[ccp4bb] LAB RESEARCH POSITION

[Greg Snyder]

A LABORATORY RESEARCH POSITION IS IMMEDIATELY AVAILABLE FOR INVESTIGATING 
INNATE IMMUNITY AND VACCINE DESIGN.
 
A full-time laboratory research specialist is available for investigating 
innate immune regulation by microbes (bacteria and viruses) and vaccine design. 
   We seek to understand 1) how microbes regulate innate immune activation, and 
 2) how this influences host response to infection.   Our goal is the 
development of safe and effective therapeutics for controlling infection, 
inflammation and disease.   We primarily use cryo-EM, X-ray crystallography and 
NMR along with complimentary biophysical and biochemical approaches to 
investigate molecular interactions of microbes and host.  As part of the 
Vaccine Research Division at the Institute of Human Virology, we utilize a 
uniquely integrated translational research platform involving clinical, basic, 
and vaccine research sciences. 

The Institute of Human Virology (IHV) was founded in 1996 to expedite 
scientific understanding of persistent human diseases, viral infection, induced 
cancers, and to develop therapeutic interventions that will improve the lives 
of patients with infectious diseases. The full-time faculty number more than 
250 M.D., M.D./Ph.D. and Ph.D. professionals, as well as adjunct faculty in 9 
African and 2 Caribbean nations. This multidisciplinary center integrates 
basic, epidemiologic, clinical  and vaccine research and translates this 
research into the development of medical therapeutics and vaccines.  The 
Clinical Care and Research Units, Basic Sciences, Cancer and Vaccine Research 
Divisions are all located within one building and directly adjacent to the 
University of Maryland medical school, hospital and Baltimore VA medical 
centers. This location provides convenient and direct access for patients as 
well as unique opportunities for translational research and therapeutic 
development. 

Qualifications and Application Procedure: This position will include a range of 
activities including supporting I) benchtop experiments (e.g., cell culture, 
protein expression and purification and characterization), II) research data 
analysis, and III) lab operations.  I am committed to the development and 
training of individuals from diverse and underrepresented backgrounds in 
science.  Interested candidates should apply to the Laboratory Research 
Specialist (#209H) position posted at the University of Maryland,  
https://umb.taleo.net/careersection/jobdetail.ftl?job=209H&lang=en   
Applications will be reviewed until the position is filled. 


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Re: [ccp4bb] COOT download site

[Frances C. Bernstein]

Pity there is not a website

cootcootgo

 Frances

=
Bernstein + Sons
*   *   Information Systems Consultants
5 Brewster Lane, Bellport, NY 11713-2803
*   * ***
 *Frances C. Bernstein
  *   ***  f...@bernstein-plus-sons.com
 *** *
  *   *** 1-631-286-1339FAX: 1-631-286-1999
=

On Thu, 4 Jun 2020, Gianluca SANTONI wrote:

The mrc website is the first non-bird related result if you search for 'coot' 
on duckduckgo (so not biased by my navigation history).



Gianluca Santoni, serial crystallographer

ESRF structural biology group
71 avenue des Martyrs
38027 Grenoble cedex (France)

On 04/06/2020 16:54, Paul Emsley wrote:

On 04/06/2020 15:41, Clemens Grimm wrote:

Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 


gives me an

"The requested URL /~emsley/software/binaries/nightlies/pre-release/ was 
not found on this server."


error since a few days.

Is the site down or has it moved?



Good grief! I haven't thought about that web site for 10 years. I had no 
idea that it was alive (not that I could do anything about it if it was).


Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/


Paul.



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Re: [ccp4bb] COOT download site

[Rosario Recacha]

Hello,

Here it appears release coot 0.9 2020

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/

Best wishes.
Rosario

On Thu, 4 Jun 2020 at 18:11, Clemens Grimm <
clemens.gr...@biozentrum.uni-wuerzburg.de> wrote:

> Zitat von Petri Kursula :
>
> > Could it be because that link is given at least here:
> > https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot
>
> That's exactly where I started from ...
>
> > 
> > Petri
> >
> > Petri Kursula
> > --
> > Professor
> > --
> > Department of Biomedicine
> > University of Bergen, Norway
> > http://www.uib.no/en/rg/petrikursula
> > petri.kurs...@uib.no
> > --
> > Faculty of Biochemistry and Molecular Medicine
> > Biocenter Oulu
> > University of Oulu, Finland
> > --
> >
> >
> >
> >
> >
> >> On 4 Jun 2020, at 17:02, Jurgen Bosch  wrote:
> >>
> >> Looks as if Clemens will be jumping straight into the future now
> >> with the new link. Were you on Coot 0.069?
> >>
> >> Jürgen
> >>
> >>> On Jun 4, 2020, at 10:54 AM, Paul Emsley
> >>> mailto:pems...@mrc-lmb.cam.ac.uk>>
> >>> wrote:
> >>>
> >>> On 04/06/2020 15:41, Clemens Grimm wrote:
>  Dear All,
> 
>  accessing the COOT download pages at
> 
> 
> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
>
>  <
> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
> >
> 
>  gives me an
> 
>  "The requested URL
>  /~emsley/software/binaries/nightlies/pre-release/ was not found
>  on this server."
> 
>  error since a few days.
> 
>  Is the site down or has it moved?
> 
> >>>
> >>> Good grief! I haven't thought about that web site for 10 years. I
> >>> had no idea that it was alive (not that I could do anything about
> >>> it if it was).
> >>>
> >>> Google finds my Coot pages using "Emsley Coot" - well, it does for me
> :-)
> >>>
> >>>
> >>> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/
> >>> 
> >>>
> >>>
> >>> Paul.
> >>>
> >>>
> 
> >>>
> >>> To unsubscribe from the CCP4BB list, click the following link:
> >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >>> 
> >>>
> >>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB
> >>> , a mailing list hosted by
> >>> www.jiscmail.ac.uk , terms &
> >>> conditions are available at
> >>> https://www.jiscmail.ac.uk/policyandsecurity/
> >>> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >> 
> >
> > 
> >
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> >
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> > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> > available at https://www.jiscmail.ac.uk/policyandsecurity/
>
>
>
> --
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -
>
> 
>
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Re: [ccp4bb] COOT download site

[Tim Gruene]

Hi Clemens,

You can download a build for Debian (testing) from
https://homepage.univie.ac.at/tim.gruene/coot_deb/bullseye/binaries/stable/

it is not the latest, but a post-0.9-release version.
I'll update it from time to time with a more recent build.

Best,
Tim

On Thu, 4 Jun 2020 15:05:20 +
Clemens Grimm  wrote:

> Hi Eleanor,
> 
> thanks for the tips. However, I am still unsure whether I really got  
> the latest pre-release version
> 
> Google sends me to:
> 
> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/devel/build-info.html
> 
> which is lacking the 0.9.x pre-release version.
> 
> With ccp4 I got packaged the 0.9 "Arteixo" pre-release but the menues
> look somehow different from that what I can see in the latest  
> presentations on Youtube ...
> 
> Clemens
> 
> Zitat von Eleanor Dodson :
> 
> > Certainly it has moved. Now latest from Emsleu Marc Cambridge.
> > Search coot in google for full address. Or it comes with ccp4
> >
> > On Thu, 4 Jun 2020 at 15:41, Clemens Grimm <
> > clemens.gr...@biozentrum.uni-wuerzburg.de> wrote:
> >  
> >> Dear All,
> >>
> >> accessing the COOT download pages at
> >>
> >> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
> >>
> >> gives me an
> >>
> >> "The requested URL
> >> /~emsley/software/binaries/nightlies/pre-release/ was not found on
> >> this server."
> >>
> >> error since a few days.
> >>
> >> Is the site down or has it moved?
> >>
> >> Thanks,
> >> Clemens
> >>
> >> --
> >> Dr. Clemens Grimm
> >> Institut für Biochemie
> >> Biozentrum der Universität Würzburg
> >> Am Hubland
> >> D-97074 Würzburg
> >> Germany
> >> e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
> >> phone : +49 0931 31 84031
> >> -
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> >>
> >> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> >> available at https://www.jiscmail.ac.uk/policyandsecurity/
> >>  
> 
> 
> 
> --
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/



-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgphjYikLWR1d.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] COOT download site

[Clemens Grimm]

Zitat von Petri Kursula :


Could it be because that link is given at least here:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot


That's exactly where I started from ...



Petri

Petri Kursula
--
Professor
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
petri.kurs...@uib.no
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
--






On 4 Jun 2020, at 17:02, Jurgen Bosch  wrote:

Looks as if Clemens will be jumping straight into the future now  
with the new link. Were you on Coot 0.069?


Jürgen

On Jun 4, 2020, at 10:54 AM, Paul Emsley  
mailto:pems...@mrc-lmb.cam.ac.uk>>  
wrote:


On 04/06/2020 15:41, Clemens Grimm wrote:

Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/  



gives me an

"The requested URL  
/~emsley/software/binaries/nightlies/pre-release/ was not found  
on this server."


error since a few days.

Is the site down or has it moved?



Good grief! I haven't thought about that web site for 10 years. I  
had no idea that it was alive (not that I could do anything about  
it if it was).


Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/  




Paul.



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--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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Re: [ccp4bb] COOT download site

[Petri Kursula]

Could it be because that link is given at least here:
https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot 

Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
http://www.uib.no/en/rg/petrikursula
petri.kurs...@uib.no
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
--





> On 4 Jun 2020, at 17:02, Jurgen Bosch  wrote:
> 
> Looks as if Clemens will be jumping straight into the future now with the new 
> link. Were you on Coot 0.069?
> 
> Jürgen 
> 
>> On Jun 4, 2020, at 10:54 AM, Paul Emsley > > wrote:
>> 
>> On 04/06/2020 15:41, Clemens Grimm wrote:
>>> Dear All,
>>> 
>>> accessing the COOT download pages at
>>> 
>>> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 
>>> 
>>>  
>>> 
>>> gives me an
>>> 
>>> "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was 
>>> not found on this server."
>>> 
>>> error since a few days.
>>> 
>>> Is the site down or has it moved?
>>> 
>> 
>> Good grief! I haven't thought about that web site for 10 years. I had no 
>> idea that it was alive (not that I could do anything about it if it was).
>> 
>> Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)
>> 
>> 
>> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ 
>> 
>> 
>> 
>> Paul.
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 
>> 
>> 
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB 
>> , a mailing list hosted by 
>> www.jiscmail.ac.uk , terms & conditions are 
>> available at https://www.jiscmail.ac.uk/policyandsecurity/ 
>> 
> 
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> 



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Re: [ccp4bb] COOT download site

[Gianluca SANTONI]

The mrc website is the first non-bird related result if you search for 
'coot' on duckduckgo (so not biased by my navigation history).



Gianluca Santoni, serial crystallographer

ESRF structural biology group
71 avenue des Martyrs
38027 Grenoble cedex (France)

On 04/06/2020 16:54, Paul Emsley wrote:

On 04/06/2020 15:41, Clemens Grimm wrote:

Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 



gives me an

"The requested URL /~emsley/software/binaries/nightlies/pre-release/ 
was not found on this server."


error since a few days.

Is the site down or has it moved?



Good grief! I haven't thought about that web site for 10 years. I had no 
idea that it was alive (not that I could do anything about it if it was).


Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/


Paul.



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Re: [ccp4bb] COOT download site

[Clemens Grimm]

Hi Eleanor,

thanks for the tips. However, I am still unsure whether I really got  
the latest pre-release version


Google sends me to:

https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/devel/build-info.html

which is lacking the 0.9.x pre-release version.

With ccp4 I got packaged the 0.9 "Arteixo" pre-release but the menues  
look somehow different from that what I can see in the latest  
presentations on Youtube ...


Clemens

Zitat von Eleanor Dodson :


Certainly it has moved. Now latest from Emsleu Marc Cambridge. Search coot
in google for full address. Or it comes with ccp4

On Thu, 4 Jun 2020 at 15:41, Clemens Grimm <
clemens.gr...@biozentrum.uni-wuerzburg.de> wrote:


Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/

gives me an

"The requested URL /~emsley/software/binaries/nightlies/pre-release/
was not found on this server."

error since a few days.

Is the site down or has it moved?

Thanks,
Clemens

--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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Re: [ccp4bb] COOT download site

[Jurgen Bosch]

Looks as if Clemens will be jumping straight into the future now with the new 
link. Were you on Coot 0.069?

Jürgen 

> On Jun 4, 2020, at 10:54 AM, Paul Emsley  wrote:
> 
> On 04/06/2020 15:41, Clemens Grimm wrote:
>> Dear All,
>> 
>> accessing the COOT download pages at
>> 
>> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 
>> 
>> gives me an
>> 
>> "The requested URL /~emsley/software/binaries/nightlies/pre-release/ was not 
>> found on this server."
>> 
>> error since a few days.
>> 
>> Is the site down or has it moved?
>> 
> 
> Good grief! I haven't thought about that web site for 10 years. I had no idea 
> that it was alive (not that I could do anything about it if it was).
> 
> Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)
> 
> 
> https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/ 
> 
> 
> 
> Paul.
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] COOT download site

[Paul Emsley]

On 04/06/2020 15:41, Clemens Grimm wrote:

Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/ 



gives me an

"The requested URL /~emsley/software/binaries/nightlies/pre-release/ 
was not found on this server."


error since a few days.

Is the site down or has it moved?



Good grief! I haven't thought about that web site for 10 years. I had no 
idea that it was alive (not that I could do anything about it if it was).


Google finds my Coot pages using "Emsley Coot" - well, it does for me :-)


https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/


Paul.



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Re: [ccp4bb] COOT download site

[Eleanor Dodson]

Certainly it has moved. Now latest from Emsleu Marc Cambridge. Search coot
in google for full address. Or it comes with ccp4

On Thu, 4 Jun 2020 at 15:41, Clemens Grimm <
clemens.gr...@biozentrum.uni-wuerzburg.de> wrote:

> Dear All,
>
> accessing the COOT download pages at
>
> http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/
>
> gives me an
>
> "The requested URL /~emsley/software/binaries/nightlies/pre-release/
> was not found on this server."
>
> error since a few days.
>
> Is the site down or has it moved?
>
> Thanks,
> Clemens
>
> --
> Dr. Clemens Grimm
> Institut für Biochemie
> Biozentrum der Universität Würzburg
> Am Hubland
> D-97074 Würzburg
> Germany
> e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
> phone : +49 0931 31 84031
> -
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] COOT download site

[Clemens Grimm]

Dear All,

accessing the COOT download pages at

http://www.ysbl.york.ac.uk/~emsley/software/binaries/nightlies/pre-release/

gives me an

"The requested URL /~emsley/software/binaries/nightlies/pre-release/  
was not found on this server."


error since a few days.

Is the site down or has it moved?

Thanks,
Clemens

--
Dr. Clemens Grimm
Institut für Biochemie
Biozentrum der Universität Würzburg
Am Hubland
D-97074 Würzburg
Germany
e-mail: clemens.gr...@biozentrum.uni-wuerzburg.de
phone : +49 0931 31 84031
-



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Re: [ccp4bb] Question about small molecule crystallography

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Dear All,

A small word of caution regarding chemical crystallography on an MX-like 
beamline - if you have a bright source, a well diffracting crystal and a pixel 
array detector it is perfectly possible to lose counts in the strongest 
reflections without noticing - certainly without going over the nominal 
detector count limits if your mosaic spread is very small

At Diamond we faced this issue with i19, which is a dedicated chemical 
crystallography beamline on an undulator source, with a Pilatus 2 detector - it 
turns out to be very very easy to exceed the count rate where the detector 
electronics can keep up. This is somewhat less of a problem with Pilatus 3 and 
Eiger 2X detectors.

So: I would strongly suggest really turning down the intensity on the beam, use 
fine slicing and be prepared to check that the data are OK before removing your 
sample. You can solve and refine the structure with e.g. SHELX and get an F^2 
calc vs. I ops plot which would show systematically under measured low angle 
reflections.

We also have a tool in development to bolt on to DIALS called screen19 which 
estimates the true peak photon rate from a “quick screening run” to offer 
insights into data collection options - https://github.com/xia2/screen19 - this 
is not perfect but you could find it useful. Our chemical crystallography users 
certainly find it helpful for planning their experiments.

Best wishes Graeme

On 4 Jun 2020, at 10:51, Alker, Andre M. 
<4599f25026c0-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Dear Jiyuan,

maybe I can add something from the small molecule crystallographer view :-)

Crystallization:
For crystallization of small molecules you normally use solvents and water or 
mixtures as mentioned already before. At my lab the most successful way to 
crystallise is evaporation. Please use small glass vials (no plastic, some 
solvents will solute them too).

You can also use crystallization kits. Here you can use Bernhard Spinglers kit 
and or the Hampton kit. The Hampton kit didn't work so well for my molecules. I 
also bought Bernhard's kit but had no time to test it so far. I have to say I'm 
only using crystallization kits at the moment as last try. Maybe that changes 
in the future.

Measurement:
Of course you can use the synchrotron for small molecules at the protein 
beamline. I'm using the PXII protein beamline at the SLS (Swiss light source) 
for my small molecules if the crystals are too small for my inhouse system or 
there is a problem with my inhouse system. To get the resolution you need for 
structure solution and a good refinement you have to change the wavelength to 
0.7Å. Collect always at least 360 degrees  in steps of 0.5 degrees or smaller. 
Use high filters and short exposure times to secure your crystal against 
radiation damage. Normally 10 to 20% of the beam and 0.01 to 0.1 sec work fine 
depending on the crystal size. Do the measurement at low temperatures as usual 
for protein crystals. Here are my parameters for the SLS-PXII beamline equipped 
with an Eiger detector (wavelength 0.7Å, biggest aperture, 20% transmission, 
step 0.1 deg/0.01 sec, 1800 degrees, 100K).

Processing, structure solution and refinement:
I process the eiger data with XDS,
for structure solution I'm using shelxs or shelxd,
for structure refinement shelxl.

But as mentioned before there are a lot of programs doing processing, structure 
solution and refinement. I just started to use Olex as well for solution and 
refinement. In very earlier times I also used hkl2000 for data processing but 
in my opinion XDS is doing a very good job for small molecule data.

Last but not least I deeply agree with Navdeep to read Mueller et al.'s 
excellent book about Crystal Structure Refinement.

Hope this helps a little bit :-)

Best regards,
André






André Alker
Senior Scientist, pCMC Analytics
Roche Pharmaceutical Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4058 Basel, Switzerland
Phone: +41-61-6880935
email: andre_m.al...@roche.com

Upcoming absences:
...

Hinweis:
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(die) namentlich genannten Empfänger bestimmt sind. Falls Sie nicht der 
Adressat dieser E-Mail sind, nehmen Sie Verbindung mit dem Absender auf und 
löschen Sie diese Mitteilung. Jede unbefugte Verwendung der in dieser 
Mitteilung enthaltenen Informationen ist untersagt.
This message is intended only for the use of the named recipient(s) and may 
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use of the information contained in this message is prohibited.


On Wed, Jun 3, 2020 at 7:40 PM Navdeep Sidhu 
mailto:sid...@gmail.com>> wrote:
Dear Jiyuan,

There was a similar question on the bulletin board some 6 years 

Re: [ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hey Paul,

I’ve attached a copy of the log after opening up coot. There is an error in 
there but not sure what it means.

IOError: [Errno socket error] [Errno 10061] No connection could be made because 
the target machine actively refused it

Cheers,

Sam

From: Paul Emsley 
Sent: 04 June 2020 11:46
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Subject: Re: [ccp4bb] Coot CCP4i2 extensions




Coot should write a log somewhere - not sure where it is - and that will record 
problems reading startup scripts. If you can find it it might be useful.



Paul.




On 04/06/2020 11:43, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hi Stuart,

Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS 
specific.

I went to the file menu and it no longer has the save mol to ccp4i2 option. I 
have tried rebooting, rolling back the update, reinstalling the update and 
nothing has changed I’m afraid. The full path to the coot executable in the 
preferences is blank but if there was a problem I don’t think coot would have 
loaded at all from the interface.

Cheers,

Sam

From: Stuart McNicholas 

Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI) 

Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see the 
problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do "Save 
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can 
use those. If not, then you do indeed still have a problem. One simple thought 
might be to reboot, if you have not already done so. Clearly Coot is, for some 
reason, not able to communicate properly. A reboot might help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot’s 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to 
the i2 gui.
I’ve rolled back the update but the bug is still present.

Cheers,

Sam





--

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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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.
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INFO:: Using Standard CCP4 Refmac dictionary from

Re: [ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hi Stuart,

Thanks for the reply, I am running on a windows 10 machine so maybe it’s OS 
specific.

I went to the file menu and it no longer has the save mol to ccp4i2 option. I 
have tried rebooting, rolling back the update, reinstalling the update and 
nothing has changed I’m afraid. The full path to the coot executable in the 
preferences is blank but if there was a problem I don’t think coot would have 
loaded at all from the interface.

Cheers,

Sam

From: Stuart McNicholas 
Sent: 04 June 2020 11:38
To: Horrell, Sam (DLSLtd,RAL,LSCI) 
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Coot CCP4i2 extensions

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see the 
problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do "Save 
mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If so you can 
use those. If not, then you do indeed still have a problem. One simple thought 
might be to reboot, if you have not already done so. Clearly Coot is, for some 
reason, not able to communicate properly. A reboot might help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) 
mailto:sam.horr...@diamond.ac.uk>> wrote:
Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot’s 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it’s impossible to save to 
the i2 gui.
I’ve rolled back the update but the bug is still present.

Cheers,

Sam





--

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 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




To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] Coot CCP4i2 extensions

[Stuart McNicholas]

Dear Sam,
   Apologies for your problem. I have tested myself on Mac and do not see
the problem, however I will try on Linux and Windows as well.

However, this menu not functioning may not mean that you cannot saves. Do
"Save mol to CCP4i2.." and "Save to CCP4i2" appear in Coot's File menu? If
so you can use those. If not, then you do indeed still have a problem. One
simple thought might be to reboot, if you have not already done so. Clearly
Coot is, for some reason, not able to communicate properly. A reboot might
help.

Best wishes,
Stuart

On Thu, 4 Jun 2020 at 10:57, Horrell, Sam (DLSLtd,RAL,LSCI) <
sam.horr...@diamond.ac.uk> wrote:

> Hello CCP4bb,
>
>
>
> I just installed the latest update and it seems to have a problem with
> Coot’s CCP4i2 extensions.
>
> The dropdown menu no longer appears when clicked so it’s impossible to
> save to the i2 gui.
>
> I’ve rolled back the update but the bug is still present.
>
>
>
> Cheers,
>
>
>
> Sam
>
>
>
>
>
>
>
> --
>
> 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
> 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
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] Question about small molecule crystallography

[Alker, Andre M.]

Dear Jiyuan,

maybe I can add something from the small molecule crystallographer view :-)

Crystallization:
For crystallization of small molecules you normally use solvents and water
or mixtures as mentioned already before. At my lab the most successful way
to crystallise is evaporation. Please use small glass vials (no plastic,
some solvents will solute them too).

You can also use crystallization kits. Here you can use Bernhard Spinglers
kit and or the Hampton kit. The Hampton kit didn't work so well for my
molecules. I also bought Bernhard's kit but had no time to test it so far.
I have to say I'm only using crystallization kits at the moment as last
try. Maybe that changes in the future.

Measurement:
Of course you can use the synchrotron for small molecules at the protein
beamline. I'm using the PXII protein beamline at the SLS (Swiss light
source) for my small molecules if the crystals are too small for my inhouse
system or there is a problem with my inhouse system. To get the resolution
you need for structure solution and a good refinement you have to change
the wavelength to 0.7Å. Collect always at least 360 degrees  in steps of
0.5 degrees or smaller. Use high filters and short exposure times to secure
your crystal against radiation damage. Normally 10 to 20% of the beam and
0.01 to 0.1 sec work fine depending on the crystal size. Do the measurement
at low temperatures as usual for protein crystals. Here are my parameters
for the SLS-PXII beamline equipped with an Eiger detector (wavelength 0.7Å,
biggest aperture, 20% transmission, step 0.1 deg/0.01 sec, 1800 degrees,
100K).

Processing, structure solution and refinement:
I process the eiger data with XDS,
for structure solution I'm using shelxs or shelxd,
for structure refinement shelxl.

But as mentioned before there are a lot of programs doing processing,
structure solution and refinement. I just started to use Olex as well for
solution and refinement. In very earlier times I also used hkl2000 for data
processing but in my opinion XDS is doing a very good job for small
molecule data.

Last but not least I deeply agree with Navdeep to read Mueller et al.'s
excellent book about Crystal Structure Refinement.

Hope this helps a little bit :-)

Best regards,
André






André Alker
Senior Scientist, pCMC Analytics
Roche Pharmaceutical Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4058 Basel, Switzerland
Phone: +41-61-6880935
email: andre_m.al...@roche.com

Upcoming absences:
...

Hinweis:
Der Inhalt dieser E-Mail kann vertrauliche Angaben enthalten, die nur für
den (die) namentlich genannten Empfänger bestimmt sind. Falls Sie nicht der
Adressat dieser E-Mail sind, nehmen Sie Verbindung mit dem Absender auf und
löschen Sie diese Mitteilung. Jede unbefugte Verwendung der in dieser
Mitteilung enthaltenen Informationen ist untersagt.
This message is intended only for the use of the named recipient(s) and may
contain confidential and/or privileged information. If you are not the
intended recipient, please contact the sender and delete this message. Any
unauthorized use of the information contained in this message is prohibited.


On Wed, Jun 3, 2020 at 7:40 PM Navdeep Sidhu  wrote:

> Dear Jiyuan,
>
> There was a similar question on the bulletin board some 6 years ago; my
> response then (links below) complements some of the other great
> suggestions already made in answer to your question:
>
>  >,
> and
>  >.
>
> I believe some 90% of small molecule structures are solved using the
> SHELX suite of programs by Prof. Sheldrick, so that should be a great
> start. The programs are very easy to use, with great defaults. (There
> used to be a joke that to solve this or that problem, all you had to do
> is start one of his programs and press enter 5 times.)
>
> As before, I'd highly recommend you read Mueller et al.'s excellent book
> with detailed tutorials. It provides the data and walks you through
> detailed examples in solving and refining small molecule structures:
>
> Peter Müller, Regine Herbst-Irmer, Anthony Spek, Thomas Schneider and
> Michael Sawaya. IUCr/Oxford, 2006
> .
>
> I'm sure you'll have much fun doing small molecules in addition to large
> molecules. We all did.
>
> All the best,
> Navdeep
>
>
> ---
> On 01.06.20 23:50, Jiyuan Ke wrote:
> > Hi Everyone,
> >
> > I want to crystallize a small organic molecule. I have very limited
> > experience in small molecule crystallography. I found that the Crystal
> > Screen HT from the Hampton research is good for both small molecule and
> > macromolecule crystallization. Plan to set up a sitting drop screen just
> > like setting up protein crystallization. I don’t know if this is the
> > proper way to do it. Is the MRC sitting drop 2-well

[ccp4bb] Coot CCP4i2 extensions

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Hello CCP4bb,

I just installed the latest update and it seems to have a problem with Coot's 
CCP4i2 extensions.
The dropdown menu no longer appears when clicked so it's impossible to save to 
the i2 gui.
I've rolled back the update but the bug is still present.

Cheers,

Sam



-- 
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 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




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

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