Re: [ccp4bb] the structures of Nucleic acid

[Natesh Ramanathan]

Dear Fu Xingke,

 Depends on what Nucleic Acid you are talking of.  If it is RNA,
you can expect some sequence to tertiary structure correspondence so you
might be able to try more MR as compared to DNA.   DNA may have double
helical architecture but less sequence to tertiary structure
correspondence, and hence DNA is less likely to have a 3D structure like
RNA specific structure for a sequence.

 SAD has become a straight forward method to avoid all these
problems to get ab-initio structure.  So many go for it directly.

Hope that helps.
Best wishes,
Natesh

On Mon, 18 Sept 2023 at 13:36, fuxingke  wrote:

> Dear Colleagues,
>  Reacently, I find the structures of Nucleic acid are solved by
> single-wavelength anomalous diffraction(SAD). So, why molecular
> replacement (MR) not?
>
> Regards
>
>
>
> Best wishes,
>
> Fu Xingke
> Institute of Physics CAS
>
> --
>
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-- 
--
"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
Associate Professor,
School of Biology and Center for High-Performance Computing (CHPC),
Founding and Current President of Cryo Electron Microscopy and 3
Dimensional Image Processing Society of India (CEM3DIPSI),
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

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

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] Structure prediction - waiting to happen

[Natesh Ramanathan]

I absolutely agree with Guenter.  This non experts speaking wrong things is
increasingly happening nowadays.  Thanks Guenter, for pointing this out.  A
theory unless it is given experimental data derived evidence it is still a
prediction (just like weather prediction, unless it is realised in the
physical world it will still be a very good knowledge based guess, which we
all revere and appreciate, even if the predicted rainfall does not occur).
Ignorance with use of Alpha-fold models by non experimental structural
biologists and non acceptable remarks that come out of these non
experimental structural biologists including the top experts in the field
and also unrelated fields, is something not at all right happening.  This
email chain also emphasises this aspect. This needs to be corrected and
addressed very seriously at a large level.  Perhaps at the same level at
which the alpha-fold success itself was propagated.   Few articles have
been published in recent journals towards this... but it has not yet
reached the mass.  *It has to  be at an even larger level, perhaps a
commentary in Nature, Science and Cell journals by the top experimental
structural biologists including Nobel Laureates in the field? It will have
more impact on the non-experts if there are Nobel Laureates included in
this task.*

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
Associate Professor,
School of Biology and Center for High-Performance Computing (CHPC),
Founding and Current President of Cryo Electron Microscopy and 3
Dimensional Image Processing Society of India (CEM3DIPSI),
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

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

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087

On Fri, 5 May 2023 at 17:57, Guenter Fritz <
guenter.fritz.phenix.c...@gmail.com> wrote:

> Dear all,
>
> taking AlphaFold models for " true" experimental structures seems to
> become a serious problem.
> I am just returning from a meeting (not a structural biology meeting) and
> saw one model after other. And the non-structural biologist used terms like
> "we calculated a structure"  or "a AlphaFold crystal structure" or "the
> structure was accurate, is was all blue".
> Alphafold models were used to predict ion channels, electron transfer
> pathways, enzyme mechanisms, and yes, not tested by experiments. Wide
> ranging conclusions were drawn on these pure models, which I would not dare
> to draw on limited experimental data.
> There is something going severely wrong.
> And don't get me wrong, I think AlphaFold and other prediction software is
> great to create testable models (like MR models) or try to figure out how
> proteins might assemble and so on.
> But I get the impression that too many of our colleagues got the
> impression that pressing a button replaces experiments.
> Seeing that grants are rejected by such arguments is alarming and we
> should do something.
>
> Best wishes,
> Guenter
>
> Very sorry to hear about your grant. I've been there. It is crushing to be
> rejected, and frustrating when the reason given is ... wrong.
>
> My journalist friends wonder why scientists don't like talking to
> journalists. This is why.  I remember when the first results from XFELs
> were published, and it was immediately declared that there was no longer a
> need for NASA, whose sole purpose (apparently) was to grow bigger and
> better crystals in space. (?!) I find the idea that AlphaFold has
> eliminated the need to solve any more structures equally ludicrous.
>
> I think the best analogy for what has happened in structural biology is
> the same impact a Star Trek style "transporter device" would have on your
> daily commute. Except this "transporter" is only accurate enough to get you
> within a mile or two of your house.  Most of the time. Don't worry, its not
> going to beam you inside a rock or into the sky, as it was trained on data
> with good Clashscores (we think). But, you are on your own getting the rest
> of the way home. This "Last Mile" of transportation networks is actually
> the most challenging, and expensive, but also the most critical. In
> structural biology, the "Last Angstrom" between prediction and actuality is
> equally important, but also fraught with difficulty. It may seem like a
> short distance, until you have to walk it. So, despite amazing progress, it
> is still premature to dismantle 

[ccp4bb] CEM3DIP Society of India, 3rd Annual Symposium on Single particle CryoEM and Cellular Tomography, 17th Dec 2022

[Natesh Ramanathan]

Dear all,

*First Announcement.*

*3rd Annual Symposium on Single particle CryoEM and Cellular Tomography,
17th Dec 2022 at IISER Pune (Hybrid Mode)*

 Cryo Electron Microscopy and 3 Dimensional Image Processing
(CEM3DIP) Society of India ( http://cem3dipsi.iisertvm.ac.in/), in
association with IISER Pune and IISER Thiruvananthapuram is conducting
the *3rd Annual Symposium on
Single particle CryoEM and Cellular Tomography on 17th December 2022 at
IISER Pune,  in Hybrid mode.   *

 Please find the program below.  Sorry for the short notice.  But
the symposium is in Hybrid mode, so many who cannot come in person will be
able to attend virtually.  All timings are in IST.   Please circulate it to
your colleagues and friends interested in structural biology using single
particle cryoEM and cellular tomography.

*3rd  CEM3DIP Society of India Annual Symposium on Single particle CryoEM
and Cellar Tomography (Over Hybrid-Platform)*
17th December 2022. Venue : IISER Pune, New Lecture Hall (NLH)
Session Time  Speakers/Chair Person Name
10:30:10:35 Inauguration by Prof. Jayant B Udgaonkar (Director IISER Pune)
10:35-10:45 Address by President CEM3DIPSI
10:45-11:45 Chairperson   Professor Jayant B Udgaonkar (Director, IISER
Pune)
10:45-11:15 Dr. Tanweer Hussain - IISc Bangalore
11:15-11:45 Dr. Vidya Mangala Prasad -  IISc Bangalore
12:00-14:15 Chairperson   Professor Mohan Wani (Director, NCCS Pune)
12:00-12:30 Dr. Dilip Kumar - Ashoka University
12:30-13:00 Dr. Shanti Swaroop Srivastava- IISER Behrampur
13:00-14:00 LUNCH BREAK  @   Posters Venue
14:00-14:15 TBA (Sponsorer talk)
14:15-15:15 Chairperson Professor M.V Hosur (Former INSA Senior Scientist)
14:15-14:45 Dr. Ramanujam Srinivasan  - NISER Bhubaneswar
14:45-15:15 Dr. Prem S Kaushal  - RCB Faridabad
15:15-15:30 Vote of thanks by Secretary CEM3DIPSI
15:30-17:30 Poster Session

There are only limited seats for this hybrid meeting.  If you are
interested
*For Free Registration email :* *cem3di...@gmail.com
 with Subject: Registration. *  and with following
details
*Your Full Name: *
*Your current Designation: *Whether you are PhD student, Postdoc or PI.
*Your affiliation *(where you are are working) :   Organisation name
(Academic/Industry).
*Whether you want to attend Offline or Online : *

 *If you are coming in person, you will have to come on your own
and make your own accommodation arrangements.*
*Tea and Lunch will be provided.*

* Industries who are interested in sponsoring this one day
CEM3DIPSI annual symposium event may please contact me by email.*

Kind regards,
Natesh
*President CEM3DIP Society of India.*

-- 
--
"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 and  Center for High-Performance Computing (CHPC)
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
Maruthamala P.O., Vithura,
Thiruvananthapuram,  695551, Kerala, India

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

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] Checking X-ray sequence (no more protein).

[Natesh Ramanathan]

Dear Jon,
 We did exactly the same back in 1999's.
1) Natesh R, Bhanumoorthy P, Vithayathil PJ, Sekar K, Ramakumar S,
Viswamitra MA. (1999). Crystal structure at 1.8 Å resolution and proposed
amino acid sequence of a thermostable xylanase from *Thermoascus
aurantiacus*. J. Mol. Biol., 288, 999-1012.


and then updated the 1.8 A crystal structure derived sequence with ultra
high resolution electron density map.  We were also able to model
additional terminal residues in ultra high resolution map (reported in 2003
paper below).

2) Natesh R, Manikandan K, Bhanumoorthy P, Viswamitra MA, Ramakumar S.
(2003). Thermostable xylanase from *Thermoascus aurantiacus* at ultrahigh
resolution (0.89 Å) at 100 K and atomic resolution (1.11 Å) at 293 K
refined anisotropically to small-molecule accuracy. Acta Crystallogr., D
59,105-117. 



I will be able happy to help off the egroup if you need more
information/help.

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,
Founding President and President Cryo Electron Microscopy and 3 Dimensional
Image Processing Society of India (CEM3DIPSI)
http://cem3dipsi.iisertvm.ac.in/
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://faculty.iisertvm.ac.in/natesh

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087

On Fri, 29 Jul 2022 at 15:45, Jon Cooper <
488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray
> sequence for a protein where it is impractical to do experimental
> sequencing, protein or DNA. The structure refines to publishable R/R-free
> and the main ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where
> alternative H-bonding networks are possible. Running alpha-fold seems an
> interesting option? Any suggestions much appreciated.
>
> Cheers, Jon.C.
>
> Sent from ProtonMail mobile
>
>
>
> --
>
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Re: [ccp4bb] sugestions on weak diffracting protein crystals

[Natesh Ramanathan]

Dear Deepak,

   I have a few suggestions:

1) First you can send it to synchrotrons, particularly microfocus beamlines
and shoot as many good in-house diffracting crystals.
2) Setting up crystallisation by micro batch method under Al's oil at
various vapour exchange rate may help.  But you have to harvest crystals at
the right time.
3) XFEL with micro crystals will also solve your problem.
4) More difficult one is to do MicroED.  You need to do a cryoFIB and do
MicroED, ie., diffraction using cryo electron microscopy and do MR with
your available model.

 Trial and perseverance will definitely lead you to the structure of your
required complex..

What is the solvent content in your protein crystal?  Based on that you can
also plan other trials.

Hope that helps.
Wish you all the very best.
Natesh



On Tue, 18 May 2021 at 15:49, Deepak Deepak  wrote:

> Dear all,
>
> I have got multiple crystals (see picture 1) of a protein (8kDa) with a
> helical aromatic oligoamide foldamer (5kDa) but these crystals *diffract
> very poorly *(see the diffraction pattern in picture 2).
>
> I prepare a 1.3mM:1.3mM complex of protein: foldamer in 20mM Tris, pH 7.5
> buffer. Crystals grew in 3-5 days in sitting and hanging drop at 20 Deg C
> and 25 Deg C in the following conditions:
>
> *- 20% PEG 400, 0.1M MES pH 6.0*
> *-20% PEG 400, 0.1M Sodium Cacodylate pH 6.0*
>
> *Multiple cryo used were:*
> *-25%Glycerol in mother solution*
>  -30% glycerol in water
> *-30%PEG 400,*
> *-35% PEG 400*
> *-20% PEG 8000 + 40% PEG 400 mix*
>
> Kindly suggest some methods/modifications on how can I improve the
> resolution and get better-diffracting crystals. Please let me know if you
> need more information.
>
> Kind regards,
> Deepak
> Ph.D. Student
>
> PS: The protein is a DNA binding protein and I have crystallized and
> solved the structure of this protein with its DNA partner and now I
> crystallized it with our foldamers but diffraction is not good. There are
> multiple structures of the Protein+DNA complex in literature but *no
> apo-protein structure *as the protein needs a binding partner to
> crystallize. *We already have solution studies showing a good binding.*
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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-- 
--
"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://faculty.iisertvm.ac.in/natesh

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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Re: [ccp4bb] request for basic crystallography online classes

[Natesh Ramanathan]

Dear Venkata,

Check with Birkbeck online crystallography certificate course here:
http://www.bbk.ac.uk/study/2020/postgraduate/programmes/TPCCRPRO_C/.

Best wishes,
Natesh

On Wed, 22 Jul 2020 at 09:22, venkata narayana Are <
venkat.sai.biochemis...@gmail.com> wrote:

> Dear Sir,
>
> My self Venkat completed Ph.D. in Biochemistry (structural biology) later
> on joined in a short project where I learned cell biology and virology. I
> have solved 15 structures during my Ph.D., further I wanting to learn
> membrane protein receptors structural biology and other complex protein
> structural biology.
>
> Here my request is, I wanted to attend crystallography lectures for
> clearing my basic concept. could you please suggest me any online classes
> or courses which are in running or going to start.
>
> Sincerely looking forward for your reply.
>
> Sincerely,
> Venkat
>
> --
>
> *Venkata Narayana Are*
>
> C/o Dr. Debasis Nayak
>
> IIT, Indore, Madhya Pradesh - 452013
>
> Mobile No: 08435214885
>
>
>
> --
>
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>


-- 
--
"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://faculty.iisertvm.ac.in/natesh

*Researcher ID*: http://www.researcherid.com/rid/C-4488-2008
*ORCID*: http://orcid.org/-0002-1145-5962
Vidwan-ID : 94134: http://iisertvm.irins.org/profile/94134
*PUBLONS*: https://publons.com/author/1520837/ramanathan-natesh#profile

Office Ph. 0091- 471-2778087



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[ccp4bb] Post Doc position : cryoEM

[Natesh Ramanathan]

Dear All,

  A postdoc position is available in my group at the School of Biology
(SoB), IISER Thiruvananthapuram (IISER-TVM), Kerala, INDIA. Our campus is
arguably one of the most picturesque in India (http://www.iisertvm
.ac.in/pages/campus), and is close to the excellent tropical mountain (e.g
Ponmudi).

  We are looking for a highly motivated, talented and self-driven
postdoctoral researcher to carry structural studies of the protein-protein,
protein-DNA and protein-drug complexes in order to understand the
structure, function and molecular mechanism of transcription
regulators in *Mycobacterium
spp*.  The postdoctoral position is funded by Institute Fellowship.  You
will be working on a project funded by MHRD (Ministry of Human Resource and
Development, Government of India).  More information about our research and
training can be found at our lab page here
http://faculty.iisertvm.ac.in/natesh/.

 You will be part of a friendly and supportive team working on
challenging projects using single-particle cryoEM and Protein
Crystallography(PX) and will benefit from additional interactions with the
wider scientific community and excellent scientific facilities and training
opportunities at IISER-TVM.

You should have a PhD (preferably fresh PhD candidate) or with
maximum 1 or 2 years of postdoctoral experience with a strong background in
protein biochemistry, molecular biology, structural biology or related
field. Applicants with experience in protein expression purification,
single-particle cryoEM and/or Protein crystallography is highly desirable.
Expertise with insect cell line expression system/cryo cellular tomography
will be an added advantage, but not necessary. If the candidate
has expertise in PX and is interested in getting trained in cryoEM you
are encouraged to apply.  The candidate should have excellent communication
skills, and be comfortable working collaboratively with other lab members.

 The individual will receive a competitive salary with On-campus
housing and work in an excellent environment.

Deadline for applications is 9th of June 2020.

For informal enquires please contact Dr Ramanathan Natesh at the email ID
nat...@iisertvm.ac.in.

JOB details:

Postdoctoral position fixed term 3 years (1 year + 2 years.  Based on
performance after 1 year, the position can be extended to 2 more years ).

Age limit is 32 years at the time of application.

Institute Fellowship amount: INR 55,000. pm  (On-campus housing will be
provided).

Qualified applicants should submit a CV along with a list of publications
and research interests, a cover letter summarizing research experience, a
research proposal (Max. 3 to 4 pages) and the names of three references to
Dr. Ramanathan Natesh (nat...@iisertvm.ac.in).  Applications will be
reviewed upon receipt. The start date for the position is tentatively
August 2020 or as early as possible.

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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Re: [ccp4bb] Contradictory result between ITC and cocrystal structure

[Natesh Ramanathan]

Dear Monika,
Did you do the proper positive and -ve control for ITC.
It is impossible that there are no changes in thermodynamics.. when it
binds..
Either your detector is not sensing it OR your experiment is not running
properly..
HTH
Best wishes,
Natesh

On Sat, 22 Feb 2020 at 12:01, monika chandravanshi <
chandravanshi.monik...@gmail.com> wrote:

> Dear All,
>
>   I have a situation, where a mutant protein does not exhibit
> any heat change upon titration with cognate ligand in the ITC experiment.
> However, it co-crystallizes with the respective cognate ligand. Also, the
> cocrystal structure reveals the conservation of the hydrogen bonding
> networks except for the mutated residues. I would like to know the possible
> reason for the no heat change in the ITC experiment.
>
> Looking forward to hearing from you.
>
> --
> *-*
>
> *With Kind Regards*
>
> *Monika Chandravanshi*
> *PhD Scholar, *
> *Department of Biosciences and Bioengineering*
> *Indian Institute of Technology Guwahati, Guwahati India*
>
> --
>
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-- 
--
"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=1

Re: [ccp4bb] CryoEM course. Third Announcement: EMBO Practical Course CEM3DIP 2020: Single particle cryoEM of macromolecular-assemblies and cellular tomography. Hurry only 6 more day left for registra

[Natesh Ramanathan]

Dear All,

The last date for registration for the *EMBO Practical course
CEM3DIP 2020: Single particle cryoEM of macromolecular-assemblies and
cellular tomography*
has been extended to *25 Sep 2019.*

 *To register for the course, please click here:*
http://meetings.embo.org/event/20-cem3dip   *(Last date 25 September
2019).  The Abstract Submission Deadline remains the same 30 Sep 2019.*

Sincerely yours,

Ramanathan Natesh, Partha Pratim Datta, Jayati Sengupta, Smarajit Polley
and Moumita Dutta,

Course Coordinators EMBO practical course CEM3DIP 2020.

Phone: *+91-471-2778087*

Please write to *cem3dip2...@iisertvm.ac.in * for
any queries/sponsorship regarding this course.

On Mon, 9 Sep 2019 at 23:16, Natesh Ramanathan 
wrote:

> *Third Announcement: Hurry up. Only 6 more days left for registration !!  
> **Applicants
> from all over the world are encouraged to apply.*
>
>
> *EMBO Practical course CEM3DIP 2020: **Single particle cryoEM of
> macromolecular-assemblies and cellular tomography*
>
>
>
> *19-30 January, 2020, at IISER & IICB Kolkata, Kolkata, India.*
>
>
> *Major topics covered include  Single particle cryoEM (Theory, hands-on
> specimen preparation, insight into data collection and hands-on image
> processing practicals). It also covers Cellular tomography (Both theory and
> sub tomogram averaging practicals) and talks on MicroED - 3D electron
> Crystallography and its application.  Speakers include  2017 Nobel Laureate
> in Chemistry  Professor Joachim Frank **(Columbia University) and other 
> **world
> leaders in their respective fields (See link below).  *
>
>
>
>*To register for the course, please click here:*
> http://meetings.embo.org/event/20-cem3dip   *(Last date 15 September
> 2019)*
>
>
>
> More details can be found below:
>
>
> The *EMBO Practical Course *Cryo Electron Microscopy and 3
> Dimensional Image Processing (*CEM3DIP 2020): **Single particle cryoEM of
> macromolecular-assemblies and cellular tomography* will be held at
> IISER-Kolkata <https://www.iiserkol.ac.in/web/en/> in Kolkata
> <https://en.wikipedia.org/wiki/Kolkata>, India and CSIR-IICB Kolkata
> <https://www.iicb.res.in/> (on specimen preparation and data collection
> hands-on sessions days).  This is an extensive 10 day practical course
> that will be held  from 19  January – 30 January 2020 at IISER-Kolkata
> (with a 1 day break, to chill out on a group excursion to historic and
> modern places of Kolkata and dinner-cum river cruise on the Ganges
> <https://en.wikipedia.org/wiki/Hooghly_River>).
>
>
>
>
>
> For Course details and to apply online go to the URL :
>
>
> http://meetings.embo.org/event/20-cem3dip
>
>
>
> Important dates :
>
> *Registration Deadline : 15 September 2019*
>
>
>
>The course will focus on structural biology using Transmission
> Electron Microscopy and aims to teach the participants the basic principles
> and practical aspects of specimen preparation, data collection, Image
> processing and 3D reconstruction in Single Particle Cryo Electron
> Microscopy(SPCryoEM) and Cellular Tomography.  This is a hands-on course,
> in which theory and practicals are tightly intertwined.  There will be
> practical session to teach sample preparation for Single particle –ve stain
> and cryoEM and data collection.  A subset of participants will be
> encouraged to bring their samples.  The topics covered will suit both the
> new entrants to the field as well as those who want to acquire an in-depth
> understanding of the fundamental principles and practical aspects.
> Applications are invited from PhD students, Post Docs and Researchers
> (Faculties/PI’s and protein crystallographers) who wish to acquire
> knowledge in SPCryoEM and Cellular Tomography.  Applicants from all over
> the world are encouraged to apply.  For more information please contact the
> course coordinator at *cem3dip2...@iisertvm.ac.in
> *.
>
>
>
> *The basic format of the course* will be theoretical lectures
> in the mornings followed by hands on practical session on specimen
> preparation, data collection and image processing on computer workstations
> in the afternoon.  Evenings will be reserved for poster presentations by
> the participants and research talks by the participants/instructors.
>
>
>
> *The instructors/speakers for the course will include:*
>
> Joachim Frank (Columbia University), Grant Jensen (Caltech), Garib N
> Murshudov (MRC-LMB), José María Carazo (CNB-CSIC), Elena Orlova (Birkbeck
> College), Elizabeth Wright (University of Wisconsin), Kelly Lee (University
> of Washington), Rajendra K Agrawal (Wadsworth Ce

[ccp4bb] CryoEM course. Third Announcement: EMBO Practical Course CEM3DIP 2020: Single particle cryoEM of macromolecular-assemblies and cellular tomography. Hurry only 6 more day left for registration

[Natesh Ramanathan]

*Third Announcement: Hurry up. Only 6 more days left for registration
!!  **Applicants
from all over the world are encouraged to apply.*


*EMBO Practical course CEM3DIP 2020: **Single particle cryoEM of
macromolecular-assemblies and cellular tomography*



*19-30 January, 2020, at IISER & IICB Kolkata, Kolkata, India.*


*Major topics covered include  Single particle cryoEM (Theory, hands-on
specimen preparation, insight into data collection and hands-on image
processing practicals). It also covers Cellular tomography (Both theory and
sub tomogram averaging practicals) and talks on MicroED - 3D electron
Crystallography and its application.  Speakers include  2017 Nobel Laureate
in Chemistry  Professor Joachim Frank **(Columbia University) and other **world
leaders in their respective fields (See link below).  *



   *To register for the course, please click here:*
http://meetings.embo.org/event/20-cem3dip   *(Last date 15 September 2019)*



More details can be found below:


The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2020): **Single particle cryoEM of
macromolecular-assemblies and cellular tomography* will be held at
IISER-Kolkata  in Kolkata
, India and CSIR-IICB Kolkata
 (on specimen preparation and data collection
hands-on sessions days).  This is an extensive 10 day practical course that
will be held  from 19  January – 30 January 2020 at IISER-Kolkata (with a 1
day break, to chill out on a group excursion to historic and modern places
of Kolkata and dinner-cum river cruise on the Ganges
).





For Course details and to apply online go to the URL :


http://meetings.embo.org/event/20-cem3dip



Important dates :

*Registration Deadline : 15 September 2019*



   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, data collection, Image
processing and 3D reconstruction in Single Particle Cryo Electron
Microscopy(SPCryoEM) and Cellular Tomography.  This is a hands-on course,
in which theory and practicals are tightly intertwined.  There will be
practical session to teach sample preparation for Single particle –ve stain
and cryoEM and data collection.  A subset of participants will be
encouraged to bring their samples.  The topics covered will suit both the
new entrants to the field as well as those who want to acquire an in-depth
understanding of the fundamental principles and practical aspects.
Applications are invited from PhD students, Post Docs and Researchers
(Faculties/PI’s and protein crystallographers) who wish to acquire
knowledge in SPCryoEM and Cellular Tomography.  Applicants from all over
the world are encouraged to apply.  For more information please contact the
course coordinator at *cem3dip2...@iisertvm.ac.in
*.



*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation, data collection and image processing on computer workstations
in the afternoon.  Evenings will be reserved for poster presentations by
the participants and research talks by the participants/instructors.



*The instructors/speakers for the course will include:*

Joachim Frank (Columbia University), Grant Jensen (Caltech), Garib N
Murshudov (MRC-LMB), José María Carazo (CNB-CSIC), Elena Orlova (Birkbeck
College), Elizabeth Wright (University of Wisconsin), Kelly Lee (University
of Washington), Rajendra K Agrawal (Wadsworth Centre), Giulia Zanetti
(Birkbeck College), Montserrat Samsó (VCU), Ana Casañal (MRC-LMB), Arjen
Jakobi (Kavli Institute), Brent L. Nannenga (Arizona State University),
Carlos Oscar S Sorzano (CNB-CSIC), Dmitry Lyumkis (Salk Instiute), Osman
Salih (EMBL-EBI), Florence Tama (Nagoya University), Jayati Sengupta
(CSIR-IICB), Manidipa Banerjee (IIT Delhi), Moumita Dutta (ICMR-NICED),
Partha Pratim Datta (IISER Kolkota), Ramanathan Natesh (IISER
Thiruvananthapuram), Smarajit Polley (Bose Institute), Somnath Dutta (IISc).



For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/20-cem3dip
**. *



The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster abstract.  Applicants should include in the section “Details
of Current research Project and Statement of Purpose” an explanation of why
attendance at the course would further the applicant's own research.  Having
some preliminary data or exposure to electron microscopy /cryoEM/
tomography will be preferred.  PhD and Postdoctoral applicants should
request their supervisor 

[ccp4bb] SEC and MALS

[Natesh Ramanathan]

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=1

[ccp4bb] EMBO Practical Course CEM3DIP 2020: Single particle cryoEM of macromolecular-assemblies and cellular tomography

[Natesh Ramanathan]

*First Announcement:*



*EMBO Practical course Cryo Electron Microscopy and 3 Dimensional Image
Processing (CEM3DIP 2020): **Single particle cryoEM of
macromolecular-assemblies and cellular tomography*



*19-30 January, 2020, at IISER Kolkata, Kolkata, India.*



The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2020): **Single particle cryoEM of
macromolecular-assemblies and cellular tomography* will be held at
IISER-Kolkata  in Kolkata
, India and IICB-Kolkata
 (on specimen preparation and data collection
hands-on sessions days).  This is an extensive 10 day practical course that
will be held  from 19  January – 30 January 2020 at IISER-Kolkata (with a 1
day break, to chill out on a group excursion to historic and modern places
of Kolkata and dinner-cum river cruise on the Ganges
).





For Course details and to apply online go to the URL :


http://meetings.embo.org/event/20-cem3dip



Important dates :

*Registration Deadline : 15 September 2019*



   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, data collection, Image
processing and 3D reconstruction in Single Particle Cryo Electron
Microscopy(SPCryoEM) and Cellular Tomography.  This is a hands-on course,
in which theory and practicals are tightly intertwined.  There will be
practical session to teach sample preparation for Single particle –ve stain
and cryoEM and data collection.  Subset of participants will be encouraged
to bring their samples.  The topics covered will suit both the new entrants
to the field as well as those who wants to acquire an in-depth
understanding  of  the fundamental principles and practical aspects.
Applications are invited from PhD students, Post Docs and Researchers
(Faculties/PI’s and protein crystallographers) who wish to acquire
knowledge in SPCryoEM and Cellular Tomography.  Applicants from all over
the world are encouraged to apply.  For more information please contact the
course coordinator at *cem3dip2...@iisertvm.ac.in
*.



*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation, data collection and image processing on computer workstations
in the afternoon.  Evenings will be reserved for poster presentations by
the participants and research talks by the participants/instructors.



*The instructors/speakers for the course will include:*

Joachim Frank (Columbia University), Grant Jensen (Caltech), Garib N
Murshudov (MRC-LMB), José María Carazo (CNB-CSIC), Elena Orlova (Birkbeck
College), Elizabeth Wright (University of Wisconsin), Kelly Lee (University
of Washington), Rajendra K Agrawal (Wadsworth Centre), Giulia Zanetti
(Birkbeck College), Montserrat Samsó (VCU), Ana Casañal (MRC-LMB), Arjen
Jakobi (Kavli Institute), Brent L. Nannenga (Arizona State University),
Carlos Oscar S Sorzano (CNB-CSIC), Dmitry Lyumkis (Salk Instiute), Osman
Salih (EMBL-EBI), Florence Tama (Nagoya University), Jayati Sengupta
(CSIR-IICB), Manidipa Banerjee (IIT Delhi), Moumita Dutta (ICMR-NICED),
Partha Pratim Datta (IISER Kolkota), Ramanathan Natesh (IISER
Thiruvananthapuram), Smarajit Polley (Bose Institute), Somnath Dutta (IISc).



For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/20-cem3dip
**.  *



The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster abstract.  Applicants should include in the section
“Details of Current research Project and Statement of Purpose” an
explanation of why attendance at the course would further the applicant's
own research.  Having some preliminary data or exposure to electron
microscopy /cryoEM/ tomography will be preferred.  PhD and
Postdoctoral applicants
should request their supervisor to send a recommendation letter, before the
application deadline, by e-mail directly to the organizer at
cem3dip2...@iisertvm.ac.in.  Only selected people from the applicants will
be contacted.  Based on the availability of funds, travel and/or
registration, accommodation bursaries for a subset of selected applicants
can be provided.  If you want to request for registration and/or
accommodation bursaries, mention that explicitly in the space for
‘Justification
for Travel Grant’ and justify your request.   All registered participants
have to present posters on their research work.  A selection of
participants will be invited to give an oral presentation of their ongoing
research work.



We shall truly appreciate if this e-mail 

Re: [ccp4bb] Generating Additional Phasing Statistics

[Natesh Ramanathan]

Dear Jason McCoy,
 You can refine the heavy atom coordinates in mlphare and you
should be able to get both the values Phasing Power and Cullis-R for your
SIRAS.
Best wishes,
Natesh

On Fri, 1 Feb 2019 at 19:24, McCoy, Jason (mccoyj5) 
wrote:

> Dear CCP4bb members,
>
> I am compiling a rebuttal for a manuscript that utilized experimental
> SIRAS phasing in order to generate coordinates that I could then use for
> molecular replacement.  For phasing, I used phenix auto-sol and I was able
> to successfully generate a suitable model for MR on a native data set.
> However, a reviewer requested additional phasing statistics, such as the
> phasing power and Cullis-R. It appears phenix auto-sol does not produce
> these statistics. I have reported the FOM pre and post density
> modification. I am looking to generate additional phasing statistics for my
> reviewer. Do you have any recommendations?
>
> Thank you in advance,
> Jason McCoy
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
--
"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=1

Re: [ccp4bb] Electron density maps for Cryo-EM structures.

[Natesh Ramanathan]

Dear Kevin,

 Are you referring to "generating a  map"  from the model (PDB
coordinates) generated from tracing the chain in the ab-initio EM map?

Best wishes,
Natesh

On Mon, 10 Sep 2018 at 09:58, Kevin Jin  wrote:

>  Dear All,
>
> Is there any sever available to create electron density maps for cryo-em
> structures? Or, we should create the maps from mmCIF. I am particularly
> interested in those cryo-em structures with high resolution, like 2.6~2.8A.
>
> Please give me an education.
>
> Thanks,
>
> Kevin
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>


-- 
--
"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=1

[ccp4bb] PhD positions in "Structural Molecular Biology" at IISER Thiruvananthapuram.

[Natesh Ramanathan]

Applications are invited from highly motivated students for admission to
the PhD programme  in the Structural Molecular Biology
  lab of Dr. Ramanathan Natesh in
the area of   Infectious Disease  (*Mycobacterium tuberculosis*  and
*Plasmodium
falciparum)   and DNA Damage Repair,  *
Under the Ph.D. Programme of Indian Institute of Science Education and
Research Thiruvananthapuram (IISER-TVM), India, starting August 2018.

For eligibility and how to apply go to :
http://www.iisertvm.ac.in/pages/phd_admissions.phpx *

Last date of receipt of the application form: 30th April 2018

The successful applicant will clone, express and purify proteins and
protein complexes for characterisation using single particle cryo-electron
microscopy and protein crystallography along with range of other
biophysical (DLS, MALS, CD, Fluorescence etc.), biochemical and molecular
biology techniques.  We are looking for candidates with strong interest in
structural biochemistry.  Ideally, these candidates will have prior expertise
in protein expression and purification.  Prior knowledge of cryo electron
microscopy and / or protein crystallography or biophysical methods is a
plus.

We have excellent facilities for doing Molecular Biology, Biochemistry,
Protein Crystallography and Single Particle cryoEM  : See
http://faculty.iisertvm.ac.in/natesh/index.php/sample-page/

Note that students who have qualification in one of the national level
tests, listed at the above application link* are eligible to apply online.
  If you are not eligible and not residing in India and you are still
interested in our Structural  Molecular Biology PhD programme, please get
in touch with me by e-mail at “nates...@hotmail.com”  to informally discuss
about your research plans in our lab.

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 PO, Vithura,
Thiruvananthapuram - 695551, Kerala, India.
nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
http://faculty.iisertvm.ac.in/natesh/
Ph. 0091- 471 - 2599403
Alternate Ph. 0091- 471-2778087
Fax.0091- 471 - 2597427

[ccp4bb] EMBO Practical Course CEM3DIP 2018: of macromolecular assemblies and cellular tomography: Final Announcement

[Natesh Ramanathan]

 *Final Announcement*

*ONLY ONE DAY LEFT for online application :*



*There is no fees for online application.  Only chosen participants will
have to pay registration fees.  Applicants from all over the world are
eligible to apply.   Applicants from EMBC member states
(http://www.embo.org/about-embo/member-states
) are in
particular encouraged  to apply.*



*EMBO Practical course Cryo Electron Microscopy and 3 Dimensional Image
Processing (CEM3DIP 2018): **of Macromolecular assemblies and Cellular
tomography*



*18-29 March, 2018, at IIT Delhi, New Delhi, India.*



The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2018): of macromolecular assemblies
and cellular tomography* will be held at IIT Delhi
 in New Delhi
, India.  This is an extensive 10
day course that will be held  from 18  March – 29 March 2018 at IIT Delhi
(with a 1 day break, to chill out at the backdrops of
Taj Mahal
, one of the seven wonders of
world).



For Course details  and to apply online go to the URL :


http://meetings.embo.org/event/18-cem3dip



Important dates :

*Registration Deadline : 15 November 2017*



   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, Image processing and 3D
reconstruction in Single Particle Cryo Electron Microscopy(SPCryoEM) and
Cellular Tomography.  This is a hands-on course, in which theory and
practicals are tightly intertwined.  There will be practical session to
teach sample preparation for Single particle –ve stain and cryoEM.   The
topics covered will suit both the new entrants to the field as well as
those who wants to acquire an in-depth understanding  of  the fundamental
principles and practical aspects.   Applications are invited from PhD
students, Post Docs and Researchers (Faculties/PI’s and protein
crystallographers) who wish to acquire knowledge in SPCryoEM and Cellular
Tomography.  Applicants from all over the world are encouraged to apply.
For more information please contact the course organizer at
*cem3dip2...@iisertvm.ac.in
*.



*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation and image processing on computer workstations in the
afternoon.  Evenings will be reserved for poster presentations by the
participants and research talks by the participants/instructors.



*The instructors/speakers for the course will include:*   Wah Chiu
(Stanford University), Jack Johnson (TSRI), Marin van Heel (CNPEM/LNNano),
Edward Morris (ICR), Paula da Fonseca (MRC-LMB), Peter Rosenthal (TFCI),
Carsten Sachse (EMBL Heidelberg), Sara Sandin (NTU), Ardan Patwardhan
(EMBL-EBI), Maya Topf (Birkbeck), Srinivasan N (IISc), Tanmay Bharath (Dunn
School of Pathology), Agnel Praveen (Birkbeck), Tanveer Hussain(IISc),
Sonja Welsh (FEI - part of Thermo Fisher Scientific), Jayati Sengupta
(IICB), Manidipa Banerjee (IIT Delhi), Ramanathan Natesh (IISER
Thiruvananthapuram), Vinothkumar KR(NCBS), Partha Pratim Datta (IISER
Kolkota), Somnath Dutta (IISc).



For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/18-cem3dip*
*.  *



The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster  abstract.  Applicants should include in the section “Current
research Project and Statement of Purpose” an explanation of why attendance
at the course would further the applicant's own research.   Having some
preliminary data or exposure to electron microscopy /cryoEM/ tomography
will be preferred.  PhD and Postdoctoral applicants should request their
supervisor to send a recommendation letter, before the application
deadline, by e-mail directly to the organizer at cem3dip2...@iisertvm.ac.in.
Only selected people from the applicants will be contacted.  Based on
availability of funds, travel and/or registration, accommodation bursaries
for subset of selected applicants can be provided.  If you want to request
for registration and/or accommodation bursaries, mention that explicityly
in the space for ‘Justification for Travel Grant’ and Justify your request.
All registered participants have to present posters on their research
work.  A selection of participants will be invited to give oral
presentation of their ongoing research work.



We shall truly appreciate if this e-mail can be circulated among your
friends, scholars and students encouraging them to 

[ccp4bb] EMBO Practical Course CEM3DIP 2018: of macromolecular assemblies and cellular tomography

[Natesh Ramanathan]

*Second  Announcement:*


*Applicants from all over the world are eligible to apply.  Applicants from
EMBC member states  (http://www.embo.org/about-embo/member-states
) are in
particular encouraged  to apply.*


*EMBO Practical course Cryo Electron Microscopy and 3 Dimensional Image
Processing (CEM3DIP2018): **of Macromolecular assemblies and Cellular
tomography*

*18-29 March, 2018, at IIT Delhi, New Delhi, India.*


The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2018): of macromolecular assemblies
and cellular tomography* will be held at  IIT Delhi
 in New Delhi
, India.  This is an extensive 10
day course that will be held  from 18  March – 29 March 2018 at IIT Delhi
(with a 1 day break, to chill out at the backdrops of
Taj Mahal
, one of the seven wonders of
world).


For Course details  and to apply online go to the URL :


http://meetings.embo.org/event/18-
cem3dip




 Important dates :

*Registration Deadline : 15 November 2017*


   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, Image processing and 3D
reconstruction in Single Particle Cryo Electron Microscopy(SPCryoEM) and
Cellular Tomography.  This is a hands-on course, in which theory and
practicals are tightly intertwined.  There will be practical session to
teach sample preparation for Single particle –ve stain and cryoEM.   The
topics covered will suit both the new entrants to the field as well as
those who wants to acquire an in-depth understanding  of  the fundamental
principles and practical aspects.   Applications are invited from PhD
students, Post Docs and Researchers (Faculties/PI’s and protein
crystallographers) who wish to acquire knowledge in SPCryoEM and Cellular
Tomography.  Applicants from all over the world are encouraged to
apply.  For more information please contact the course organizer at
*cem3dip2...@iisertvm.ac.in
*.


*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation and image processing on computer workstations in the afternoon.
  Evenings will be reserved for poster presentations by the participants
and research talks by the participants/instructors.


*The instructors/speakers for the course will include:*  Wah Chiu (Stanford
University), Jack Johnson (TSRI), Marin van Heel (Leiden University),
Edward Morris (ICR), Paula da Fonseca (MRC-LMB), Peter Rosenthal (TFCI),
Carsten Sachse (EMBL Heidelberg), Sara Sandin (NTU), Ardan Patwardhan
(EMBL-EBI), Maya Topf (Birkbeck), Srinivasan N (IISc), Tanmay Bharath (Dunn
School of Pathology), Agnel Praveen (Birkbeck), Tanveer
Hussain(IISc), Sonja Welsh (FEI - part of Thermo Fisher Scientific), Jayati
Sengupta (IICB), Manidipa Banerjee (IIT Delhi), Ramanathan Natesh (IISER
Thiruvananthapuram), Vinothkumar KR(NCBS), Partha Pratim Datta (IISER
Kolkota), Somnath Dutta (IISc).


For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/18-cem3dip*
*. *

The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster  abstract.  Applicants should include in the section “Current
research Project and Statement of Purpose” an explanation of why attendance
at the course would further the applicant's own research.   Having some
preliminary data or exposure to electron microscopy /cryoEM/ tomography
will be preferred.  PhD and Postdoctoral applicants should request their
supervisor to send a recommendation letter, before the application
deadline, by e-mail directly to the organizer at cem3dip2...@iisertvm.ac.in.
  Only selected people from the applicants will be contacted.  Based on
availability of funds, travel and/or registration, accommodation bursaries
for subset of selected applicants can be provided.  If you want to request
for registration and/or accommodation bursaries, mention that explicityly
in the space for ‘Justification for Travel Grant’ and Justify your
request.   All
registered participants have to present posters on their research work.  A
selection of participants will be invited to give oral presentation of
their ongoing research work.


We shall truly appreciate if this e-mail print out can be displayed at your
Institute notice board and 

[ccp4bb] EMBO Practical Course CEM3DIP 2018: of macromolecular assemblies and cellular tomography

[Natesh Ramanathan]

*First Announcement:*

*EMBO Practical course Cryo Electron Microscopy and 3 Dimensional Image
Processing (CEM3DIP 2018): **of Macromolecular assemblies and Cellular
tomography*

*18-29 March, 2018, at IIT Delhi, New Delhi, India.*

The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2018): of macromolecular assemblies
and cellular tomography* will be held at  IIT Delhi
 in New Delhi
, India.  This is an extensive 10
day course that will be held  from 18  March – 29 March 2018 at IIT Delhi
(with a 1 day break, to chill out at the backdrops of
Taj Mahal
, one of the seven wonders of
world).

For Course details  and to apply online go to the URL :


http://meetings.embo.org/event/18-cem3dip

 Important dates :

*Registration Deadline : 15 November 2017*

   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, Image processing and 3D
reconstruction in Single Particle Cryo Electron Microscopy(SPCryoEM) and
Cellular Tomography.  This is a hands-on course, in which theory and
practicals are tightly intertwined.  There will be practical session to
teach sample preparation for Single particle –ve stain and cryoEM.   The
topics covered will suit both the new entrants to the field as well as
those who wants to acquire an in-depth understanding  of  the fundamental
principles and practical aspects.   Applications are invited from PhD
students, Post Docs and Researchers (Faculties/PI’s and protein
crystallographers) who wish to acquire knowledge in SPCryoEM and Cellular
Tomography.  Applicants from all over the world are encouraged to
apply.  For more information please contact the course coordinator at
*cem3dip2...@iisertvm.ac.in
*.

*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation and image processing on computer workstations in the
afternoon.  Evenings will be reserved for poster presentations by the
participants and research talks by the participants/instructors.

*The instructors/speakers for the course will include:* Tony Crowther
(MRC-LMB), Wah Chiu (Stanford University), Jack Johnson (TSRI), Marin van
Heel (Leiden University), Edward Morris (ICR), Paula da Fonseca (MRC-LMB),
Peter Rosenthal (TFCI), Carsten Sachse (EMBL Heidelberg), Sara Sandin
(NTU), Ardan Patwardhan (EMBL-EBI), Maya Topf (Birkbeck), Srinivasan N
(IISc), Tanmay Bharath (Dunn School of Pathology), Agnel Praveen
(Birkbeck), Tanveer Hussain(IISc), Sonja Welsh (FEI - part of Thermo Fisher
Scientific), Jayati Sengupta (IICB), Manidipa Banerjee (IIT Delhi),
Ramanathan Natesh (IISER Thiruvananthapuram), Vinothkumar KR(NCBS), Partha
Pratim Datta (IISER Kolkota), Somnath Dutta (IISc).

For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/18-cem3dip*
*. *

The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster  abstract.  Applicants should include in the section “Current
research Project and Statement of Purpose” an explanation of why attendance
at the course would further the applicant's own research.   Having some
preliminary data or exposure to electron microscopy /cryoEM/ tomography
will be preferred.  PhD and Postdoctoral applicants should request their
supervisor to send a recommendation letter, before the application
deadline, by e-mail directly to the organizer at cem3dip2...@iisertvm.ac.in
.  Only selected people from the applicants will be contacted.  Based on
availability of funds, travel and/or registration, accommodation bursaries
for subset of selected applicants can be provided.  If you want to request
for registration and/or accommodation bursaries, mention that explicityly
in the space for ‘Justification for Travel Grant’ and Justify your
request.   All
registered participants have to present posters on their research work.  A
selection of participants will be invited to give oral presentation of
their ongoing research work.

We shall truly appreciate if this e-mail print out can be displayed at your
Institute notice board and circulated among your friends, scholars and
students encouraging them to apply for this course.

Sincerely yours,
Ramanathan Natesh, Manidipa Banerjee and Vinothkumar Kutti Ragunath,
Course Coordinators CEM3DIP 2018.
Phone: +91-471-2599403

Please write to cem3dip2...@iisertvm.ac.in for any queries regarding this
course.
-- 
--

Re: [ccp4bb] on the resoution of crystal

[Natesh Ramanathan]

Dear John,

  In protein crystallography, the ranges customarily applied to
resolution are:

 Low resolution  --> worse than 2.7 A
 Medium resolution -->  better than 2.7 A but worse than 1.8 A
 High resolution -->  better than 1.8 Aand worse than 1.2 A
 Atomic resolution --> better than 1.2 A  and worse than 0.95 A
Ultra high resolution --> better than 0.95 A

There is a very nice diagram for you in Fig. 5 of  Wlodawer et al., FEBS J.
2008 Jan; 275(1): 1–21.
:
at this link:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465431/figure/F5/

   You should think in terms of reciprocal space and diffraction.
Higher angle of diffraction w.r.t. the incident beam means High Resolution,
which means lower number.

Best wishes,
Natesh

On 5 February 2017 at 17:39,  <
0ef8f1cfe4cc-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dear All,
>
> For one protein crystal, its resolution was 1.8 A. For another crystal for
> the same protein,  its resolution was 3.8 A. In literature, do we call the
> 1.8 A crystal as the high resolution crystal (because of quality), or do we
> call the 3.8 A crystal as the high resolution crystal (because of 3.8 was
> larger than 1,8)?
>
> Best regards.
>
> John
>



-- 
--
"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
Ramalingaswami Fellow-DBT, Assistant Professor
Indian Institute of Science Education and Research Thiruvananthapuram
(IISER-TVM),
1st floor, Dept. of Computer Science & Engg. Building,
CET Campus, Engineering College P.O.,
Trivandrum,  695016, Kerala, India

nat...@iisertvm.ac.in
http://www.researcherid.com/rid/C-4488-2008
http://faculty.iisertvm.ac.in/~natesh
Ph. 0091- 471-2599403
Fax.0091-471-2597427