Re: [ccp4bb] mmCIF and CIF

[Folmer Fredslund]

Dear Oliviero,

The suggestion made by Tim Grüne is probably best, you didn't specify 
exactly what you have in the mmCIF file.


Anyway, openbabel should be able to read mmCIF files and write a CIF, 
(https://openbabel.org/wiki/MmCIF)


Best regards,
Folmer

On 2017-11-14 14:16, Oliviero Carugo wrote:

Dears,

does anybody know how to transform an mmCIF file of the Protein Data 
Bank into a CIF file (the slightly different format used in small 
molecule crystallography)?


Thanks,

Oliviero

[ccp4bb] Postdoctoral research position

[Demetres D. Leonidas]

Postdoctoral research position: molecular biologist/bioinformatician
A 2-year Post-Doctoral position is available immediately in the
Laboratory of Molecular Biology and Genomics in the Department of
Biochemistry and Biotechnology of the University of Thessaly, located in
the city of Larissa. The selected candidate will work in the framework
of a national Research Infrastructure program on Synthetic Biology.
Research in the Laboratory of Molecular Biology and Genomics focuses on
various aspects of insect olfaction, reproduction and evolution, aiming
at the development of new approaches for control of insects of
agricultural or medical importance. We are seeking a highly motivated
and creative scientist with a track record of successful research. A
good bioinformatics background is strongly desired. The ideal candidate
should be able to analyze raw sequencing data, perform genome assembly
and annotation and have a good understanding of comparative and
functional genomics. At the same time, he/she should be able to design
and perform experiments in support of the bioinformatics analyses.
Candidates should have a PhD and should have training in one or more of
the following disciplines: bioinformatics, molecular biology,
biochemistry, cell biology, and genome-wide technologies. Familiarity
with insect rearing is desirable but not essential. Curriculum Vitae, a
brief letter describing interests and prior experience and names of
three references should be sent to: kmath...@bio.uth.gr.

Research position: MSc Bioinformatician
A 2-year position for an MSc Bioinformatician is available immediately
in the Laboratory of Molecular Biology and Genomics in the Department of
Biochemistry and Biotechnology of the University of Thessaly, located in
the city of Larissa. The selected candidate will work in the framework
of a national Research Infrastructure program on Synthetic Biology.
Research in the Laboratory of Molecular Biology and Genomics focuses on
various aspects of insect olfaction, reproduction and evolution, aiming
at the development of new approaches for control of insects of
agricultural or medical importance. We are seeking a highly motivated
individual with a BSc in Biology or related science and an MSc in
Bioinformatics. The successful candidate will be involved in raw
sequencing data analysis, genome assembly and annotation and comparative
and functional genomics studies. His/her research could also lead to a
PhD. Curriculum Vitae, a brief letter describing interests and prior
experience and names of three references should be sent to:
kmath...@bio.uth.gr.

--
---
Dr. Demetres D. Leonidas
Professor of Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis
41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


---
Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus.
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[ccp4bb] cryoEM course in Prato

[Alex de Marco]

Dear All,

I would like to remind you about the “*Prato cryoEM course*” from* 9th to
13th of April 2018*.

Registrations will close on December 1st, and currently there are still
sits available.



The course aims at PhD students and researchers with little experience in
cryoEM or that are planning to use cryoEM to bring their projects to the
next level.

It will comprise a series of lectures covering all steps of Single-particle
cryoEM and Subtomogram Averaging (from sample preparation to data
collection and image processing). Practical sessions will give the students
the opportunity to perform image processing for both single particle and
subtomogram averaging.



The software used for the practical sessions will be:

-  SIMPLE and CTFFIND for single particle analyses

-  Dynamo for the subtomogram averaging.





More information about the course can be found on
http://simplecryoem.com/Prato/workshop2018.html

or should you have any more questions feel free to contact us.



Looking forward to see you in Tuscany





Alex, Hans and Dominika









--



Alex de Marco, PhD

Associate Professor



Monash University

*Dept. of Biochemistry and Molecular Biology*

*ARC Centre of Excellence in Advanced Molecular Imaging*

23 Innovation Walk, 3800 Clayton (Australia)

P: +61 3 99053791 <%2B61%2003%2099053791>

M: *+61 4 11041429*

Email: alex.dema...@monash.edu

Web: www.demarco-lab.com

[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 

Re: [ccp4bb] mmCIF and CIF

[Tim Gruene]

Dear Oliviero,

depending where the mmCIF originates from, and provided you have data with it, 
it might be easiest to go
mmCIF -> PDB -> SHELXL (via PDB2INS) -> CIF (via the SHELXL ACTA command).

Best,
Tim

On Tuesday, November 14, 2017 2:16:06 PM CET Oliviero Carugo wrote:
> Dears,
> 
> does anybody know how to transform an mmCIF file of the Protein Data
> Bank into a CIF file (the slightly different format used in small
> molecule crystallography)?
> 
> Thanks,
> 
> Oliviero

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/104
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


signature.asc
Description: This is a digitally signed message part.

Re: [ccp4bb] Regarding Patents

[Keller, Jacob]

>>Isn’t that exactly the idea of a patent? Instead of keeping the invention
a trade secret (occasionally a viable alternative) you publish the invention,
and the inventor (and in general, the supporting institutions) can get
rewarded if someone plans to use the idea commercially.

I agree with this especially because someone else is, after all, going to 
commercialize it and charge money for it.







Best, BR

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Abhishek 
Anan
Sent: Saturday, November 4, 2017 05:31
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Regarding Patents

I second Gert's thoughts
Best,
Abhishek

On Sat, Nov 4, 2017 at 10:21 AM, Gert Vriend 
> wrote:
A related question. If you have a crystal structure and found a novel ligand 
binding site that can be used to regulate protein activity, could you patent 
such "binding site"? If not, how to make the best use of such findings?

I would say that the best one can do with important novel 
data/information/knowledge/insights is to publish it so the world can benefit 
from it.

Gert

[ccp4bb] mmCIF and CIF

[Oliviero Carugo]

Dears,

does anybody know how to transform an mmCIF file of the Protein Data 
Bank into a CIF file (the slightly different format used in small 
molecule crystallography)?


Thanks,

Oliviero

[ccp4bb] SAD Phasing in a home lab - RE: [ccp4bb]

[Conn Mallett]

Dear Yuvaraj,

Jim Pflugrath worked with a few brilliant high school student interns one of 
the summers before he retired and made this video to demonstrate how easy it is 
to do a ‘halide swish’ to incorporate iodide into crystals of macromolecules 
for home laboratory de-novo SAD phasing using Cu X-ray radiation:

https://www.youtube.com/watch?v=45Qc3jOPaKY

Disclaimer: This is not an advert for any product or service by any company, no 
animals or high school students were harmed in the making of this video.  Vegan 
friendly, Gluten-free, non-GMO.  All rights reserved ☺

Good Luck,

-Conn

Conn Mallett, PhD
Senior Account Manager
Rigaku Oxford Diffraction
Carlsbad, CA 92008

Tel: 7136146891
conn.mall...@rigaku.com
Skype: conn.mallett


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of YUVARAJ I
Sent: Tuesday, November 14, 2017 4:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb]

Dear all
What are the chemicals which give an anomalous signal at home 
source (Cu Kα radiation) apart from Lathanides and Zinc acetate. What are the 
things I should taken care of to get sufficient anomalous signal to solve the 
structure.

I have crystal data without anomalous signal at 1.76A  resolution. What are 
theoretical ways possible to solve the structure when there is no homologous 
structures available in the PDB.

Note: There is one cysteine and  one methionine  in 176 AA length protein.

Thanks
Yuvaraj

--

[ccp4bb] EMBO Practical Course on Characterization of macromolecular complexes by integrative structural biology

[Marco Marcia]

Dear ccp4 community,
I would like to draw your attention to the following course, which is 
now open for registration:


EMBO Practical Course on *Characterization of macromolecular complexes 
by integrative structural biology*

May 12-19, 2018
EPN campus
Grenoble, France
http://meetings.embo.org/event/18-characterization

This course has been held biennially since 2002, and covers various 
topics that include methods for expressing and purifying complexes, 
characterizing them biophysically, and probing their structures. It is 
addressed to PhD students and postdocs interested in the structural 
biology of large multisubunit complexes.


*Deadline for registration: 28 February 2018*

We are looking forward to receiving your applications!
Marco
on behalf of the organizing committee: Marco Marcia, Montserrat Soler 
Lopez, Carlo Petosa, Estelle Mossou, Daniele De Sanctis



--
_

Dr. Marco MARCIA
Group Leader
EMBL Grenoble
71 Avenue des Martyrs, room 254
38042 Grenoble Cedex 09
France
phone (lab): 0033-(0)47620-7634/7040
phone (office): 0033-(0)47620-7759
fax: 0033-(0)47620-7199
email: mmar...@embl.fr
web: https://embl.fr/research/unit/marcia/

Re: [ccp4bb] AW: [ccp4bb] High R/Rfree

[Eleanor Dodson]

Remember  DNA can generate some very strong reflections along the stacking
axis.

But 2outliers" can mean anything - as Herman says look at the images.

Aimless shows you a plot of where they are - and gives a list.. - they may
be associated with ice rings? or just diffraction problems.



On 14 November 2017 at 08:24,  wrote:

> Dear Radhika,
>
>
>
> What reason does Xtriage give for declaring the reflections to be
> outliers? Too weak, too strong, other reasons? As was mentioned before,
> what is the resolution of your data? In cases like this, it is always good
> to have a look at the diffraction images to see if there is some problem
> there like streaks, ice rings etc.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Radhika Singh
> *Gesendet:* Dienstag, 14. November 2017 00:45
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] High R/Rfree
>
>
>
> Hello All,
>
>
>
> I am currently working on the structure of a DNA protein complex.  The
> data has been processed in space group P1 (53.042   59.527   78.526 105.24
> 98.03 106.99 P 1, Rpim 11.7%).  At this stage I have almost 85% model is
> complete but my R/Rfree is stuck as 26%/34%.
>
>
>
> I have some concerns and questions:
>
> * Xtriage says there are a large number of outliers; however no
> pseudotranslational symmetry is detected by the program.  What are the
> other reasons for outliers?
>
>
>
> * I am trying phenix.refine for refinement with the default settings. Is
> there any special setting that can help me?
>
>
>
> I would like to have some suggestions about my problem.
>
>
>
> Thanks in advance
>
>
>
> Radhika
>
>
>

[ccp4bb]

[Eleanor Dodson]

Most metals give a reasonable anomalous signal at CiKa.
at 1.75A S f" is ~ 0.8   Se ~ 1.4

That is not very strong -  you would need pretty good data to see the
signal, but aimless analyses the CCanom for you.


There are lots of sites to tell you what f" is likely to be for all atom
types- CHOOCH in CCP4 does that.
Eleanor



On 14 November 2017 at 10:01, YUVARAJ I  wrote:

> Dear all,
> How to change the origin of  the reflection from the default value in
> imosflm or DIALS during Indexing. Is there any way to do it in CCP4i or
> CCP4i2 GUI.
>
> Thanks
> Yuvaraj
> --
>
>
>
>
>

Re: [ccp4bb] change the origin of the origin of the reflection

[Harry Powell]

Hi

I'll assume you mean that you want to change the direct beam position - in 
iMosflm it's easy, and the best way for you to proceed is to follow the 
tutorial on the website - see files on 

http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/documentation.html

especially 


http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/documentation/tutorial.html

If you want to do it in DIALS, I would recommend looking at the "Correcting 
poor initial geometry" tutorial - 


https://dials.github.io/documentation/tutorials/correcting_poor_initial_geometry_tutorial.html

I don't know of a sensible way to do it directly in ccp4i or ccp4i2 - perhaps 
someone here can enlighten both of us.

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 




On 14 Nov 2017, at 09:30, YUVARAJ I wrote:

> Dear all,
> How to change the origin of  the reflection from the default value in imosflm 
> or DIALS during Indexing. Is there any way to do it in CCP4i or CCP4i2 GUI. 
> 
> Thanks 
> 
> Yuvaraj
> 
> 

[ccp4bb]

[YUVARAJ I]

Dear all,
How to change the origin of  the reflection from the default value in
imosflm or DIALS during Indexing. Is there any way to do it in CCP4i or
CCP4i2 GUI.

Thanks
Yuvaraj
--

[ccp4bb]

[YUVARAJ I]

Dear all
What are the chemicals which give an anomalous signal at home
source (Cu *K*α radiation) apart from Lathanides and Zinc acetate. What are
the things I should taken care of to get sufficient anomalous signal to
solve the structure.

I have crystal data without anomalous signal at 1.76A  resolution. What are
theoretical ways possible to solve the structure when there is no
homologous structures available in the PDB.

Note: There is one cysteine and  one methionine  in 176 AA length protein.

Thanks
Yuvaraj

--

[ccp4bb] change the origin of the origin of the reflection

[YUVARAJ I]

Dear all,
How to change the origin of  the reflection from the default value in
imosflm or DIALS during Indexing. Is there any way to do it in CCP4i or
CCP4i2 GUI.

Thanks

Yuvaraj

[ccp4bb] AW: [ccp4bb] High R/Rfree

[Herman . Schreuder]

Dear Radhika,

What reason does Xtriage give for declaring the reflections to be outliers? Too 
weak, too strong, other reasons? As was mentioned before, what is the 
resolution of your data? In cases like this, it is always good to have a look 
at the diffraction images to see if there is some problem there like streaks, 
ice rings etc.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Radhika 
Singh
Gesendet: Dienstag, 14. November 2017 00:45
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] High R/Rfree

Hello All,

I am currently working on the structure of a DNA protein complex.  The data has 
been processed in space group P1 (53.042   59.527   78.526 105.24  98.03 106.99 
P 1, Rpim 11.7%).  At this stage I have almost 85% model is complete but my 
R/Rfree is stuck as 26%/34%.

I have some concerns and questions:
* Xtriage says there are a large number of outliers; however no 
pseudotranslational symmetry is detected by the program.  What are the other 
reasons for outliers?

* I am trying phenix.refine for refinement with the default settings. Is there 
any special setting that can help me?

I would like to have some suggestions about my problem.

Thanks in advance

Radhika