Re: [ccp4bb] New density quiz

2023-08-31 Thread Martin Noble 
You sure that’s not a stray bit of polypeptide ?

On 31 Aug 2023, at 11:54, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

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your login details.
I dont know what it is - but thats a beautiful map! What was in the 
crystallisation pot, do you know?
Eleanor

On Tue, 29 Aug 2023 at 18:22, Bijelic, Aleksandar 
>
 wrote:
Dear CCP4 members,

I found the attached density in some of my structures and would highly 
appreciate suggestions what molecule this could be. The density is always 
located above an aromatic amino acid and close to the adjacent ASU (like in the 
attached picture). The mother liquid included MES/Tris as buffer, PEG8000 as 
precipitant, and ammonium sulfate as additive. Some tartrate "impurity" could 
also be included. My best guess currently is PEG. Looking forward to your 
suggestions.

Cheers
Aleks



Von meinem/meiner Galaxy gesendet




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[ccp4bb] Position in drug discovery structural biology/biophysics in Newcastle

2022-04-05 Thread Martin Noble 

Dear all,

Could I draw your attention to a great position that we have available to join 
a two year, MRC DPFS-funded project to provide structural and biophysical input 
to a drug discovery project in the CRUK Newcastle Drug Discovery Unit.

The project is pursuing an exciting structural hypothesis to develop therapies 
to address an unmet need for treatments for patients with ovarian cancer.  It 
is currently in early lead optimisation, and the post holder will be joining a 
well founded team to develop and apply techniques of structural biology 
(crystallography/cryo EM), biophysics (SPR/ITC), and cellular and cell-free 
assays to progress the project towards clinical candidate selection.

Because the work will be conducted in a group that has been instrumental in the 
development of licensed drugs, this post will offer the holder an insight into 
authentic and effective modern structure based drug discovery.  It would 
especially suit someone looking to round off their structural biology skills 
with a view to pursuing careers in academic or industrial drug discovery.

Informal approaches can be made directly to myself 
(martin.no...@newcastle.ac.uk<mailto:martin.no...@newcastle.ac.uk>) or Jane 
Endicott (jane.endic...@newcastle.ac.uk<mailto:jane.endic...@newcastle.ac.uk>), 
but anyone considering the position should apply through the Newcastle 
University portal using the URL:

https://jobs.ncl.ac.uk/job/Newcastle-Research-AssistantAssociate/778968301/

This link also offers further particulars for the post, for which the closing 
date is 22nd April.

With best wishes,

Martin




Martin Noble
Professor of Structural Biology and Anticancer Drug Design
Translational and Clinical Research Institute
Faculty of Medical Sciences
Newcastle University
Paul O’Gorman Building
The Medical School
Framlington Place
Newcastle Upon Tyne
NE2 4HH

Tel: (+44) 191 2084466
E-mail: martin.no...@ncl.ac.uk<mailto:martin.no...@ncl.ac.uk>
Drug discovery: http://research.ncl.ac.uk/drugdiscovery
Cell cycle research: http://research.ncl.ac.uk/cellcyclestructuralbiology

[cid:image006.png@01D7EB56.7C328740][cid:ACA0812E-C952-4B02-9D0E-AC7188E3F4DF@ncl.ac.uk]




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Re: [ccp4bb] CCP4i2 Export and Deposition task

2020-11-27 Thread Martin Noble 
Thanks Huw: I am equally at fault for initiating a module without documenting 
it.


On 27 Nov 2020, at 11:32, Nikolas 
mailto:nikolas.ca...@gmail.com>> wrote:

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your login details.
Dear Huw,

thanks a lot for your reply. Indeed the "Prepare and validate files for 
deposition" is the task I was using. My issue was accessing the output files, 
which was solved with your tutorial. I looking for the file in the folders when 
I should have saved it by clicking on the icons.

Thanks,
Nikolas

Il giorno gio 26 nov 2020 alle ore 23:43 Huw Jenkins 
<288da93ae744-dmarc-requ...@jiscmail.ac.uk>
 ha scritto:
Hi,

> On 26 Nov 2020, at 17:59, Nikolas 
> mailto:nikolas.ca...@gmail.com>> wrote:
>
> I am trying to prepare and export the files for a structure solved in CCP4i2 
> but so far the only tasks available are the "Prepare and validate" and "Merge 
> experimental data .." tasks.

Yes the first of these "Prepare and validate files for deposition" is the one 
you want.

> I have tried to look for the tutorial but both the icon and the input page 
> illustrated are different from the ones I can see in the software.

Is this the one found from "Help/Tutorials" - > "Task Documentation" within 
CCP4i2? Unfortunately that appears to be an outdated list of documentation and 
so links to the old (CCP4-7.0) "Prepare files for deposition" task. As you've 
spotted the interface has changed completely in CCP4-7.1.

Probably the closest thing to documentation for the new task is my presentation 
at this year's CCP4 study weekend 
here:https://www.youtube.com/watch?v=hd3pKgLpLM8=420

Apologies - writing documentation for this has been on my to-do list for a long 
time.

Best regards,


Huw


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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 

Hi Stuart,

If the wait til Python3 is the issue, surely we are close to pushing the 
trigger ?
Are we confident that other things (like fortran libraries and ad-hos python 
and shell scripts) are good to go ?

M.

Sent from my iPad

On 18 Nov 2020, at 10:13, Stuart McNicholas  
wrote:


Possibly. But i2 itself cannot be fully international until Python3, since 
sqlite in Python2 does not support unicode. Unless we drop sqlite, of course, 
but there will be other libraries that cause problems.

On Wed, 18 Nov 2020 at 09:44, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Thanks Stuart,

Of course, since we ar enow in teh 21st Century, maybe we should make these 
problems go away, if necessaryby dropping those elements of the suite that 
can’t handle international, modeern scientists ?


Sent from my iPad

On 18 Nov 2020, at 09:20, Stuart McNicholas 
mailto:stuart.mcnicho...@york.ac.uk>> wrote:


Yes, Martin, we should. I think we're catching and warning about non-ASCII now. 
I'll check if whitespace is in the check as well, and if not add it.

On Wed, 18 Nov 2020 at 09:12, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>>
 wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk<mailto:2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk<mailto:kevin.cow...@york.ac.uk>
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437<https://orcid.org/-0002-0189-1437>
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://w<http://www.york.ac.uk/docs/disclaimer/email.htm>ww.york.ac.uk/docs/disclaimer/email.htm<http://www.york.ac.uk/docs/disclaimer/email.htm>


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk<mailto:kevin.cow...@york.ac.uk>
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437<https://orcid.org/-

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 
Thanks Stuart,

Of course, since we ar enow in teh 21st Century, maybe we should make these 
problems go away, if necessaryby dropping those elements of the suite that 
can’t handle international, modeern scientists ?


Sent from my iPad

On 18 Nov 2020, at 09:20, Stuart McNicholas  
wrote:


Yes, Martin, we should. I think we're catching and warning about non-ASCII now. 
I'll check if whitespace is in the check as well, and if not add it.

On Wed, 18 Nov 2020 at 09:12, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk<mailto:19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>>
 wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk<mailto:2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk<mailto:kevin.cow...@york.ac.uk>
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437<https://orcid.org/-0002-0189-1437>
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://w<http://www.york.ac.uk/docs/disclaimer/email.htm>ww.york.ac.uk/docs/disclaimer/email.htm<http://www.york.ac.uk/docs/disclaimer/email.htm>


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk<mailto:kevin.cow...@york.ac.uk>
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437<https://orcid.org/-0002-0189-1437>
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://w<http://www.york.ac.uk/docs/disclaimer/email.htm>ww.york.ac.uk/docs/disclaimer/email.htm<http://www.york.ac.uk/docs/disclaimer/email.htm>



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Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

2020-11-18 Thread Martin Noble 
Should be caught in ccp4.setup-sh ? Or in ccp4i2 launch binary ?


Sent from my iPad

On 17 Nov 2020, at 13:13, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk> wrote:



⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Dear Kevin,
   Glad you worked it out. Sorry I missed earlier messages. This is another 
common Windows problem - not just spaces either, but anything not ASCII 
alphanumeric is likely to cause problems.

Stuart

On Tue, 17 Nov 2020 at 12:54, Kevin Cowtan 
<2ba34e97fcaf-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi all

The problem turned out to be that the user had a space in their username. 
Creating a new account solved it.

Regards,

On Tue, 17 Nov 2020 at 10:23, Kevin Cowtan 
mailto:kevin.cow...@york.ac.uk>> wrote:
Hi!

I have a student trying to run i2, and a task to import merged data from cif 
which works fine for the other students is failing at the pointless step.

The logfiles are identical up to pointless (apart from the random free-R flag 
assignment), but the problem occurs in pointless. The log file output is as 
follows:


 Input command lines 


# Task 4.3.1 pointless running pointless

# Mini-MTZ input to HKLIN:

#   Data type   parameter  jobannotation

NAME PROJECT 2b463 CRYSTAL xtal DATASET dest

HKLIN 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\4_2b463_obsout_import_merged.mtz

HKLOUT 
C:\Users\xxx\CCP4I2_PROJECTS\2b463\CCP4_JOBS\job_4\job_3\job_1\MTZUNMERGEDOUT.mtz

choose spacegroup P 61


 End of input



**

**

* POINTLESS  *

*   1.12.2   *

**

*   Determine Laue group from unmerged intensities   *

* Phil Evans MRC LMB, Cambridge  *

* Uses cctbx routines by Ralf Grosse-Kunstleve et al.*

**

**



 ERROR 


$TEXT:Reference: $$ Please cite $$

P.R.Evans, 'Scaling and assessment  of data quality' Acta Cryst. D62, 72-82  
(2006).

http://journals.iucr.org/d/issues/2006/01/00/ba5084/index.html;>

PDF

P.R.Evans, 'An introduction to data reduction: space-group determination, 
scaling and intensity statistics' Acta Cryst. D67, 282-292 (2011)

http://journals.iucr.org/d/issues/2011/04/00/ba5158/index.html;>

PDF

$$


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm


--
Professor Kevin Cowtan
Email:  kevin.cow...@york.ac.uk
Pronouns:   Please use he/him or they/them when referring to me in professional 
contexts
Address:York Structural Biology Laboratory, Department of Chemistry
University of York, York, YO10 5DD, UK
ORCiD:  -0002-0189-1437
Web:https://www.york.ac.uk/chemistry/staff/academic/a-c/kcowtan/
Disclaimer: 
http://www.york.ac.uk/docs/disclaimer/email.htm



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Re: [ccp4bb] CCP4 tutorials (files)

2020-07-30 Thread Martin Noble 
Hi Rafael,

CCP4 ships with lots of tutorial data.

If you launch CCP4i2, then there is a Help/Tutorials menu which will introduce 
those techniques through CCP4i2, and help you identify file locations if you 
want to have a crack at command line structure determination.

Best wishes

Martin

On 30 Jul 2020, at 15:10, Rafael Marques 
mailto:rafael_mmsi...@hotmail.com>> wrote:

⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Hello folks.

During the quarantine I am trying to use some softwares on CCP4 that I have 
never used before and also to learn how to solve structures differently than 
the usual MR (for me). However, the ccp4 tutorial website is down and error 404 
is everywhere. Does anybody know a link where I can find files for doing SAD, 
MAD, MR, SIRAS and so on?

Many thanks in advance

__

Rafael Marques da Silva
Mestrando em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +55 16 99766-0021

   "A sorte acompanha uma mente bem treinada"





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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

2020-06-09 Thread Martin Noble 
Dear all,

This is a very good idea for development: with many of us port-forwarding to 
access resources from home, the capacity to specify a non-standard port for ssh 
connections in i2 can in principle allow submission from a home laptop to a 
work-based server…very efficient !

Please keep me in the loop if this fix has worked, and i may end up using it 
myself.

With best wishes,

Martin

On 9 Jun 2020, at 09:17, Stuart McNicholas 
<19a0c5f649e5-dmarc-requ...@jiscmail.ac.uk>
 wrote:

⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.
Dear Michael,
   I think that the port number is hardwired in CCP4i2 on line 439 of 
$CCP4/share/ccp4i2/core/CCP4JobServer.py

transport = paramiko.Transport((sP.machine, 22))

also there are various calls to the "paramiko" library which handles ssh, which 
do not pass a port number and so default to 22.

This is all bad.

I have attached a replacement for this file. Could you try making a backup of 
the above file and copying the attached file in its place.
I have put a constant for the port number in the line

PARAMIKO_PORT=22

near the top of the file. Then change this port number for what is suitable for 
you.

If this works, then I will make the port number an option in the program. If 
not, then I will try something else.


Best wishes,
Stuart McNicholas

On Mon, 8 Jun 2020 at 17:40, Michael Weyand 
mailto:michael.wey...@uni-bayreuth.de>> wrote:
Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] A grumble

2019-11-10 Thread Martin Noble 
So does the CCP4 program csymmatch
Best wishes,
Martin


On 10 Nov 2019, at 16:55, R. D. Oeffner 
mailto:rd...@cam.ac.uk>> wrote:

The program phenix.famos (or phenix.find_alt_orig_sym_mate) does exactly that 
for a pair of pdb files.

Robert

From: Eugene Osipov
Sent: Sunday, November 10, 2019 11:49 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] A grumble
By the way, may be someone has a script to move several isomorphous structures 
to the same origin and rename chains according to reference structure?


пт, 8 нояб. 2019 г. в 14:02, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
I have just downloaded two isomorphous coordinates from the pdb
5arb and 5arc  deposited by the same team


Tried to compare and they are on different origins.

I know it doesnt affect the crystallography
It is easily corrected

BUT it seems bad practice to me

Eleanor




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--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O


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Re: [ccp4bb] conversion from pdb to cif format changes R factors ... why?

2018-10-03 Thread Martin Noble 
On observation is that I have a brand new pipeline for this that will be 
released as soon as the main distribution has
gemmi installed…this is based on far newer code developed by John Berrisford 
and Eugene Krissinel.  It does, however,
still rely on a zero cycle REFMAC run...

On 3 Oct 2018, at 12:16, Martin Noble 
mailto:martin.no...@newcastle.ac.uk>> wrote:

I will check that there is not a new keyword that needs to be set for TLS to be 
used as provided.
M.


On 3 Oct 2018, at 12:09, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:

That was my thought exactly. Eleanor has been faster. Indeed if the TLS 
parameters get not passed to the refmac subjob it will not be taken into 
account. It did work previously, but there have been some changes recently and 
it might be that there is something broken now. It would be good to check this, 
because it should be fixed.

Christian

Am 03.10.2018 um 11:53 schrieb Eleanor Dodson:
That is a serious bug in the deposition task.
You can find the refmac command script if you search in the Job list 
directories. If it does not invoke TLS when there are TLS records provided that 
is a fixable bug..

Eleanor

On Wed, 3 Oct 2018 at 10:51, Antonio Ariza 
mailto:antonio.ar...@path.ox.ac.uk>> wrote:
Hi Christian,

Yes, I used TLS refinement for all the structures I deposited … but the TLS 
parameters were included in the deposition task, so I  assumed the programme 
would know that it needs to take these into account.

Anyway …  I guess that in order to correct the remarks in the headers of the 
curated coordinates in the PDB, I'll have to alter all the cif files manually 
and then resubmit them to the deposition server.


Cheers,


Tony

--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE
e-mail: antonio.ar...@path.ox.ac.uk<mailto:antonio.ar...@path.ox.ac.uk>
Tel: 00 +44 1865 285655

Links to my public profiles:
ResearchGate<https://www.researchgate.net/profile/Antonio_Ariza>
LinkedIn<https://www.linkedin.com/in/antonioariza1>
GoogleScholar<https://scholar.google.co.uk/citations?user=9pAIKV0J=en>
Twitter<https://twitter.com/DrAntonioAriza?lang=en>

Check out my latest paper!!!
Structural insights into the function of ZRANB3 in replication stress 
response<http://www.nature.com/articles/ncomms15847>



From: Christian Roth 
mailto:christianroth...@gmail.com>>
Sent: 02 October 2018 20:52
To: Antonio Ariza; CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] conversion from pdb to cif format changes R factors ... 
why?


Hi Tony,


is that for all structures or just some? I recall there was a problem when one 
has used TLS refinement. The deposition task runs a 0 cycle refmac job to 
recreate the statistics. If there is a difference, e.g no TLS included that 
might explain the difference.


Cheers


Christian

Am 02.10.2018 um 19:25 schrieb Antonio Ariza:
Hi all,

I'm wondering if anyone else has noticed this ... or is there something I am 
missing here?

One of the reviewers of my latest manuscript just pointed out that the R 
factors in my validation reports are significantly different (i.e. worse) than 
those I stated in the paper. So, I checked and indeed they are. I tracked the 
difference in the numbers down to the point where I used "Prepare files for 
deposition" in ccp4i2. This is the first time I used this programme to convert 
my pdb and mtz files into cif files, instead of trying to deposit the pdb and 
mtz files as I've always done. The conversion, however, changed the R factors 
... and seemingly nothing else as the coordinates of  both files are still the 
same.

Any idea why the programme does this? Is there another programme I can use that 
doesn't do this? It's annoying because now I have to redeposit the data for the 
10 structures I've submitted for this paper.

Here are the remarks of the pdb file and the remarks of the resulting cif file, 
as you can see they are the same except for the R factors.

PDB:
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :   1.67
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :  49.13
REMARK   3   DATA CUTOFF(SIGMA(F)) : NONE
REMARK   3   COMPLETENESS FOR RANGE(%) :  97.26
REMARK   3   NUMBER OF REFLECTIONS :   35463
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD  : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE (WORKING + TEST SET) : 0.20233
REMARK   3   R VALUE(WORKING SET) :  0.20068
REMARK   3   FREE R VALUE :  0.23658
REMARK   3   FREE R VALUE TEST SET SIZE   (%) :  4.7
REMARK   3   FREE R VALUE TEST SET COUNT  :  1759
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOL

Re: [ccp4bb] conversion from pdb to cif format changes R factors ... why?

2018-10-03 Thread Martin Noble 
I will check that there is not a new keyword that needs to be set for TLS to be 
used as provided.
M.


On 3 Oct 2018, at 12:09, Christian Roth 
mailto:christianroth...@gmail.com>> wrote:

That was my thought exactly. Eleanor has been faster. Indeed if the TLS 
parameters get not passed to the refmac subjob it will not be taken into 
account. It did work previously, but there have been some changes recently and 
it might be that there is something broken now. It would be good to check this, 
because it should be fixed.

Christian

Am 03.10.2018 um 11:53 schrieb Eleanor Dodson:
That is a serious bug in the deposition task.
You can find the refmac command script if you search in the Job list 
directories. If it does not invoke TLS when there are TLS records provided that 
is a fixable bug..

Eleanor

On Wed, 3 Oct 2018 at 10:51, Antonio Ariza 
mailto:antonio.ar...@path.ox.ac.uk>> wrote:
Hi Christian,

Yes, I used TLS refinement for all the structures I deposited … but the TLS 
parameters were included in the deposition task, so I  assumed the programme 
would know that it needs to take these into account.

Anyway …  I guess that in order to correct the remarks in the headers of the 
curated coordinates in the PDB, I'll have to alter all the cif files manually 
and then resubmit them to the deposition server.


Cheers,


Tony

--

Dr. Antonio Ariza
University of Oxford
Sir William Dunn School of Pathology
South Parks Road
Oxford
OX1 3RE
e-mail: antonio.ar...@path.ox.ac.uk
Tel: 00 +44 1865 285655

Links to my public profiles:
ResearchGate
LinkedIn
GoogleScholar
Twitter

Check out my latest paper!!!
Structural insights into the function of ZRANB3 in replication stress 
response



From: Christian Roth 
mailto:christianroth...@gmail.com>>
Sent: 02 October 2018 20:52
To: Antonio Ariza; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] conversion from pdb to cif format changes R factors ... 
why?


Hi Tony,


is that for all structures or just some? I recall there was a problem when one 
has used TLS refinement. The deposition task runs a 0 cycle refmac job to 
recreate the statistics. If there is a difference, e.g no TLS included that 
might explain the difference.


Cheers


Christian

Am 02.10.2018 um 19:25 schrieb Antonio Ariza:
Hi all,

I'm wondering if anyone else has noticed this ... or is there something I am 
missing here?

One of the reviewers of my latest manuscript just pointed out that the R 
factors in my validation reports are significantly different (i.e. worse) than 
those I stated in the paper. So, I checked and indeed they are. I tracked the 
difference in the numbers down to the point where I used "Prepare files for 
deposition" in ccp4i2. This is the first time I used this programme to convert 
my pdb and mtz files into cif files, instead of trying to deposit the pdb and 
mtz files as I've always done. The conversion, however, changed the R factors 
... and seemingly nothing else as the coordinates of  both files are still the 
same.

Any idea why the programme does this? Is there another programme I can use that 
doesn't do this? It's annoying because now I have to redeposit the data for the 
10 structures I've submitted for this paper.

Here are the remarks of the pdb file and the remarks of the resulting cif file, 
as you can see they are the same except for the R factors.

PDB:
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) :   1.67
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) :  49.13
REMARK   3   DATA CUTOFF(SIGMA(F)) : NONE
REMARK   3   COMPLETENESS FOR RANGE(%) :  97.26
REMARK   3   NUMBER OF REFLECTIONS :   35463
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD  : THROUGHOUT
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE (WORKING + TEST SET) : 0.20233
REMARK   3   R VALUE(WORKING SET) :  0.20068
REMARK   3   FREE R VALUE :  0.23658
REMARK   3   FREE R VALUE TEST SET SIZE   (%) :  4.7
REMARK   3   FREE R VALUE TEST SET COUNT  :  1759
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED   :  20
REMARK   3   BIN RESOLUTION RANGE HIGH   :1.670
REMARK   3   BIN RESOLUTION RANGE LOW:1.714
REMARK   3   REFLECTION IN BIN (WORKING SET) : 2221
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) :82.65
REMARK   3   BIN R VALUE   (WORKING SET) :0.392
REMARK   3   BIN FREE R VALUE SET COUNT  :  113
REMARK   3

[ccp4bb] Postdoctoral positions in Drug Discovery at Newcastle University

2018-09-07 Thread Martin Noble 

Dear all,

May I draw your attention to recruitment that we have in process for structural 
biologists to join our drug-discovery team here at the Northern Institute for 
Cancer Research ?

There is a deadline of 12th September for a post currently advertised at

https://www.jobs.ac.uk/job/BMG197/research-assistant-associate-structural-biology-a146128r

Structural biologists at NICR form part of an extremely enjoyable and 
pleasingly effective drug discovery program that brings together talents from 
chemistry, cancer bioscience and structure/biophysics to discover next 
generation small molecular therapies for cancer.  The structure and biophysics 
team comprises about 8 people who each work on one or more projects. Our 
responsibilities are is to make proteins, build assays, and solve structures, 
and to play a full role in the design process for iterative medicinal chemistry.

Each target has a team drawn from each of the disciplines, and teamwork is an 
essential part of what we are about.  When we are blowing Newcastle’s trumpet, 
we highlight that the group here has played important roles in delivering two 
drugs to the clinic that have been approved for cancer therapy in the last two 
years.  We are optimistic that this winning streak will continue, and are 
looking for staff who share our enthusiasm for making cutting edge structural 
and biophysical work really count.

Applicaitons should be made through the university website, but Prof. Jane 
Endicott (jane.endic...@ncl.ac.uk) or I can be 
approached informally to learn more.

With thanks and best wishes,

Martin




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[ccp4bb] Open, CRUK-supported (free to attendees ), one day meeting on structural biology in drug discovery, Newcastle 20th February 2018

2018-02-05 Thread Martin Noble 



CRUK Centre Network Meeting:
Accelerating Cancer Drug Discovery Through Structural Biology
Centre for Life, Newcastle upon Tyne, Tuesday February 20th, 2018

This free one-day meeting is open to anyone with an interest in the use of 
structural biology and fragment-based hit finding to accelerate drug discovery 
in oncology and beyond.   There are opportunities for poster presentations and 
short talks and we are keen to have lab-active researchers attend.

Highlights include:
Plenary Speaker: Peter Parker, “Mechanisms, Monitoring and Medicines”
Sessions on “What makes a good target”, “Fragment approaches” “Success stories”.
Lunchtime panel discussions on “Getting your protein into a drug discovery 
programme”, “How to find your first hit” and “Funding opportunities”

The full programme and the link to register can be found on the meeting web 
site at:

http://bit.ly/2jSxj86

Please note the revised registration deadline of Monday February 12th, 2018.


Professor Jane Endicott
Northern Institute for Cancer Research
Newcastle University
Paul O’Gorman Building
Medical School
Framlington Place
Newcastle upon Tyne
NE2 4HH UK

E-mail: jane.endic...@ncl.ac.uk
Tel: +44 (0)191 208 4422
FAX: +44 (0)191 208 4301

[ccp4bb] RA/SRA position in Drug Discovery at Newcastle University - application deadline 24/1/2018

2018-01-18 Thread Martin Noble 


Dear all,

Could I direct your attention to the availability of an RA/SRA  position to 
join the structure/biophysics team in the Drug Discovery program of the NICR, 
Newcastle University.

The post is tenable for up to 2 years, and will allow someone to join an 
extremely well resourced drug discovery team with a proven track record of 
delivering compounds into clinical use, clinical trials, or as biological 
probes in the community.  Our team works closely with academic and commercial 
partners, most recently through a deeply enjoyable alliance arrangement with 
Astex Pharmaceuticals. As suc,h this post will provide excellent exposure to 
the process of drug discovery at the interface between academia and industry.  
I, for one, absolutely love the work we do here.

Further details of the post are available at:

https://vacancies.ncl.ac.uk/ViewVacancyV2.aspx?enc=mEgrBL4XQK0+ld8aNkwYmC6FKAyPHkUPcqMIqVslWXTolydxzocO1yGR2RteD5RM+62NqK7jkZzHc0EdQQdQNYuUb7dyy44HLf7xCrKK0v6lLmKCe6c/4JYe/sqY/BNsNa2hWLrNQAAZR5HNviboNG2yopdB/y7X0lvIqWE18nc=

although informal questions can be addressed to myself 
(martin.no...@ncl.ac.uk) or Jane Endicott 
(jane.endic...@ncl.ac.uk).

With thanks and best wishes,

Martin

[ccp4bb] CRUK-supported anticancer drug discovery post in Newcastle

2015-11-11 Thread Martin Noble 
Dear all,

CRUK recently granted a Network Accelerator Award to a consortium of drug 
discovery groups (CRT Discovery labs, The Beatson Institute in Glasgow, the 
ICR, Leicester, Manchester, and Newcastle) to fund cross-institutional 
structural and biophysical work towards drug discovery.  

Through this funding, there is now a post available at the Northern Institute 
for Cancer Research in Newcastle for someone to carry out protein expression, 
purification, crystallization and structure-determination for drug-discovery 
projects drawn from diverse CRUK-funded research.

The post will be an excellent opportunity for any-one interested in drug 
discovery and in particular for someone thinking about a career in academic or 
industrial drug discovery.  It brings lots of opportunities to interact with 
colleagues at Manchester, the ICR, CRT, Glasgow, Belfast and Leicester in 
addition to Newcastle.  The post is for three years in the first instance, but 
the grant is awarded for 5 years in total.

For job details, please google

A27694T  site:ncl.ac.uk

Informal queries about the job can be made to 

Prof Jane Endicott (jane.endic...@ncl.ac.uk) or Prof Martin Noble 
(martin.no...@ncl.ac.uk).

but in any case. please make formal applicaiotn through the Newcastle 
University website.

With best wishes,

Martin

Martin Noble
Professor of Structural Biology and Anticancer Drug Design
Paul O’Gorman Building
Newcastle University Medical School, 
Framlington Place
Newcastle Upon Tyne, NE2 4HH
United Kingdom

Tel: +44 (0)191 2084466
E-mail: martin.no...@ncl.ac.uk

[ccp4bb] Studentships in Newcastle

2015-06-18 Thread Martin Noble 
Dear all,

Please find attached an advert for a Ph.D. studentship to apply structural 
biology and inhibitor design
to tackle protein arginine methyl transferases in a collaboration between the 
departments of chemistry and
the Northern Institute for Cancer Research.

Best wishes,

Martin Noble



Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 208 4466









PhDadvertNCL.pdf
Description: PhDadvertNCL.pdf

[ccp4bb] Post with Jane Endicott and Martin Noble at Newcastle University

2014-02-18 Thread Martin Noble 
Dear BBers,

I’d like to draw your attention to a post available from immediately until 
March 2016 working on interdisciplinary structural biology of CDK-containing 
complexes involved in regulating transcription and/or the cell-cycle. The post, 
which will be held at the Northern Institute for Cancer Research, provides an 
opportunity to blend X-ray crystallography with techniques spanning the 
biophysical to the cell biological.
The closing date for applications, which should deb made therough the Newcastle 
University website, is 2nd March 2014.
Job details are available at:

https://www15.i-grasp.com/fe/tpl_newcastle02.asp?newms=jjid=52465aid=14216

I found this by googling “A1762R” and Newcastle

Informal enquiries can be made to me offline.

Best wishes,

Martin

[ccp4bb] CCP4 Grant Renewal

2013-04-12 Thread Martin Noble 


Dear BBer,

As I hope you are all aware CCP4 has been well supported throughout its 
existence by BBSRC grant income. This Research Council funding is vital for the 
continued success of the CCP4 collaboration and to support its software 
development, distribution, and out-reach activities. This core funding has 
underpinned CCP4's activities and enabled us to generate commercial license 
income to complement the core grant.

On the 24th April 2013, we will be submitting  our five-yearly grant-renewal 
application to the BBSRC.  This will be reviewed over the next few months, and 
will be considered in the highly competitive, responsive mode funding meeting 
of BBSRC committee D in September/October.

We are writing to ask those of you who are keen that CCP4 should continue in 
its work to help in ensuring a positive outcome to this application.  
Historically, we have been fortunate to draw on letters of support that we have 
uploaded to the BBSRC, and which have had a number and weight that has helped 
to make the case for funding indisputable.  This year, BBSRC have indicated 
that this approach presents challenges to them in respect of identifying 
independent refereeing downstream. We are therefore proposing instead to 
collect and hold letters of support from users of the suite who wish to voice 
such support, but to provide the BBSRC with a summary analysis of those letters 
rather than with the letters themselves.

To keep numbers appropriate, we would really need to receive some sort of 
letter from PIs, Reserch Fellows, and senior postdocs.  Those letters should be 
specific about the high-impact work that CCP4 sustains, and ideally should 
reference the workplan that WG1 has agreed for the current renewal. This 
relates specifically to work packages as follows

WP0: Cloud infrastructure, facilitating mobility of data and projects from 
site to site, ( especially synchrotrons to home lab to laptop) and providing 
access to powerful compute-resources to apply challenging algorithms to 
difficult problems.  Headed up by Eugen Krissinel

WP1: Improved integration of structure-determination with data collection at 
the synchrotron.  This involves feed-forward (better data passed  from data 
analysis to structure determination) and feed-back (better informed decision 
making at the synchrotron as a result of better use of automated pipelines to 
know how useful the data are as soon as possible). Headed up by

WP2: Improved models for MR.  This is to build on AMPLE to make better models 
for molecular replacement: an exciting area that will make unsolveable 
structures solveable.  Headed by Airlie McCoy and Dan Rigden

WP3: Atom-free and reparameterized atomic refinement.  A tool to make EM-models 
and/or poor homology models into a better starting point for solving 
structures.  Not unlike the morphing from PHENIX, but significantly different 
and possibly better.  Headed by Kevin Cowtan

WP4: Extending the statistical model for refinement to confront the real-world 
issues that data is compromised (overlapped, from multiple crystals, collected 
while the crystal is being zapped by a death-star(TM) grade death beam). Headed 
by Garib Murshudov

If you are such a person, or could persuade such a person to contribute, then 
please could we ask for your help.  Letters and/or e-msils should go to Keith 
Wilson (keith.wil...@york.ac.ukmailto:keith.wil...@york.ac.uk) AS SOON AS 
POSSIBLE, and no later than 16th April.

Many thanks for your help and support,

Martin

Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466

Re: [ccp4bb] CCP4 Grant Renewal

2013-04-12 Thread Martin Noble 

Hi Phil,

Since these will be mostly used for numbers, and supplied only if BBSRC change 
their mind about wanting to see the specific letters, I would say that people 
doing high impact research (which should include anyone who has been funded), 
might contribute their penny's worth.  We will be completely transparent about 
the process that we have gone through to gauge support, and the BBSRC can make 
of it what they will.  With that said, however, I would think that individuals 
who are named recipients of support from the grant would probably be a step too 
far. That would leave you as having to write a letter :-)

best wishes,

Martin

Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466
Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466






On 12 Apr 2013, at 11:19, Phil Evans 
p...@mrc-lmb.cam.ac.ukmailto:p...@mrc-lmb.cam.ac.uk
 wrote:


I assume that Exec members should not write a letter? Or should we?
Phil

On 12 Apr 2013, at 10:46, Martin Noble 
martin.no...@newcastle.ac.ukmailto:martin.no...@newcastle.ac.uk wrote:



Dear BBer,

As I hope you are all aware CCP4 has been well supported throughout its 
existence by BBSRC grant income. This Research Council funding is vital for the 
continued success of the CCP4 collaboration and to support its software 
development, distribution, and out-reach activities. This core funding has 
underpinned CCP4's activities and enabled us to generate commercial license 
income to complement the core grant.

On the 24th April 2013, we will be submitting  our five-yearly grant-renewal 
application to the BBSRC.  This will be reviewed over the next few months, and 
will be considered in the highly competitive, responsive mode funding meeting 
of BBSRC committee D in September/October.

We are writing to ask those of you who are keen that CCP4 should continue in 
its work to help in ensuring a positive outcome to this application.  
Historically, we have been fortunate to draw on letters of support that we have 
uploaded to the BBSRC, and which have had a number and weight that has helped 
to make the case for funding indisputable.  This year, BBSRC have indicated 
that this approach presents challenges to them in respect of identifying 
independent refereeing downstream. We are therefore proposing instead to 
collect and hold letters of support from users of the suite who wish to voice 
such support, but to provide the BBSRC with a summary analysis of those letters 
rather than with the letters themselves.

To keep numbers appropriate, we would really need to receive some sort of 
letter from PIs, Reserch Fellows, and senior postdocs.  Those letters should be 
specific about the high-impact work that CCP4 sustains, and ideally should 
reference the workplan that WG1 has agreed for the current renewal. This 
relates specifically to work packages as follows

WP0: Cloud infrastructure, facilitating mobility of data and projects from 
site to site, ( especially synchrotrons to home lab to laptop) and providing 
access to powerful compute-resources to apply challenging algorithms to 
difficult problems.  Headed up by Eugen Krissinel

WP1: Improved integration of structure-determination with data collection at 
the synchrotron.  This involves feed-forward (better data passed  from data 
analysis to structure determination) and feed-back (better informed decision 
making at the synchrotron as a result of better use of automated pipelines to 
know how useful the data are as soon as possible). Headed up by

WP2: Improved models for MR.  This is to build on AMPLE to make better models 
for molecular replacement: an exciting area that will make unsolveable 
structures solveable.  Headed by Airlie McCoy and Dan Rigden

WP3: Atom-free and reparameterized atomic refinement.  A tool to make EM-models 
and/or poor homology models into a better starting point for solving 
structures.  Not unlike the morphing from PHENIX, but significantly different 
and possibly better.  Headed by Kevin Cowtan

WP4: Extending the statistical model for refinement to confront the real-world 
issues that data is compromised (overlapped, from multiple crystals, collected 
while the crystal is being zapped by a death-star(TM) grade death beam). Headed 
by Garib Murshudov

If you are such a person, or could persuade such a person to contribute, then 
please could we ask for your help.  Letters and/or e-msils should go to Keith 
Wilson (keith.wil...@york.ac.ukmailto:keith.wil...@york.ac.uk) AS SOON AS 
POSSIBLE, and no later than 16th April.

Many thanks for your help and support,

Martin

[ccp4bb] Structural biology to support anticancer drug discovery at the NICR, Newcastle University

2013-03-18 Thread Martin Noble 

Dear all,

As per the attached, we are really pleased to announce up to four positions to 
join a structural biology team supporting drug discovery in the Northern 
Institute for Cancer Research and the Chemistry Department, Newcastle 
University.  The structural biology positions, supported by an exciting 
Alliance Partnership between Newcastle University, CRT, and Astex 
Pharmaceuticals, will help to complete a highly interdisciplinary team of 
clinicians, bioscientists, and medicinal and computational chemists working to 
deliver next generation cancer therapies. We plan to appoint a Senior Research 
Associate, up to two more junior postdocs, and a technician.

If the possibility appeals, then please hunt out and complete the online 
application on the Newcastle University website 
(www.ncl.ac.uk/vacancieshttp://www.ncl.ac.uk/vacancies).

martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk or
jane.endic...@ncl.ac.ukmailto:jane.endic...@ncl.ac.uk

With best wishes,

Martin




Newcastle University has a strong track-record in cancer research and cancer 
drug discovery, hosting the Cancer Research UK Newcastle Cancer Drug Discovery 
Programme.  The programme has attracted £17M over the past 5 years in direct 
funding, and in collaboration with industry partners has generated compounds 
for clinical trials.  Currently, the programme has 5 projects at various stages 
of small-molecule drug discovery from hit identification to lead optimisation.
Astex Pharmaceuticals™ is a dynamic company striving to make an impact in the 
fight against cancer and other major diseases.  The Company has a team of 
highly qualified and motivated individuals who want to make a difference to 
patients by playing a key role in the development of novel therapies.  Great 
value is placed on strategic partnerships with leading academic institutes, 
which is seen as an important means to maximise patient benefit from 
internationally outstanding science.
Newcastle University and Cancer Research Technology have recently established a 
5-year research alliance with Astex Pharmaceuticals that will provide 
significant additional resource for the joint exploitation of innovative 
targets in cancer.  To support the expanded Programme and alliance, Newcastle 
University is seeking to recruit new staff with expertise in medicinal 
chemistry, structural biology and drug discovery bioscience.   Applicants who 
have experience in the discovery/development of small molecule anticancer 
therapeutics or validation of therapeutic targets are invited to apply, 
although high calibre candidates with expertise in other disease areas are also 
encouraged.  Further details of this exciting opportunity to join a large and 
successful team of researchers at the cutting edge of cancer drug discovery are 
available at:
www.ncl.ac.uk/vacancieshttp://www.ncl.ac.uk/vacancies
The positions can be found under the heading “Search for Job Vacancies” and 
selecting NICR. The closing date for all positions is the 10th of April. 
Interviews for the posts will be held during the weeks commencing 22nd and 29th 
of April.

Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.ukmailto:martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 246 4466

[ccp4bb] Crystallographer/Structural biologist to support anti-cancer drug discovery in Newcastle

2013-01-04 Thread Martin Noble 



Dear (and hopefully still festive) all,

We would like to draw attention to an opportunity to join the structural 
biology laboratory of Martin Noble and Jane Endicott in the Northern Institute 
for Cancer Research, Newcastle University.  This post, funded for up to 2 years 
by the MRC/DPFS, is for a crystallographer to join a team of clinical and 
translational researchers who are developing inhibitors of a promising kinase 
pathway as a potential novel strategy for the treatment of a range of tumors.

The project is at an extremely exciting stage, and the timeline for appointment 
is therefore rather short: The deadline for applications is 15th January, and 
shortlisted candidates will be notified by e-mail before Friday January 18th.  
Interviews will take place on Thursday January 24th.

Application is through the Newcastle University website, via the URL:

https://www15.i-grasp.com/fe/tpl_newcastle02.asp?newms=jjid=47164aid=14216

Best wishes,

Martin Noble and Jane Endicott

[ccp4bb] Structural Biology job vacancy

2011-04-20 Thread Martin Noble 
Structural Biologist – Crysalin Limited, Upper Heyford, Oxfordshire

Crysalin Limited is a venture capital backed structural biology company 
recently spun out of the University of Oxford’s Biophysics Laboratory. It is 
based upon the pioneering work of Professor Martin Noble and Dr. John Sinclair. 
 Crysalin is developing novel protein nanoassemblies to address the problems of 
the crystallization step in structure based drug design. 

The successful candidate will join a small group of motivated industrial 
professionals at our Upper Heyford facility focussed on this developing this 
technology.

Candidates will have significant experience of the x-ray crystallography 
process from crystal manipulation to structural refinement. Specifically the 
ideal candidate will have demonstrated experience in crystal mounting, data 
collection, structural solution and refinement. The following additional 
technical skills would be of value: molecular biology, protein purification, 
protein design and engineering, electron microscopy and atomic force 
microscopy. 

The ideal candidate will be self-motivated, have experience in team working 
environments and have proven presentation and interpersonal skills. 

Crysalin offers an opportunity to work at the cutting edge of structural 
biology research with expert groups both at the University of Oxford and at 
Crysalin.  A competitive salary and options package will be provided. 

Please reply with a C.V. to Ceri Lewis , Crysalin Limited, 77 Heyford Park, 
Upper Heyford , Oxfordshire, OX25 5HD or  Email- recruitm...@crysalin.com.

[ccp4bb] Lectureship at Laboratory of Molecular Biophysics, Oxford University

2010-01-21 Thread Martin Noble 

Dear all,

Could I draw your attention to a lectureship recently advertised here in Oxford
at the Laboratory of Molecular Biophysics ? We are looking to appoint a
new faculty member to join a growing body of structural biologists in
a beautiful new building that offers excellent facilities. Applicants should 
have a track record in interdisciplinary strutural biology, ideally including 
active NMR projects.  Deadline for applications is 29th January and, as acting 
head of the laboratory, I'd be happy to answer any questions you may have about 
the post offline.

Best wishes,

Martin Noble
=
Prof. Martin E.M. Noble
Acting Head, Laboratory of Molecular Biophysics,
New Biochemistry
South Parks Road,
Oxford OX1 3QU, U.K.

Phone: (+44) 1865 613221
e-mail:  martin.no...@bioch.ox.ac.uk




UNIVERSITY OF OXFORD

MEDICAL SCIENCES DIVISION

DEPARTMENT OF BIOCHEMISTRY

University Lecturership in Biochemistry, Structural Cell Biology - in 
association with an Official Fellowship at Somerville College

Salary £42,351 pa - £56,917 per annum 

Applications are invited for a University Lecturership in Biochemistry, 
Structural Cell Biology - in the Department of Biochemistry, Oxford University, 
a permanent academic post upon the successful completion of a probationary 
period. A Tutorial Fellowship at Somerville College is attached to this 
position.

 The successful applicant will join a team of biophysicists and structural 
biologists at the heart of a vibrant community of biomedical scientists within 
the attractive new Biochemistry Building in Oxford. The principal duty will be 
to establish and lead a world-class research programme in the area of 
structural cellular biology, exploiting multiple techniques, ideally including 
NMR spectroscopy.  The successful applicant will have, or show promise of, 
developing an international reputation for scholarship and research, and will 
contribute to and benefit from a full role in the academic life of the 
Biochemistry Department and Somerville College.

Oxford was the highest ranked biochemistry department to be individually rated 
in the recent Research Assessment Exercise, with 75% of the returned 
researchers characterised as world-leaders in their field, and structural 
biology identified as a particular strength. Appointment of this post is part 
of an extensive recruitment process within this area of research.

Committed to equality and valuing diversity

The University will especially welcome applications from women and ethnic 
minorities meeting the selection criteria, who are under-represented among its 
academic staff (section 38 of the Sex Discrimination Act 1975 and section 48 of 
the Race Relations Act 1976 apply).

Further particulars for the post are available on the university website at 
http://www.admin.ox.ac.uk/fp.  For an informal discussion, please contact 
Professor Kim Nasmyth, Professor of Biochemistry and Head of Department on: 
(01865) 613212. 

Applications (seven copies except from candidates overseas who need send only 
one), should be sent to: The Head of Department, Department of Biochemistry, 
South Parks Road, Oxford OX1 3QU, UK, quoting reference: AL09062.   The closing 
date for receipt of applications is Friday, 29 January 2010.