[ccp4bb] Computational Crystallography Newsletter (CCN) submissions

[Nigel Moriarty]

Folks

Calling for articles and short communications of interest to
structural biologists. The initial deadline for submission for the
January 2018 issue is 20 December 2017.

The Computational Crystallography Newsletter (CCN) is an electronic
newsletter for structural biologists, and is published online every 6
months. Feature articles, meeting announcements and reports can be
submitted to me at any time for consideration. Submission of text by
email or word-processing files using the CCN templates is requested.
Past newsletters and a Microsoft Word template are available at
www.phenix-online.org/newsletter.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

Re: [ccp4bb] sending dewar to synchrotrons

[Edward Snell]

This typically happens in the US when any label is left on the Dewar that 
implies it contains liquid nitrogen, i.e. the green diamond label or any 
indication of previous hazardous shipment. The synchrotron sometimes ships them 
back wet (and adds these labels) There are special shipment rules and training 
required in this case.

The shipper should be shipped dry and needs to be labeled “Dry Shipper, 
Non-Regulated”. SSRL used to have information on this on its SMB user portal 
but they have updated this and I could not find it recently.

Note that in the US shipping a dry shipper that is still full with liquid 
nitrogen when improperly labeled carries a stiff penalty.

Cheers,

Eddie

Edward Snell Ph.D.
President and CEO Hauptman-Woodward Medical Research Institute
BioInnovations Chaired Professorship, University at Buffalo, SUNY
700 Ellicott Street, Buffalo, NY 14203-1102
hwi.buffalo.edu
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
[cid:image002.png@01D3621F.2C27CB30]
Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas, 
Leonard M.
Sent: Monday, November 20, 2017 4:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] sending dewar to synchrotrons

To expand, we have been shipping to SSRL, though I don’t think it has anything 
to do with them.  It is being returned by the carrier, FedEx, on the way out.  
TheFedEx people down here have been very difficult to work with by providing no 
information.

Mostly I am just venting and wanted to see if this is isolated, more widespread 
then anybody thinks or random.  The occasional problem I can see but this is 
twice in a row so it just got me wondering.

Len


On Nov 20, 2017, at 2:45 PM, Loll,Patrick 
> wrote:

Ouch. Can you expand on this? E.g, what carrier? What synchrotron? And who 
returns them—the carrier?

We just sent a dewar to APS via FedEx last week, and we had no problems (other 
than the fact that FedEx didn’t come to pick it up until 7:30 PM…)

Cheers,
Pat Loll


On 20 Nov 2017, at 3:14 PM, Thomas, Leonard M. 
> wrote:

Hello All,

General inquiry here, I have been sending dewars out to synchrotrons for many 
years now and all of a sudden we have run into them being returned due to 
incomplete paper work or hazardous problems.  I was just wondering if anyone 
else had had this happen in the past and what you may have done to overcome it 
besides sending the dewar out a week yearly in hopes you have time to turn it 
around.  It has been rather frustrating.

Len Thomas

Leonard Thomas, Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://structuralbiology.ou.edu/mcl

---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu

Leonard Thomas
lmtho...@ou.edu

Re: [ccp4bb] sending dewar to synchrotrons

[Matthew Bratkowski]

SSLR always returns your dewars containing liquid nitrogen and with
hazardous liquid nitrogen stickers on the dewars.  If you are shipping the
dewar dry, you should not need the stickers.  If you do not take the
stickers off before re-shipping them, the dewar is likely to be returned.
We had this issue once.

Matt

On Mon, Nov 20, 2017 at 2:14 PM, Thomas, Leonard M.  wrote:

> Hello All,
>
> General inquiry here, I have been sending dewars out to synchrotrons for
> many years now and all of a sudden we have run into them being returned due
> to incomplete paper work or hazardous problems.  I was just wondering if
> anyone else had had this happen in the past and what you may have done to
> overcome it besides sending the dewar out a week yearly in hopes you have
> time to turn it around.  It has been rather frustrating.
>
> Len Thomas
>
> Leonard Thomas, Ph.D.
> Macromolecular Crystallography Laboratory
> Oklahoma COBRE in Structural Biology
> Price Family Foundation Institute of Structural Biology
> University of Oklahoma
> Department of Chemistry and Biochemistry
> Stephenson Life Sciences Research Center
> 101 Stephenson Parkway
> Norman, OK 73019-5251
> Office
> :
> (405)325-1126 <(405)%20325-1126>
> lmtho...@ou.edu
> http://structuralbiology.ou.edu/mcl
>
>

Re: [ccp4bb] sending dewar to synchrotrons

[Chun Luo]

Not sure if this helps.

 

We ship proteins with dry ice. The dry ice label has lines for Shipper and 
Recipient (Consignee) addresses which are often not filled out. We had one 
package returned for not filling them out.

 

Also check your bill. FedEx charge the return.

 

--Chun

 

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas, 
Leonard M.
Sent: Monday, November 20, 2017 1:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] sending dewar to synchrotrons

 

To expand, we have been shipping to SSRL, though I don’t think it has anything 
to do with them.  It is being returned by the carrier, FedEx, on the way out.  
TheFedEx people down here have been very difficult to work with by providing no 
information. 

 

Mostly I am just venting and wanted to see if this is isolated, more widespread 
then anybody thinks or random.  The occasional problem I can see but this is 
twice in a row so it just got me wondering.

 

Len

 

 

On Nov 20, 2017, at 2:45 PM, Loll,Patrick  > wrote:

 

Ouch. Can you expand on this? E.g, what carrier? What synchrotron? And who 
returns them—the carrier?

We just sent a dewar to APS via FedEx last week, and we had no problems (other 
than the fact that FedEx didn’t come to pick it up until 7:30 PM…)

Cheers,
Pat Loll




On 20 Nov 2017, at 3:14 PM, Thomas, Leonard M.  > wrote:

Hello All,

General inquiry here, I have been sending dewars out to synchrotrons for many 
years now and all of a sudden we have run into them being returned due to 
incomplete paper work or hazardous problems.  I was just wondering if anyone 
else had had this happen in the past and what you may have done to overcome it 
besides sending the dewar out a week yearly in hopes you have time to turn it 
around.  It has been rather frustrating.  

Len Thomas

Leonard Thomas, Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu  
http://structuralbiology.ou.edu/mcl


---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com  
pj...@drexel.edu  

 

Leonard Thomas

lmtho...@ou.edu  

 

 

 

Re: [ccp4bb] sending dewar to synchrotrons

[Thomas, Leonard M.]

To expand, we have been shipping to SSRL, though I don’t think it has anything 
to do with them.  It is being returned by the carrier, FedEx, on the way out.  
TheFedEx people down here have been very difficult to work with by providing no 
information.

Mostly I am just venting and wanted to see if this is isolated, more widespread 
then anybody thinks or random.  The occasional problem I can see but this is 
twice in a row so it just got me wondering.

Len


On Nov 20, 2017, at 2:45 PM, Loll,Patrick 
> wrote:

Ouch. Can you expand on this? E.g, what carrier? What synchrotron? And who 
returns them—the carrier?

We just sent a dewar to APS via FedEx last week, and we had no problems (other 
than the fact that FedEx didn’t come to pick it up until 7:30 PM…)

Cheers,
Pat Loll

On 20 Nov 2017, at 3:14 PM, Thomas, Leonard M. 
> wrote:

Hello All,

General inquiry here, I have been sending dewars out to synchrotrons for many 
years now and all of a sudden we have run into them being returned due to 
incomplete paper work or hazardous problems.  I was just wondering if anyone 
else had had this happen in the past and what you may have done to overcome it 
besides sending the dewar out a week yearly in hopes you have time to turn it 
around.  It has been rather frustrating.

Len Thomas

Leonard Thomas, Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://structuralbiology.ou.edu/mcl


---
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu


Leonard Thomas
lmtho...@ou.edu

Re: [ccp4bb] [Off-topic] Comparison of the same structure built by many people

[Mark J. van Raaij]

This one?http://scripts.iucr.org/cgi-bin/paper?SE0260

Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij
 Original message From: Shintaro Aibara 
 Date: 20/11/2017  21:25  (GMT+01:00) To: 
CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [Off-topic] Comparison of the same 
structure built by many people 
Dear All,
Apologies for the slightly off-topic, but I was wondering if anybody knew of a 
paper/textbook where a protein model was built by multiple people (ranging from 
novice to experienced builders) and compared. I believe the conclusion was that 
while the overall trace was broadly correct, experienced builders maintained 
better geometry compared to beginners.
I distinctly remember reading it a couple of years ago but cannot seem to find 
the figure. If anybody knows of this figure/paper/textbook it would be much 
appreciated if you could point me in the direction.
Yours faithfully,
Shintaro

[ccp4bb] [Off-topic] Comparison of the same structure built by many people

[Shintaro Aibara]

Dear All,

Apologies for the slightly off-topic, but I was wondering if anybody knew
of a paper/textbook where a protein model was built by multiple people
(ranging from novice to experienced builders) and compared. I believe the
conclusion was that while the overall trace was broadly correct,
experienced builders maintained better geometry compared to beginners.

I distinctly remember reading it a couple of years ago but cannot seem to
find the figure. If anybody knows of this figure/paper/textbook it would be
much appreciated if you could point me in the direction.

Yours faithfully,
Shintaro

[ccp4bb] sending dewar to synchrotrons

[Thomas, Leonard M.]

Hello All,

General inquiry here, I have been sending dewars out to synchrotrons for many 
years now and all of a sudden we have run into them being returned due to 
incomplete paper work or hazardous problems.  I was just wondering if anyone 
else had had this happen in the past and what you may have done to overcome it 
besides sending the dewar out a week yearly in hopes you have time to turn it 
around.  It has been rather frustrating.

Len Thomas

Leonard Thomas, Ph.D.
Macromolecular Crystallography Laboratory
Oklahoma COBRE in Structural Biology
Price Family Foundation Institute of Structural Biology
University of Oklahoma
Department of Chemistry and Biochemistry
Stephenson Life Sciences Research Center
101 Stephenson Parkway
Norman, OK 73019-5251
Office: (405)325-1126
lmtho...@ou.edu
http://structuralbiology.ou.edu/mcl

[ccp4bb] BCA BSG Winter Meeting 2017

[Mark Roe]

From: BCA >
Subject: BCA BSG Winter Meeting 2017
Date: 20 November 2017 at 10:11:16 GMT
To: >
Reply-To: BCA >


[https://gallery.mailchimp.com/08691b2f140331942d32952fd/images/10fd2806-7391-4b27-abb4-7eaca2f98669.jpg]


Biological Structures Winter Meeting 2017
The joy and pain of structural biology research
Monday 18 December, 2017
Cavendish Laboratory, Cambridge



REGISTER 
HERE



The Biological Structures Group Winter meeting “The Joy and Pain of Structural 
Biology Research” will be held on Monday December 18th, 2017 at the Cavendish 
Laboratory at the University of Cambridge.

The meeting is aimed at giving the audience an insight into the "joy and pain" 
of protein crystallographic/structural biology research. Speakers have been 
asked to choose a particular piece of published work from any stage of their 
career and speak about the "real" story behind it - the people, the chance 
meeting, the experimental process, the 100's of failed trials that eventually 
led to "perfect" experiment. The aim here is to give the audience a deeper 
insight into the processes that lead to the wonderful science that structural 
biology reveals.

The meeting will be opened by Professor Malcolm Longair, a former head of the 
department who has recently published a book describing the scientific history 
of the Cavendish Laboratory. He will present a seminar about the contributions 
of Perutz, Kendrew, Crick, Watson and Bragg at the Cavendish that help shape 
structural biology research.

Additional speakers include: the 2017 Nobel Prize winner Richard Henderson, 
Judith Howard Sir Tom Blundell, Randy Read, Pamela Williams, Ben Bax and Janet 
Thornton.

Key publications identified by the speakers will be assembled as a pdf-file 
that can be downloaded from the BSG website. A publication associated with the 
contents this meeting is planned to appear in the journal Nature Structural & 
Molecular Biology in 2018.

There will be opportunities to visit the small museum in the Cavendish 
Laboratory that houses many of the historically important pieces of apparatus 
which contributed to major discoveries by members of the Laboratory. Dr. David 
Ward will also be available to show the scanning helium microscope that can be 
used for non-destructive imaging of biological samples and describe the new 
features being developed to extend the resolution below 100 nm.

We are looking forward to seeing you this December!




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[ccp4bb] Core EMDB developer position

[Ardan Patwardhan]

Dear all

Just a reminder that the deadline for this post is fast approaching 
(24/11/2017) -  https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01079 


We are looking for a person with a  a structural biology/bioinformatics 
background and some programming experience looking to move away from research 
and into a professional software development career path. This is an exciting 
opportunity to work with EMDB software infrastructure including data 
deposition, searching visualisation, validation and data mining.

Best wishes

Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

Re: [ccp4bb] Scripting for COOT

[B.Lohkamp]

Just for completeness the pythonic command line way:

coot --pdb input.pdb --auto input.mtz --python -c 
'set_go_to_atom_molecule(0); set_go_to_atom_chain_residue_atom_name("B", 
42, " CA ")'


Bernhard

On 17/11/2017 09:00, Martín Martínez Ripoll wrote:

We have used it in this way...

coot --pdb  input.pdb   ---auto  input.mtz   --script  script.com

and then, in file "script.com", you write the corresponding instructions...

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")

Martin
_
Dr. Martin Martinez-Ripoll
Research Professor Emeritus
xmar...@iqfr.csic.es
Department of Crystallography & Structural Biology
www.xtal.iqfr.csic.es
www.xtal.iqfr.csic.es/Cristalografia/
Telf.: +34 917459550
Consejo Superior de Investigaciones Científicas
Spanish National Research Council


-Mensaje original-
De: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] En nombre de Paul
Emsley
Enviado el: jueves, 16 de noviembre de 2017 17:32
Para: CCP4BB@JISCMAIL.AC.UK
Asunto: Re: [ccp4bb] Scripting for COOT

On 16/11/2017 13:28, Edward A. Berry wrote:

(set-go-to-atom-molecule 0)
(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")


Would those be also on the command line, or where?


You can use them on the command line like this:

coot --pdb input.pdb -c '(set-go-to-atom-molecule
0)(set-go-to-atom-chain-residue-atom-name "B" 42 " CA ")'