - do two-wavelength MAD.  This shouldn't be an
afterthought to the SAD experiment, though, but properly planned as one
comprehensive experiment.  Using the inflection and remote energies might
be a good idea because it maximizes the differences between the two
datasets.

Inverse beam can be powerful but also poses challenges.  I use this
technique only if I fail otherwise.

All best.


Andreas





On Tue, Aug 27, 2019 at 3:55 AM Nukri Sanishvili  wrote:

> Hi Lindsey,
> Obviously, one would need a lot more information to properly diagnose the
> problem and I am sure much smarter people them me will ask you for that.
> But just to move the task by couple of steps, I want to point out couple of
> things.
> 1. Trivial question: did you have the anomalous option turned on during
> data processing? (Just like from the IT help - is your computer turned on?)
> 2. How much data did you collect for each half of the inverse beam
> geometry? If you have enough, try phasing with only one half. When done
> properly, inverse beam experiment is great but it can easily get tricky
> introducing systematic errors and thus swamping anomalous signal.  If you
> redo the inverse beam, use little wider wedges, say, 5-10 degrees.
> 3. I thought an example of diffraction image would not give any useful
> information but... Judging by how smooth the background is on your Pilatus
> image, I am guessing you have used a lot of exposure. Can you calculate how
> much dose did you put in your crystal? If you are going to re-do the
> experiment, I would suggest reducing the exposure level and collecting more
> data.
> 4. Because you are not showing f' and f" plots, I am guessing that you are
> doing SAD. If it fails and you end up redoing your experiment and you have
> crystals for it, you might want to try 2-wavelength MAD but for that you
> would need to know exactly where is inflection point and collect one of the
> datasets there.
>
> Good luck!
> Nukri
>
> On Mon, Aug 26, 2019 at 5:45 PM L. Doyle  wrote:
>
>> I have some Seleno-Methionine protein crystals (12 SeMet of 211 amino
>> acids, incorporation verified by Mass Spec). I've already collected several
>> datasets (ALS BL5.0.2) but I seem to be losing (rejecting?) a lot of
>> anomalous signal during data processing. I'm most familiar with HKL2000,
>> but I have tried XDS and DIALS auto-processing. Here is a scan:
>> https://ibb.co/LZqm33p and here is an example of a frame:
>> https://ibb.co/gR3ZR47. Each frame is 0.25° and I'm using inverse beam
>> with wedge size 1°. Maybe I need to adjust my collection strategy? All
>> previous datasets have been in space group P 21 with dimensions of approx.
>> 24.5Å, 85Å, 40Å, 90°, 96.5°, 90°. I'm sure there are additional things I
>> can be doing in HKL but I've run out of ideas. Any advice or
>> recommendations would be appreciated. Please let me know if you need
>> additional information.
>>
>> Thank you,
>> Lindsey
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>>
>
> --
>
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[ccp4bb] Senior Scientist Structural Biology GPCR's

[L. Raats]

Senior Scientist Structural Biology GPCR's
Based in a Belgian Biotechnology company

To strengthen the capabilities of their Structural Biology group, they are
looking for a Senior Scientist Structural Biology under the leadership of a
GPCR expert in the field. You will be part of multidisciplinary drug
discovery project teams, as well as able to act as a project leader
yourself. Furthermore you will be coaching Reasearch Associates.

You have a PhD and Post-doc or relevant industrial experience in the field.
You are familiar with a wide array of techniques and have previously worked
on GPCR's.

Informal inquiries may be made to Lorin Raats (l.ra...@qtcrecruitment.com).



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Re: [ccp4bb] SEC and MALS

[Petri Kursula]

Hi,
that's typical behaviour for an elongated/disordered molecule, given that SEC 
separates based on hydrodynamic radius, not MW.
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula 

petri.kurs...@uib.no 
--
Faculty of Biochemistry and Molecular Medicine
University of Oulu, Finland
--






> On 27 Aug 2019, at 07:57, Natesh Ramanathan  wrote:
> 
> Dear  Friends,
> 
> Can you share your experience with examples of MALS giving lower 
> molecular weight (Eg. Monomer) and  SEC giving higher molecular weight (Eg. 
> Dimer),  for the same protein sample?
> 
>   If you have/know any published paper, can you please point me to that 
> reference paper or send me the paper?
> 
> Many thanks.
> Best regards,
> Natesh  
> 
> 
> -- 
> --
> "Live Simply and do Serious Things .. "
> - Dorothy Mary Crowfoot Hodgkin OM, FRS
> 
> "In Science truth always wins"
> - Max Ferdinand Perutz OM FRS
> --
> Dr. Ramanathan Natesh
> Assistant Professor, 
> School of Biology,
> Indian Institute of Science Education and Research Thiruvananthapuram 
> (IISER-TVM),
> Maruthamala P.O., Vithura,
> Thiruvananthapuram,  695551, Kerala, India
> 
> nat...@iisertvm.ac.in 
> http://www.researcherid.com/rid/C-4488-2008 
> 
> ORCID: http://orcid.org/-0002-1145-5962 
> 
> https://publons.com/author/1520837/ramanathan-natesh#profile 
> 
> http://faculty.iisertvm.ac.in/natesh 
> 
> Office Ph. 0091- 471-2778087
> 
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