Re: [ccp4bb] AW: [EXTERNAL] Re: identifying bound ions

2018-08-02 Thread Kay Diederichs
Dear Herman,

this is part of the X-UTIL package that can be ftp-ed from
 ftp://xray.bmc.uu.se/pub/gerard/xutil/
The webpage http://xray.bmc.uu.se/usf/installation.html says that you will need 
a license from Gerard Kleywegt.

best,

Kay



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[ccp4bb] Fw: AsCA 2018 Programme Announcement

2018-08-02 Thread Christopher Squire
?[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/d231daa0bdac4db99817bc87d65a4b98]


Dear Colleagues,

The full agenda for the AsCA 2018/CRYSTAL 32 
Conference is now available online. We invite 
you to explore our programme of oral presentations, poster presentations, and 
workshops, displaying outstanding science from Asia, Australia and New Zealand, 
and from around the world.

If you haven't already, register today at 
the early-bird rate to connect with the scientific community, and our 
speakers, and start planning your schedule. It's 
peak season in December so we recommend you book your 
accommodation early.

Likewise, if you haven't submitted your abstract yet, we kindly request your 
support by submitting contributions to the AsCA 2018/CRYSTAL 32 conference at 
your earliest convenience before the deadlines (1 September 2018 for Oral, 1 
November 2018 for Poster). The online abstract submission link is 
http://asca2018.org/call-for-abstracts/.

The conference will run from 2-5 December 2018.

We look forward to seeing you there. In the meantime, if you have any questions 
please visit the conference website or contact us via 
email.

Kind regards,
Dr. Christopher Squire (University of Auckland), Professor Ted Baker 
(University of Auckland), Professor Kurt Krause (University of Otago) and the 
AsCA 2018/CRYSTAL 32 Committee.



[https://az659834.vo.msecnd.net/eventsairseasiaprod/production-uoaevents-public/74ff1f66f2454a1badc85ad293b9e939]








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[ccp4bb] New RFP to support International Space Station (ISS) Crystallization Experiments – First Step Proposals Due Aug 24th

2018-08-02 Thread Marc Giulianotti
ISS National Lab Microgravity Molecular Crystallization Growth RFP landing 
page: https://www.iss-casis.org/mmcg

The purpose of this Request for Proposals (RFP) is to solicit applications 
directed toward utilization of the ISS National Laboratory by commercial and 
academic investigators in the field of molecular crystal growth. Microgravity 
has been used for more than 30 years to improve outcomes of crystal analyses 
through production of higher quality and larger crystals. To examine the 
readiness and requirements of this marketplace for a more commercial approach 
to crystallization on the ISS National Laboratory, CASIS held a subject matter 
expert workshop in October 
2015 
with experts across the field of crystallography. The mission of this workshop 
was to outline the basic science requirements for a long-term crystallization 
program onboard the ISS National Laboratory, including accessibility and 
timing, flight and ground resources, education, and funding. CASIS is 
harnessing the information gained from the workshop and the ongoing support of 
this group to implement an ISS National Laboratory program for repetitive, 
low-cost crystallization in microgravity. The program, now known as the CASIS 
Microgravity Molecular Crystal Growth (MMCG) Program, seeks to provide a 
platform for discovery to users across many disciplines—commercial, other 
government agencies, academia, and private research. (More details about the 
MMCG Program can be found here: https://www.iss-casis.org/workshops/2018-mmcg/.)

In 2016, CASIS issued a RFP soliciting 
proposals
 for support service for the MMCG program. As a result of this RFP, service 
contracts were awarded to four different entities; the University of Alabama at 
Birmingham, Teledyne Brown Engineering, the Bionetics Corporation, and 
Techshot, Inc. More details about the entities and the services they can 
provide under this solicitation can be found in the MMCG Program 
Overview 
and at the 2018 MMCG workshop 
website.

At this time, CASIS seeks proposals that can utilize the services provided 
through our MMCG Program Support Services Providers.
ISS National Lab Microgravity Molecular Crystallization Growth RFP landing 
page: https://www.iss-casis.org/mmcg


Marc Giulianotti, PhD
Sr. Assoc. Program Scientist
CENTER FOR THE ADVANCEMENT
OF SCIENCE IN SPACE (CASIS)
OFFICE: 321.419.9222
www.iss-casis.org

[cid:image001.png@01D38AEA.74CC4200]

Info on:
NIH Chips in Space: http://casistissuechip.blogspot.com/
NSF Tissue Engineering: 
https://www.iss-casis.org/research-on-the-iss/solicitations/tissue-engineering-2017/
MMCG RFP: https://www.iss-casis.org/mmcg




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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Diana Tomchick
I’ll second the use of ACORN. I was able to solve an RNA duplex structure with 
1.4 Å data using the program, and it only took about 20 minutes of CPU time on 
an old (~5 years) Mac Pro.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Aug 2, 2018, at 9:00 AM, Mark J. van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:


When I was at Santiago de Composrela Univ., we have had success with the CCP4 
program ACORN even at around 1.2 Å resolution. Also peptides, no heavy atoms.
Didn't do this myself though I have to admit, but could put you in contact with 
the people who did.

Mark J van Raaij
CNB-CSIC
wwwuser.csic.es/~mjvanraaij


Mark J van Raaij
CNB-CSIC
wwwuser.csic.es/~mjvanraaij

 Original message 
From: Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>>
Date: 02/08/2018 14:53 (GMT+01:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Structure solution - hexapeptide

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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UT Southwestern


Medical Center



The future of medicine, today.




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[ccp4bb] VB: [ccp4bb] Senior Postdoctoral Position on solid-state NMR on membrane proteins (umea, Sweden)

2018-08-02 Thread Gerhard Gröbner
Postdoctoral position in Chemistry (NMR-based structural biology)

This postdoctoral position is part of a project where we investigate the 
structure of membrane-coupled
proteins of the Bcl-2 family by using mainly solid-state NMR methods 
(complementary also neutron
scattering approaches). The Bcl-2 family regulates how nature removes damaged, 
infected and redundant
cells via a strictly controlled process, named programmed cell death 
(apoptosis).

The employment that is placed on the Department of Chemistry is full-time for a 
period of two years,
starting at a date decided in agreement between the two parties.

Project description

This postdoctoral position is part of a research project where we will 
investigate the regulation of
programmed cell death at the molecular level with focus on the structure of the 
proteins and biological
membranes involved in this important process. Important key players in the 
mitochondrial (intrinsic) cell
death pathway are membrane-active proteins of the Bcl-2 family. Family members 
with opposite
functions meet at the outer membrane of mitochondria, where they determine the 
fate of a cell, namely to
live or to die. The main objective of this project is to understand the 
function – and underlying structural
properties – of these proteins and their interaction with the mitochondrial 
membrane environment. For
this purpose we will use structural biological methods focusing on solid-state 
NMR spectroscopy of
lipid-protein complexes. By applying advanced solid-state NMR approaches, we 
will be able to provide
structural insight into the molecular mechanism by which the survival membrane 
protein Bcl-2 and its
antagonist, the cell-killing Bax protein, interact with each other at the 
mitochondrial membrane and
thereby determine the fate of the cell. In addition, we will also use neutron 
reflectometry on these lipid
protein complexes. The Postdoc will primarily study the membrane bound Bcl-2 
proteins. The
Department of Chemistry offers access to an excellent research infrastructure 
within the KBC
environment (www.kbc.umu.se) with access to solid phase/liquid 850 MHz NMR and 
neutron sources in
Europe (mainly ESS/ISIS). The work will be carried out in a multidisciplinary 
environment.

Qualifications

The required qualification is a doctoral degree or a foreign degree that is 
deemed equivalent to a
doctorate in chemistry, biochemistry, biophysics or equivalent field. Priority 
should be given to
candidates who have completed their doctoral degree no more than three years 
before the closing date of
the application, unless special circumstances exist. Previous extensive 
experience of protein structure
determination by solid-fast NMR is required and previous experience with 
membrane proteins is highly
meriting. You shall have a keen interest in the area of NMR-based structural 
biology and be prepared to
take on scientific and technological challenges. Training and/or experience in 
biochemistry, structural
biology and/or biophysical chemistry, as well as neutron scattering on 
biological samples are a strong
merit. You must be creative with good teamwork skills, be initiative-driven and 
have a high degree of
independence. Good knowledge of English, both written and spoken, and a very 
good ability to write
scientific publications is required.

Application

A complete application should contain the following documents:

• A cover letter including a description of your qualifications, research 
interests and motivation for
applying, and your contact information (maximum 2 pages)
• A curriculum vitae, including a publication list
• Copies of your PhD thesis and relevant publications
• Copies of degree certificates or equivalent, including documentation of 
completed academic courses
and obtained grades
• Name and contact information of at least two reference persons

The application can be written in Swedish or English. Applications must be 
submitted via our recruiting
system (https://umu.mynetworkglobal.com/en/what:job/jobID:211361/). Log on and 
apply via the button at the bottom of the page. Reference number: AN 
2.2.1-989-18. The last day to apply is 2018-08-15.

For more information please contact Professor Gerhard Gröbner, phone: 
+4690-7866346, email: gerhard.
grob...@umu.se




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Re: [ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread Charles Ballard - UKRI STFC
[cid:a3a4faea-08e2-46af-88de-3bde456d9124@fed.cclrc.ac.uk]


Sorry for spamming you all on this, but these images keep on getting stripped 
for Armin and myself.

On 2 Aug 2018, at 16:51, Charles Ballard - UKRI STFC wrote:

> Begin forwarded message (on behalf of Armin Wagner)
> From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
> Date: 2 August 2018 at 09:17:48 BST
> To: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
> Dear Eleanor,
>
> We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
> allows collecting data above and below the absorption edges of Ca, K, Cl, S 
> and even P. Crystal, solvent and loop absorption are of course a problem for 
> the longest wavelengths, but so far we have done quite a fair amount of 
> studies around these absorption edges with strong signal above the edge and 
> obviously no signal below. Resolution in our setup is limited to around 3.2 A 
> at 5 A wavelength, but for anomalous difference fourier maps this is 
> sufficient. I have attached an example for a disulphide bridge which should 
> illustrate it better.
>
> Best regards,
>
>Armin
>
>
>
> [cid:image001.png@01D42A41.AE0B8B60]
>
> From: Eleanor Dodson 
> mailto:eleanor.dod...@york.ac.uk>>
> Date: Wednesday, 1 August 2018 at 19:09
> To: Armin Wagner 
> mailto:armin.wag...@diamond.ac.uk>>
> Cc: "ccp4bb@jiscmail.ac.uk" 
> mailto:ccp4bb@jiscmail.ac.uk>>
> Subject: Re: [ccp4bb] Sulphate or phosphate?
>
> I am not sure if you gave your wave length but it is always worth doing an 
> anomalous map, and looking at relativr peak heights for your known S 
> positions and the putative sulphate or phosphate.
> There are small differences in the expected f" at most wavelengths.
>
> Chemical arguments are doubtless better of Course!
> Eleanor
>
> On 1 August 2018 at 16:54, 
> armin.wag...@diamond.ac.uk 
> mailto:armin.wag...@diamond.ac.uk>> wrote:
> Dear David,
>
> The long-wavelength beamline I23 at Diamond 
> (http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
> phosphorous edge. While data quality will be obviously compromised by 
> absorption effects (we are working on this), for a reasonably well 
> diffracting crystal like yours we should be able to get anomalous difference 
> fourier maps from data collected above and below the sulphur edge (lambda ~5 
> A) to answer your question.
>
> We’ve published some test crystal work around the sulphur edge a while ago, 
> you might want to have a look here:
> https://doi.org/10.1016/j.nimb.2016.12.005
>
> The beamline is currently in an advanced commissioning phase accepting a 
> limited number of projects. So, please get into touch if you are interested. 
> We are currently sorting out a few more hardware and software aspects before 
> we can run the beamline as a standard user facility, but we have made a lot 
> of progress over the past months. There will be more details here on the 
> bulletin board ahead of the next call for proposals in autumn.
>
> Best regards,
>
>Armin
>
>
> Postdoc position for long-wavelength crystallography:
> https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html
>
>
>
>
> On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
> mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
> schul...@cornell.edu> wrote:
>
>How can one distinguish between a sulphate or phosphate in an electron
>density map? Both are present in the mother liquor, and resolution is in
>the range of 1.75 - 2.25 A
>
>
>--
>===
>All Things Serve the Beam
>===
>David J. Schuller
>modern man in a post-modern world
>MacCHESS, Cornell University
>
> schul...@cornell.edu
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or 
> privileged material, and are for the use of the intended addressee only. If 
> you are not the intended addressee or an authorised recipient of the 
> addressee please notify us of receipt by returning the e-mail and do not use, 
> copy, retain, distribute or disclose the information in or attached to the 
> e-mail.
> Any opinions expressed within this e-mail are those of the individual and not 
> necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
> 

[ccp4bb] Fwd: [ccp4bb] Sulphate or phosphate? (Armin's figures)

2018-08-02 Thread Charles Ballard - UKRI STFC
Begin forwarded message:

[cid:image001.png@01D42A41.AE0B8B60]




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[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread Charles Ballard - UKRI STFC
Begin forwarded message (on behalf of Armin Wagner)
From: ahw78 mailto:armin.wag...@diamond.ac.uk>>
Date: 2 August 2018 at 09:17:48 BST
To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>>
Cc: ccp4bb mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?
Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This allows 
collecting data above and below the absorption edges of Ca, K, Cl, S and even 
P. Crystal, solvent and loop absorption are of course a problem for the longest 
wavelengths, but so far we have done quite a fair amount of studies around 
these absorption edges with strong signal above the edge and obviously no 
signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
mailto:eleanor.dod...@york.ac.uk>>
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner mailto:armin.wag...@diamond.ac.uk>>
Cc: "ccp4bb@jiscmail.ac.uk" 
mailto:ccp4bb@jiscmail.ac.uk>>
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, you 
might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:
https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University

schul...@cornell.edu



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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom



Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread George Sheldrick
A particularly useful command line option in SHELXT for such cases is 
-L15 to try all trigonal and hexagonal space groups. SHELXT is included 
in recent CCP4 distributions and is also available with documentation 
from shelx.uni-goettingen.de


George

On 02.08.2018 15:53, Aaron Finke wrote:

Hi Kristof,

Direct methods/charge flipping won’t work if your data quality is poor 
below ~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small 
molecule crystals have more stringent standards for data quality. If 
your Rmerge is 50% or more, it’s probably just noise and not useful 
for direct methods.


If SHELXT doesn’t work on the full data set, try cutting the data down 
to 0.9 Å or even 1 Å. I have had limited success doing that on some 
particularly bad data sets.  Alternatively, run SHELXD at full 
resolution indefinitely (NTRY 0) until it finds a solution. It could 
take days, but you may get something.


As a last resort, if you think this hexapeptide may have any secondary 
structure, you may want to try ab initio MR with ARCIMBOLDO.


Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu 

On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>> 
wrote:


Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, 
there should be 3 Nmol/asym

- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not 
able to solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s 
hardly any homologous models



Has anyone encountered a similar problem please, and could provide 
any possible solutions?

(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry
University of Goettingen
Tammannstr.  4
D37077 Goettingen
Germany
Tel: +49 551 3933021 or +49 5594 227312




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[ccp4bb] CCP4/IFSC MX2018 Macromolecular Crystallography School - Sao Carlos, Brazil.

2018-08-02 Thread João Renato Carvalho Muniz
Dear Colleagues,

We are pleased to announce the IFSC/CCP4 Molecular Crystallography School
“From data processing to structure refinement and beyond”, held at Sao
Carlos Institute of Physics (IFSC), University of Sao Paulo (USP), Sao
Carlos, SP, Brazil.

All details can be found at http://www.ifsc.usp.br/mx2018

Dates: November 14th through 24th, 2018

Venue: Sao Carlos Institute of Physics (IFSC), University of Sao Paulo
(USP), Sao Carlos, SP, Brazil.

The school comprises:
Theoretical and in-depth tutorial training on state-of-the-art methods in
macromolecular crystallography;
Main Topics: Diffraction data processing; Phasing and structure
determination; and Model refinement and validation;
Crystallographic computation workshop: will feature many modern
crystallographic software packages taught by the authors and other experts.
The daily schedule will be organized into three sessions – lectures,
tutorials, and hands-on activities, with interactive troubleshooting of the
technical difficulties the participants face in their projects.

Applicants: Graduate students, postdoctoral researchers and young
scientists at the assistant professor level, are encouraged to apply. Only
25 applicants will be selected for participation. Participants of the
workshop are strongly encouraged to bring their own problem datasets so the
problems can be addressed during the hands-on/discussion sessions.

Application: Application deadline is September 30th. The application form,
program, contact info and other details can be found at
http://www.ifsc.usp.br/mx2018

The registration for application is free. Few scholarships to cover travel
expenses for students from Brazil and Latin America will be available.
Accommodation expenses will be covered to all participants. More
instructions will be provided once the selection process is completed.

We hope to see you at the school.
Garib, Kyle, Ronan, Richard, and Joao.


Joao Muniz
Sao Carlos Institute of Physics (IFSC)
University of Sao Paulo (USP)
Laboratorio de Biologia Estrutural (LBEst)
Sao Carlos, SP, Brazil.



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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Mark J. van Raaij

When I was at Santiago de Composrela Univ., we have had success with the CCP4 
program ACORN even at around 1.2 Å resolution. Also peptides, no heavy 
atoms.Didn't do this myself though I have to admit, but could put you in 
contact with the people who did.
Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij

Mark J van RaaijCNB-CSICwwwuser.csic.es/~mjvanraaij
 Original message From: Kristof Van Hecke 
 Date: 02/08/2018  14:53  (GMT+01:00) To: 
CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Structure solution - hexapeptide 
Dear all, 

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10 
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12 
- SG = P3(1)12 or P3(2)12 

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,. 
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions? 
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof 


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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Aaron Finke
Hi Kristof,

Direct methods/charge flipping won’t work if your data quality is poor below 
~1Å. Take a look at your Rmerge, as Jeffrey mentioned. Small molecule crystals 
have more stringent standards for data quality. If your Rmerge is 50% or more, 
it’s probably just noise and not useful for direct methods.

If SHELXT doesn’t work on the full data set, try cutting the data down to 0.9 Å 
or even 1 Å. I have had limited success doing that on some particularly bad 
data sets.  Alternatively, run SHELXD at full resolution indefinitely (NTRY 0) 
until it finds a solution. It could take days, but you may get something.

As a last resort, if you think this hexapeptide may have any secondary 
structure, you may want to try ab initio MR with ARCIMBOLDO.

Aaron

--
Aaron Finke
Staff Scientist, MacCHESS
Cornell University
e-mail: af...@cornell.edu

On Aug 2, 2018, at 8:53 AM, Kristof Van Hecke 
mailto:kristofrg.vanhe...@gmail.com>> wrote:

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Jeffrey, Philip D.
"Very decent" means different things to different people.  Is your Rmerge < 20% 
in the 0.84 Å shell ?  If so that's a small molecule quality data set and 
something like that should solve relatively straightforwardly with e.g. SHELXT. 
 However the classical program would be SHELXD and perhaps a CPU day or three 
(speaking from recent experience with data that did not go quite as far).

If it doesn't solve, then there's probably something interesting about the 
data.  P3x 1 2 is a rare space group in both protein world and small molecule 
world.  I would suggest checking for signs of twinning and dropping back to 
point group 3.

You should not be surprised  if your bulk solvent content is almost 
non-existent and you have 5 molecules in the asymmetric unit.

Cheers
Phil Jeffrey
Princeton

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kristof Van 
Hecke [kristofrg.vanhe...@gmail.com]
Sent: Thursday, August 02, 2018 8:53 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Structure solution - hexapeptide

Dear all,

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12
- SG = P3(1)12 or P3(2)12

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,.
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions?
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Christopher Squire
Hi agree,

Try SHELXT. I have just solved several tetrapeptides, linear and cyclic, and 
with up to 5 molecules per au. Shelxt solved them exceptionally easily at 
0.77-0.89 angstrom resolution. Most of the oxygens and nitrogens were picked by 
the software correctly. You know you have the right solution if you have the 
correct form of the amino acids, D- or L-form - assuming you know the sequence! 
Does a really good job of picking the space group too.

Good luck!

Chris.


From: CCP4 bulletin board  on behalf of 
graeme.win...@diamond.ac.uk 
Sent: 03 August 2018 1:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Structure solution - hexapeptide

Kristof,

Just checking - have you tried SHELXT? Feeding in umerged HKL file

I appreciate that this is direct methods but the tool is pretty powerful

Also: you could find processing the data with different tools helps…

Best wishes Graeme (who dabbles in “small" molecule stuff, too)

> On 2 Aug 2018, at 08:53, Kristof Van Hecke  
> wrote:
>
> Dear all,
>
> I’m trying to solve a structure of a (modified) hexapeptide:
> - inhouse (very decent) data up to 0.8 Angstrom
> - average redundancy = 10
> - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
> should be 3 Nmol/asym
> - ‘large’ unit cell of about a=54, b=54, c=12
> - SG = P3(1)12 or P3(2)12
>
> As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
> solve this via Direct Methods, Charge Flipping etc,.
> Trying MR (with Phaser) doesn’t give any results either, as there’s hardly 
> any homologous models
>
>
> Has anyone encountered a similar problem please, and could provide any 
> possible solutions?
> (building in heavy atoms isn’t my first option at the moment,. )
>
>
> Thank you very much
>
> Regards
>
> Kristof
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


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This e-mail and any attachments may contain confidential, copyright and or 
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are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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Re: [ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread graeme.win...@diamond.ac.uk
Kristof,

Just checking - have you tried SHELXT? Feeding in umerged HKL file

I appreciate that this is direct methods but the tool is pretty powerful

Also: you could find processing the data with different tools helps… 

Best wishes Graeme (who dabbles in “small" molecule stuff, too) 

> On 2 Aug 2018, at 08:53, Kristof Van Hecke  
> wrote:
> 
> Dear all, 
> 
> I’m trying to solve a structure of a (modified) hexapeptide:
> - inhouse (very decent) data up to 0.8 Angstrom
> - average redundancy = 10 
> - according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
> should be 3 Nmol/asym
> - ‘large’ unit cell of about a=54, b=54, c=12 
> - SG = P3(1)12 or P3(2)12 
> 
> As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
> solve this via Direct Methods, Charge Flipping etc,. 
> Trying MR (with Phaser) doesn’t give any results either, as there’s hardly 
> any homologous models
> 
> 
> Has anyone encountered a similar problem please, and could provide any 
> possible solutions? 
> (building in heavy atoms isn’t my first option at the moment,. )
> 
> 
> Thank you very much
> 
> Regards
> 
> Kristof 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


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This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
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[ccp4bb] Structure solution - hexapeptide

2018-08-02 Thread Kristof Van Hecke
Dear all, 

I’m trying to solve a structure of a (modified) hexapeptide:
- inhouse (very decent) data up to 0.8 Angstrom
- average redundancy = 10 
- according to the Matthews coefficient of 1.88 with 34.77 %solvent, there 
should be 3 Nmol/asym
- ‘large’ unit cell of about a=54, b=54, c=12 
- SG = P3(1)12 or P3(2)12 

As there’s (presumably) only C, H, N and O in the structure, I’m not able to 
solve this via Direct Methods, Charge Flipping etc,. 
Trying MR (with Phaser) doesn’t give any results either, as there’s hardly any 
homologous models


Has anyone encountered a similar problem please, and could provide any possible 
solutions? 
(building in heavy atoms isn’t my first option at the moment,. )


Thank you very much

Regards

Kristof 


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


[ccp4bb] refmac error

2018-08-02 Thread Leonid Sazanov
Hi, after updating to ccp4/7.0, I get this error when trying to run Refmac:

Dictionary path has not been defined
Check the environment variable CLIBD_MON
Current value of CLIBD_MON is
/mnt/nfs/clustersw/shared/ccp4/7.0/ccp4-7.0/lib/data/monomers
It should be set to wherever_dict/dic/
===> Error: Wrong path for the dictionary files
 Refmac:  Wrong path for the dictionary files

How to resolve this?
Many thanks!



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[ccp4bb] FW: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread armin.wag...@diamond.ac.uk

Dear all,

Sorry, now with the attachment of an anomalous difference fourier above and 
below the sulphur edge. 

Best regards,

   Armin


On 02/08/2018, 09:17, "CCP4 bulletin board on behalf of 
armin.wag...@diamond.ac.uk"  wrote:

Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This 
allows collecting data above and below the absorption edges of Ca, K, Cl, S and 
even P. Crystal, solvent and loop absorption are of course a problem for the 
longest wavelengths, but so far we have done quite a fair amount of studies 
around these absorption edges with strong signal above the edge and obviously 
no signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner 
Cc: "ccp4bb@jiscmail.ac.uk" 
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, 
you might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:

https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University

schul...@cornell.edu



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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any 
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which you may sustain as a result of software viruses which may be transmitted 
in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England 
and Wales with its registered office at 

Re: [ccp4bb] [EXTERNAL] Re: identifying bound ions

2018-08-02 Thread Andrew Leslie
Hi Herman,

  We can run it stand alone, (i.e. "which xpand” points to an 
exe that runs) but we have the Uppsala suite installed on our machine.

Cheers,

Andrew

> On 2 Aug 2018, at 07:38, herman.schreu...@sanofi.com wrote:
> 
> Dear Kay,
> 
> I have looked at XPAND and it looks like it is part of the O-package. Do you 
> know if it can also be used stand-alone?
> 
> Best,
> Herman 
> 
> -Ursprüngliche Nachricht-
> Von: Kay Diederichs [mailto:kay.diederi...@uni-konstanz.de] 
> Gesendet: Mittwoch, 1. August 2018 15:00
> An: CCP4BB@JISCMAIL.AC.UK; Schreuder, Herman /DE
> Betreff: [EXTERNAL] Re: identifying bound ions
> 
> Dear Herman,
> 
> the "water scrutinizer" option of XPAND does this -. 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.msg.ucsf.edu_local_programs_ono_manuals_xpand-5Fman.html-23S7=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=xDNvO2p9KWi88plMQdKeBus0tAym2doLwUPdQNfYRG8=sEx3IqjhUIdjbiqizdljtA1eTlNHUhuaNKMHipOp6L4=
>  
> 
> best wishes,
> 
> Kay
> 
> On Tue, 31 Jul 2018 12:39:01 +, herman.schreu...@sanofi.com wrote:
> 
>> Dear BB,
>> 
>> I know it has been discussed some time ago, but a google search did not come 
>> up with anything useful.
>> 
>> I need a program which analyzes the bound waters and suggests whether a 
>> particular water might be a chloride, calcium, sulfate, sodium or something 
>> else. Preferably a program that can be run off-line (not a web server), but 
>> if there is no choice, we will use a webserver as well.
>> 
>> Thank you for your suggestions!
>> Herman
>> 
>> 
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=xDNvO2p9KWi88plMQdKeBus0tAym2doLwUPdQNfYRG8=7Fy9spg-ZpKgzdg0fT25uD-PzjkXI5bt48_hAD-zTSo=
>>  
>> 
> 
> 
> 
> 
> 
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[ccp4bb] Workshop on nMX at ECM31, the programme is now online

2018-08-02 Thread John R Helliwell

Dear Colleagues,
The Workshop on nMX at ECM31, the programme is now online at:-
https://ecm31.ecanews.org/en/neutron-macromolecular-crystallography.php
There is still time to register.
Best wishes,
John 
Emeritus Professor John R Helliwell DSc



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Re: [ccp4bb] Sulphate or phosphate?

2018-08-02 Thread armin.wag...@diamond.ac.uk
Dear Eleanor,

We can tune the wavelength over a large range (lambda = 1.2 – 6 A). This allows 
collecting data above and below the absorption edges of Ca, K, Cl, S and even 
P. Crystal, solvent and loop absorption are of course a problem for the longest 
wavelengths, but so far we have done quite a fair amount of studies around 
these absorption edges with strong signal above the edge and obviously no 
signal below. Resolution in our setup is limited to around 3.2 A at 5 A 
wavelength, but for anomalous difference fourier maps this is sufficient. I 
have attached an example for a disulphide bridge which should illustrate it 
better.

Best regards,

Armin



[cid:image001.png@01D42A41.AE0B8B60]

From: Eleanor Dodson 
Date: Wednesday, 1 August 2018 at 19:09
To: Armin Wagner 
Cc: "ccp4bb@jiscmail.ac.uk" 
Subject: Re: [ccp4bb] Sulphate or phosphate?

I am not sure if you gave your wave length but it is always worth doing an 
anomalous map, and looking at relativr peak heights for your known S positions 
and the putative sulphate or phosphate.
There are small differences in the expected f" at most wavelengths.

Chemical arguments are doubtless better of Course!
Eleanor

On 1 August 2018 at 16:54, 
armin.wag...@diamond.ac.uk 
mailto:armin.wag...@diamond.ac.uk>> wrote:
Dear David,

The long-wavelength beamline I23 at Diamond 
(http://www.diamond.ac.uk/Instruments/Mx/I23.html) can go all way down to the 
phosphorous edge. While data quality will be obviously compromised by 
absorption effects (we are working on this), for a reasonably well diffracting 
crystal like yours we should be able to get anomalous difference fourier maps 
from data collected above and below the sulphur edge (lambda ~5 A) to answer 
your question.

We’ve published some test crystal work around the sulphur edge a while ago, you 
might want to have a look here:
https://doi.org/10.1016/j.nimb.2016.12.005

The beamline is currently in an advanced commissioning phase accepting a 
limited number of projects. So, please get into touch if you are interested. We 
are currently sorting out a few more hardware and software aspects before we 
can run the beamline as a standard user facility, but we have made a lot of 
progress over the past months. There will be more details here on the bulletin 
board ahead of the next call for proposals in autumn.

Best regards,

Armin


Postdoc position for long-wavelength crystallography:
https://vacancies.diamond.ac.uk/vacancy/post-doctoral-research-associate-355285.html




On 31/07/2018, 14:38, "CCP4 bulletin board on behalf of David Schuller" 
mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of 
schul...@cornell.edu> wrote:

How can one distinguish between a sulphate or phosphate in an electron
density map? Both are present in the mother liquor, and resolution is in
the range of 1.75 - 2.25 A


--
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University

schul...@cornell.edu



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1


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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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[ccp4bb] AW: [EXTERNAL] Re: identifying bound ions

2018-08-02 Thread Herman . Schreuder
Dear Kay,

I have looked at XPAND and it looks like it is part of the O-package. Do you 
know if it can also be used stand-alone?

Best,
Herman 

-Ursprüngliche Nachricht-
Von: Kay Diederichs [mailto:kay.diederi...@uni-konstanz.de] 
Gesendet: Mittwoch, 1. August 2018 15:00
An: CCP4BB@JISCMAIL.AC.UK; Schreuder, Herman /DE
Betreff: [EXTERNAL] Re: identifying bound ions

Dear Herman,

the "water scrutinizer" option of XPAND does this -. 
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.msg.ucsf.edu_local_programs_ono_manuals_xpand-5Fman.html-23S7=DwIFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ=xDNvO2p9KWi88plMQdKeBus0tAym2doLwUPdQNfYRG8=sEx3IqjhUIdjbiqizdljtA1eTlNHUhuaNKMHipOp6L4=
 

best wishes,

Kay

On Tue, 31 Jul 2018 12:39:01 +, herman.schreu...@sanofi.com wrote:

>Dear BB,
>
>I know it has been discussed some time ago, but a google search did not come 
>up with anything useful.
>
>I need a program which analyzes the bound waters and suggests whether a 
>particular water might be a chloride, calcium, sulfate, sodium or something 
>else. Preferably a program that can be run off-line (not a web server), but if 
>there is no choice, we will use a webserver as well.
>
>Thank you for your suggestions!
>Herman
>
>
>
>
>
>
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