Re: [ccp4bb] Mosflm Error Msg

[Frank von Delft]

It would be nice though if imosflm did the killing for you - it happens 
to me a large fraction of the time on windows.  (I imagine windows 
doesn't make mosflm's life easy, mind you.)


phx


On 04/02/2015 05:11, Keller, Jacob wrote:

No--but thanks to you I just found it hanging in the process manager and killed 
it, which seems to have done the trick. Guess I should have thought of that 
sooner...

Thanks for the help,

Jacob

-Original Message-
From: Edward A. Berry [mailto:ber...@upstate.edu]
Sent: Tuesday, February 03, 2015 11:51 PM
To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Mosflm Error Msg

Is the old mosflm.lp open in an editor?
Some editors will put a lock on the file which would prevent mosflm from 
overwriting or renaming it.

On 02/03/2015 11:38 PM, Keller, Jacob wrote:

Dear Crystallographers,

Has anyone come across this message before with imosflm in Win7? I think 
restarting cures it, but I've got other jobs going...

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] Mosflm Error Msg

[Keller, Jacob]

No--but thanks to you I just found it hanging in the process manager and killed 
it, which seems to have done the trick. Guess I should have thought of that 
sooner...

Thanks for the help,

Jacob

-Original Message-
From: Edward A. Berry [mailto:ber...@upstate.edu] 
Sent: Tuesday, February 03, 2015 11:51 PM
To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Mosflm Error Msg

Is the old mosflm.lp open in an editor?
Some editors will put a lock on the file which would prevent mosflm from 
overwriting or renaming it.

On 02/03/2015 11:38 PM, Keller, Jacob wrote:
> Dear Crystallographers,
>
> Has anyone come across this message before with imosflm in Win7? I think 
> restarting cures it, but I've got other jobs going...
>
> JPK
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>
>

Re: [ccp4bb] Mosflm Error Msg

[Edward A. Berry]

Is the old mosflm.lp open in an editor?
Some editors will put a lock on the file which would prevent mosflm from 
overwriting or renaming it.

On 02/03/2015 11:38 PM, Keller, Jacob wrote:

Dear Crystallographers,

Has anyone come across this message before with imosflm in Win7? I think 
restarting cures it, but I've got other jobs going...

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

[ccp4bb] Mosflm Error Msg

[Keller, Jacob]

Dear Crystallographers,

Has anyone come across this message before with imosflm in Win7? I think 
restarting cures it, but I've got other jobs going...

JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

Re: [ccp4bb] proton scattering by X-rays

[Tim Gruene]

Hi Colin,

I understood the jest, of course.

Now I got curious: At 2theta=0, the scattering from H is 1e, so I assume
the the scattering length for its nucleus is 1e/1860 = 0.00054.
According to the data from Phil Coppens web site, the atomic scattering
factor for H reaches this value at sin theta / lambda = 1.95, i.e.
d=0.26A. That's far away from the wavelength 'we' use, but not too far
off from the resolution limit on a Silver source (0.31A), is it?

I am not sure this can be totally neglected. Am I wrong?

Cheers,
Tim

On 02/03/2015 04:03 PM, Colin Nave wrote:
> Hi Tim
> Although my SHELX comment was in jest, your point illustrates the programs 
> versatility. You are also right about the flat(ish) form factor for the 
> proton.
> To get to a resolution where there is a cross over would require a very short 
> wavelength. Other processes would then dominate. A nice source for this is 
> the x-ray data booklet from LBL, in particular the chapter on scattering of 
> x-rays from electrons and atoms. 
> http://xdb.lbl.gov/Section3/Sec_3-1.html
> Interestingly fig 3-1 in this does not include coherent scattering from 
> nuclei presumably because it is negligible compared with the other processes 
> - in practice Ian was correct in saying that a proton is effectively 
> invisible to x-rays of the energy we usually use.
> 
> Colin
> 
> 
> -Original Message-
> From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
> Sent: 02 February 2015 22:08
> To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb
> Subject: Re: [ccp4bb] proton scattering by X-rays
> 
> Hi Colin,
> 
> you can add f' for every atom type in SHELXL yourself, so in that sense, it 
> has been incorporated in SHELX. Bear in mind that the nucleus is point-like 
> to X-rays at ordinary wavelengths so that it should not have a form factor 
> like the electron cloud but a constant scattering length - just as they do 
> for neutron scattering.
> 
> You can do the maths at what resolution the form factor and the constant
> 1:1860 scattering length contribution cross. It is not ridiculously small but 
> nowhere near 0.8A. Charge density people may need to take this into account, 
> but I don't know if they do.
> 
> Cheers,
> Tim
> 
> On 02/02/2015 04:03 PM, Colin Nave wrote:
>> “As you say the proton itself is invisible to X-rays.”
>> Not quite! The ratio of scattering between electrons and protons should go 
>> as the inverse square of the masses.
>> Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but 
>> doubtless it has been incorporated in to SHELX.
>> Colin
>>
>>
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
>> Ian Tickle
>> Sent: 02 February 2015 13:35
>> To: ccp4bb
>> Subject: Re: [ccp4bb] proton scattering by X-rays
>>
>>
>> Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, 
>> it must have at least some partial electron around it for the (possibly 
>> partial) covalent bond, enough to diffract X-rays anyway.  As you say the 
>> proton itself is invisible to X-rays.
>> Cheers
>> -- Ian
>>
>> On 2 February 2015 at 13:08, Peter Moody 
>> mailto:pcem1bigfi...@gmail.com>> wrote:
>> Dear BB
>>
>> I have (again) realised how limited by understanding of our subject is.
>>
>> In Nature’s online site 
>> http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
>>  there is a paper describing an X-ray structure determined with sub-atomic 
>> data (nice!).  The figures show density for H+ as well as H-. In my simple 
>> way I had assumed that any X-ray scattering from the nucleus was negligible, 
>> and that the electrons are responsible for this. I would expect a proton 
>> (i.e. H+) alone to be invisible to X-rays, and certainly not to look similar 
>> to a hydride (with two electrons in (electron density) maps. What have I 
>> missed?  Could someone please explain, or point me to a suitable reference?
>>
>> Best wishes, Peter
>> (please use peter.mo...@le.ac.uk to reply 
>> directly)
>>
>> http://www2.le.ac.uk/departments/biochemistry/staff/moody
>>
>>
>>
> 
> --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> 
> GPG Key ID = A46BEE1A
> 
> 

-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



signature.asc
Description: OpenPGP digital signature

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

[Alexandre OURJOUMTSEV]

Dear Bernhard,

For the unplaced model, it can only be a Babinet model to improve the scaling,

This is not fully true, and the flat mask correction can be used as well. 
Please look :

Fokine, A. & Urzhumtsev, A.G. (2002) "On the use of low resolution data for 
translation search in molecular replacement". Acta Cryst., A58, 72-74

Fokine, A., Capitani, G., Grütter, M.G. & Urzhumtsev, A. (2003) "Bulk-solvent 
correction for fast translation search in molecular replacement: service 
programs for AMoRe and CNS". J. Appl.Cryst., 36, 352-355.

Best regards,

Sacha Urzhumtsev


De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Bernhard Rupp 
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Envoyé : mardi 3 février 2015 14:49
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Bulk solvent correction in Phaser MR LF

Hi Fellows,

I cannot find the proper reference for the implementation of bulk solvent 
corrections in the
Phaser Molecular replacement likelihood functions.  For the unplaced model, it 
can only be a Babinet model to improve the scaling, and I believe that is 
implemented via a
Babinet rescaled function for sigma A including the coordinate error.

Can anybody help me where to find that?
Thx, BR

[ccp4bb] MrBump Behaves Strangely

[Keller, Jacob]

Dear Crystallographers,

I am trying to get MrBump to complete a partial solution, but on my windows7 
machine, the CCP4i interface essentially freezes (cannot see logfiles therein, 
nothing responds, although it does not completely die), and those log files 
which I think are the correct ones have ceased changing. Nevertheless, the 
process continues on 2 cores and 800 MB RAM as phaser.exe.

Is something broken here, maybe phaser has gone incognito mode, or something 
else? It's happened the last few days any time I've tried to run MrBump. Any 
thoughts?

...And please spare me any parathyrophobia--we don't need to beat that dead 
horse!

JPK



***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***

[ccp4bb] [Job Posting] Software developer position at DNASTAR (Madison, WI USA)

[Steve Darnell]

Greetings,

My company is hiring software developers for our structural biology group in 
Madison, WI USA. If interested, please submit applications to 
res...@dnastar.com.

Best regards,
Steve Darnell

--
DNASTAR is a leading developer of desktop computer software for molecular 
biologists. Established in 1984, our products are used by pharmaceutical, 
biotech and academic researchers in more than 65 countries. 

Due to company growth, we seek an experienced software developer to join our 
development team. Five or more years of experience using Java and C++ in a 
commercial development environment are required. Bachelor's or advanced degree 
in computer science and/or life science domain and experience developing 
software for life scientists are preferred. Position is available in our 
structural biology group, which focuses on 3D protein structure prediction, 
protein-protein docking, and computational protein engineering. 

We have a team oriented work environment, along with a competitive health, 
dental and 401k benefits package. 

To apply, send resume and salary requirements to res...@dnastar.com. No calls 
please.

--
Steve Darnell, Ph.D.
Senior Scientist
DNASTAR, Inc.
3801 Regent Street
Madison, WI 53705 USA

Re: [ccp4bb] Bulk solvent correction in Phaser MR LF

[Randy Read]

Hi Bernhard,

You're right, it's a Babinet-style correction to the SigmaA curve for the 
effect of neglecting bulk solvent in the model.  We gave a formula in equation 
19 of the main Phaser reference (McCoy et al., 2007), but actually we've 
changed the form of this since then.  It looks like the equation wasn't given 
in the documentation, so I've just updated that:

http://www.phaser.cimr.cam.ac.uk/index.php/Keywords#SOLPARAMETERS

Best wishes,

Randy Read

On 3 Feb 2015, at 13:49, Bernhard Rupp (Hofkristallrat a.D.) 
 wrote:

> Hi Fellows,
>  
> I cannot find the proper reference for the implementation of bulk solvent 
> corrections in the
> Phaser Molecular replacement likelihood functions. For the unplaced model, it 
> can only
> be a Babinet model to improve the scaling, and I believe that is implemented 
> via a
> Babinet rescaled function for sigma A including the coordinate error.
>  
> Can anybody help me where to find that?
> Thx, BR

--
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research  Tel: + 44 1223 336500
Wellcome Trust/MRC Building   Fax: + 44 1223 336827
Hills RoadE-mail: rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk

[ccp4bb] proton scattering by X-rays

[Marcus Winter]

Hi, Colin,





... I've been carrying a (very beaten up) 5'' x 3'' (April 1986) edition of the 
LBL ‘X-ray Data Booklet’ around in my briefcase for the past ¼ century or more. 
 (An invaluable reference work.)  So, I’m most pleased to follow the link that 
you refer to now, to the online version.  What progress.  Fantastic !!  
Definitely, though, I’ll not forsake this here little book.





Many Thanks and Very Best Regards,



Marcus.





-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Colin Nave
Sent: Tuesday, February 03, 2015 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] proton scattering by X-rays



Hi Tim

Although my SHELX comment was in jest, your point illustrates the programs 
versatility. You are also right about the flat(ish) form factor for the proton.

To get to a resolution where there is a cross over would require a very short 
wavelength. Other processes would then dominate. A nice source for this is the 
x-ray data booklet from LBL, in particular the chapter on scattering of x-rays 
from electrons and atoms.

http://xdb.lbl.gov/Section3/Sec_3-1.html

Interestingly fig 3-1 in this does not include coherent scattering from nuclei 
presumably because it is negligible compared with the other processes - in 
practice Ian was correct in saying that a proton is effectively invisible to 
x-rays of the energy we usually use.



Colin





-Original Message-

From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de]

Sent: 02 February 2015 22:08

To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb

Subject: Re: [ccp4bb] proton scattering by X-rays



Hi Colin,



you can add f' for every atom type in SHELXL yourself, so in that sense, it has 
been incorporated in SHELX. Bear in mind that the nucleus is point-like to 
X-rays at ordinary wavelengths so that it should not have a form factor like 
the electron cloud but a constant scattering length - just as they do for 
neutron scattering.



You can do the maths at what resolution the form factor and the constant

1:1860 scattering length contribution cross. It is not ridiculously small but 
nowhere near 0.8A. Charge density people may need to take this into account, 
but I don't know if they do.



Cheers,

Tim



On 02/02/2015 04:03 PM, Colin Nave wrote:

> “As you say the proton itself is invisible to X-rays.”

> Not quite! The ratio of scattering between electrons and protons should go as 
> the inverse square of the masses.

> Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but 
> doubtless it has been incorporated in to SHELX.

> Colin

>

>

> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

> Ian Tickle

> Sent: 02 February 2015 13:35

> To: ccp4bb

> Subject: Re: [ccp4bb] proton scattering by X-rays

>

>

> Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, 
> it must have at least some partial electron around it for the (possibly 
> partial) covalent bond, enough to diffract X-rays anyway.  As you say the 
> proton itself is invisible to X-rays.

> Cheers

> -- Ian

>

> On 2 February 2015 at 13:08, Peter Moody 
> mailto:pcem1bigfi...@gmail.com>>
>  wrote:

> Dear BB

>

> I have (again) realised how limited by understanding of our subject is.

>

> In Nature’s online site 
> http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
>  there is a paper describing an X-ray structure determined with sub-atomic 
> data (nice!).  The figures show density for H+ as well as H-. In my simple 
> way I had assumed that any X-ray scattering from the nucleus was negligible, 
> and that the electrons are responsible for this. I would expect a proton 
> (i.e. H+) alone to be invisible to X-rays, and certainly not to look similar 
> to a hydride (with two electrons in (electron density) maps. What have I 
> missed?  Could someone please explain, or point me to a suitable reference?

>

> Best wishes, Peter

> (please use 
> peter.mo...@le.ac.uk>
>  to reply

> directly)

>

> http://www2.le.ac.uk/departments/biochemistry/staff/moody

>

>

>



--

Dr Tim Gruene

Institut fuer anorganische Chemie

Tammannstr. 4

D-37077 Goettingen



GPG Key ID = A46BEE1A





--

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 attachment

Re: [ccp4bb] proton scattering by X-rays

[Colin Nave]

Hi Tim
Although my SHELX comment was in jest, your point illustrates the programs 
versatility. You are also right about the flat(ish) form factor for the proton.
To get to a resolution where there is a cross over would require a very short 
wavelength. Other processes would then dominate. A nice source for this is the 
x-ray data booklet from LBL, in particular the chapter on scattering of x-rays 
from electrons and atoms. 
http://xdb.lbl.gov/Section3/Sec_3-1.html
Interestingly fig 3-1 in this does not include coherent scattering from nuclei 
presumably because it is negligible compared with the other processes - in 
practice Ian was correct in saying that a proton is effectively invisible to 
x-rays of the energy we usually use.

Colin


-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
Sent: 02 February 2015 22:08
To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb
Subject: Re: [ccp4bb] proton scattering by X-rays

Hi Colin,

you can add f' for every atom type in SHELXL yourself, so in that sense, it has 
been incorporated in SHELX. Bear in mind that the nucleus is point-like to 
X-rays at ordinary wavelengths so that it should not have a form factor like 
the electron cloud but a constant scattering length - just as they do for 
neutron scattering.

You can do the maths at what resolution the form factor and the constant
1:1860 scattering length contribution cross. It is not ridiculously small but 
nowhere near 0.8A. Charge density people may need to take this into account, 
but I don't know if they do.

Cheers,
Tim

On 02/02/2015 04:03 PM, Colin Nave wrote:
> “As you say the proton itself is invisible to X-rays.”
> Not quite! The ratio of scattering between electrons and protons should go as 
> the inverse square of the masses.
> Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but 
> doubtless it has been incorporated in to SHELX.
> Colin
> 
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
> Ian Tickle
> Sent: 02 February 2015 13:35
> To: ccp4bb
> Subject: Re: [ccp4bb] proton scattering by X-rays
> 
> 
> Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, 
> it must have at least some partial electron around it for the (possibly 
> partial) covalent bond, enough to diffract X-rays anyway.  As you say the 
> proton itself is invisible to X-rays.
> Cheers
> -- Ian
> 
> On 2 February 2015 at 13:08, Peter Moody 
> mailto:pcem1bigfi...@gmail.com>> wrote:
> Dear BB
> 
> I have (again) realised how limited by understanding of our subject is.
> 
> In Nature’s online site 
> http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129
>  there is a paper describing an X-ray structure determined with sub-atomic 
> data (nice!).  The figures show density for H+ as well as H-. In my simple 
> way I had assumed that any X-ray scattering from the nucleus was negligible, 
> and that the electrons are responsible for this. I would expect a proton 
> (i.e. H+) alone to be invisible to X-rays, and certainly not to look similar 
> to a hydride (with two electrons in (electron density) maps. What have I 
> missed?  Could someone please explain, or point me to a suitable reference?
> 
> Best wishes, Peter
> (please use peter.mo...@le.ac.uk to reply 
> directly)
> 
> http://www2.le.ac.uk/departments/biochemistry/staff/moody
> 
> 
> 

--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


-- 
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, 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
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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

[ccp4bb] Postdoc position in Structural Characterization of the Sec Translocon machinery - Stockholm University

[Matthew Bennett]

Postdoc position in Structural Characterization of the Sec Translocon machinery.

Daniel Daley and Arne Elofsson, DBB and SciLifeLab Stockholm University


A post-doc position is immediately available in membrane biochemistry and 
structural biology at Stockholm University. The position aims to understand how 
proteins are inserted into cellular membrane by the Sec translocon. The project 
will endeavor to trap substrate proteins during the insertion process and 
determining which ancillary modules and chaperones are recruited. Downstream 
analysis will include mass spectrometry and cryo-EM. The ultimate goal is to 
provide novel structural information about the machinery by combining this 
experimental information with structural modeling.

The initial part of the project will be performed in the Daley lab at DBB and 
the cryo-EM will be done at the new facility at Stockholm University/SciLife.

 The position is funded by a grant from the University to DD and AE. The 
position is a two-year postdoc position with a full salary. Regulations at the 
University limit this position to researchers with a PhD not older than three 
years.

Applicants should possess a PhD in Biochemistry or a related discipline, and be 
proficient with standard molecular methods such as cloning and protein 
purification. A high level of motivation and good communication skills are 
required. The position will be a joint appointment between the SciLife Lab 
Stockholm and The Department of Biochemistry and Biophysics at Stockholm 
University. Requests for more information as well as applications can be sent 
to Associate Professor Daniel Daley (dda...@dbb.su.se). Please include a cover 
letter, CV and the email address of at least two references. Applications will 
remain open until the position is filled.

[ccp4bb] INSTRUCT course on Computational Tools Combining Atomic and Volume Data

[Tom Burnley]

Instruct with CCP-EM is proud to announce the following workshop:

'INSTRUCT course on Computational Tools Combining Atomic and Volume Data'

* Event Details
There is increasing overlap between structural biology disciplines, a
common example being the interpretation of volume data from electron
cryo-microscopy (cryoEM) in terms of atomic models from crystallography
(MX) and nuclear magnetic resonance spectroscopy (NMR). A wide variety of
tools exist to perform rigid-body or flexible fitting. If docking of models
is successful, then one can obtain atomistic detail of large
multi-component complexes, leading to a better understanding of cellular
machinery.

However, because of the limited resolution of cryoEM volumes, fitting of
atomic models is not straightforward, and there is a strong danger of
overfitting. The course will give an overview of the issues involved, an
introduction to selected tools from the cryoEM, MX and NMR fields, and a
discussion of validation. There will be a mixture of lectures and hands-on
practicals. The course will highlight software available from CCISB
partners.

The course is aimed at both electron microscopists wishing to interpret
their volume models, and scientists from MX/NMR looking to understand the
increasing amount of cryoEM data available. The course is open to
investigators at all levels, but participants should have collected, or be
close to collecting, relevant structural data. We will work with examples
from the PDB and EMDB, but participants can bring their own data to look at
if they wish.

The course is limited to 20 delegates which will be selected from all
applicants.  A maximum of 60 applicants can register interest.

Applications will close on Friday 20th February and the 20 successful
applicants will be notified by 2nd March.

* For more information:

https://www.structuralbiology.eu/support/whats-on/calendar-events/computational-tools-combining-atomic-and-volume-data

* For registration:

https://eventbooking.stfc.ac.uk/news-events/instruct-course--on-computational-tools-combining-atomic-and-volume-data-263

* Confirmed tutors:

Maya Topf (Birkbeck)
Alan Roseman (Manchester)
Garib Murshudov (MRC-LMB Cambridge)
Paul Emsley (MRC-LMB Cambridge)
Agnel Praveen Joseph (STFC)
Ardan Patwardhan (EBI)
Stuart McNicholas (York)

Best wishes,

Tom

-- 
Dr Tom Burnley, PhD
Science and Technology Facilities Council (STFC)
The Research Complex At Harwell
Rutherford Appleton Laboratory, R92
OX11 0FA
01235 56 7871

[ccp4bb] Bulk solvent correction in Phaser MR LF

[Bernhard Rupp (Hofkristallrat a.D.)]

Hi Fellows,

 

I cannot find the proper reference for the implementation of bulk solvent
corrections in the

Phaser Molecular replacement likelihood functions. For the unplaced model,
it can only

be a Babinet model to improve the scaling, and I believe that is implemented
via a 

Babinet rescaled function for sigma A including the coordinate error.

 

Can anybody help me where to find that?

Thx, BR

 

 

Re: [ccp4bb] serial MR / refinement

[Marcin Wojdyr]

Dear Eike,

we have a simple automation exactly for this problem: a pipeline called
DIMPLE. In Diamond it's run automatically after data collection, if the
user provided pdb file.

If you have CCP4 installed try:

dimple file.mtz file.pdb output_dir

The last arg is a directory where you want results to be put.
The results include pictures of blobs of el. density not accounted for
by the model -- places where a ligand is suspected.

Best,
Marcin


On Tue, Feb 03, 2015 at 12:00:20PM +0100, Eike Schulz wrote:
> Dear all,
> 
> I am looking for a way to automate molecular replacement and refinement 
> runs.
> 
> From ligand / fragment screening trials we have many datasets of the same 
> protein with various resolutions (2.8 – 1.2Å). The apo-structure is known 
> and well refined. The cell constants are fairly similar but not in all 
> cases identical, hence I would prefer a MR run prior to the refinement. 
> 
> I am sure this can somehow be realised with some shell-script but maybe 
> there is some more sophisticated way of realising this? 
> 
> I would also be happy for partial solutions or general advise to the 
> problem.
> 
> Best regards
> 
> Eike

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[ccp4bb] serial MR / refinement

[Eike Schulz]

Dear all,

I am looking for a way to automate molecular replacement and refinement 
runs.

>From ligand / fragment screening trials we have many datasets of the same 
protein with various resolutions (2.8 – 1.2Å). The apo-structure is known 
and well refined. The cell constants are fairly similar but not in all 
cases identical, hence I would prefer a MR run prior to the refinement. 

I am sure this can somehow be realised with some shell-script but maybe 
there is some more sophisticated way of realising this? 

I would also be happy for partial solutions or general advise to the 
problem.

Best regards

Eike

Re: [ccp4bb] OFF TOPIC: Cooling system for columns

[Roger Dodd]

Hi Chiara,

We also have an Avant at room temperature. My recommendation would be to
forgo using a water bath. Instead you can achieve a prep near enough to 4C
by doing 2 things: Firstly, keep your columns stored in the cold room or a
fridge to pre-chill them before use. Secondly, make your buffers up with
chilled water and then either put them in an ice bucket or you could get a
bottle jacket (much like a wine bottle cooler) and use that. If you want to
make extra sure of a low temperature, you could keep the ice frozen longer
using some cold packs from the freezer. GE have tested this setup with some
thermocouples and find the temperature drop across the column goes from 6C
at the top to 7C at the bottom even with a 16/600 column, so it should
definitely be fine for a shorter 10/300.

Having said all that, our local Äkta specialist from GE assures us that,
except for pathological cases, room temperature preps are generally OK,
especially if your protein is immobilised on a column - proteins are pretty
stable under those conditions. And, of course, the fraction collector can
be chilled to 6C, so as soon as your samples come off the column they will
be chilled.

--
Roger B. Dodd, PhD
Cambridge Institute for Medical Research
University of Cambridge School of Clinical Medicine
Wellcome Trust/MRC Building
Cambridge Biomedical Campus
Hills Road
Cambridge
CB2 0XY

On Tue Feb 03 2015 at 10:15:26 AM Chiara Rapisarda <
chiara.rapisa...@pasteur.fr> wrote:

> Hello,
>
> we have an AKTA Avant that we keep at room temperature. We would like to
> be able to use it for preps at 4 degrees, so we would like to keep the FPLC
> columns (type 10/30 from GE) in the cold. We were thinking of buying a
> circulating water bath and connect it somehow to the columns through a
> jacket. Has anybody had any experience with that? We looked also into
> buying the hot pocket from Fisher Scientific but it is a bit out of our
> budget.
> Any suggestions are very welcome.
>
> Chiara
>
>
>
> POSTDOC
> Structural Biology of
> Bacterial secretion
> Department of Structural Biology and Chemistry
>
> INSTITUT PASTEUR
>
> 25 rue du Docteur Roux
> 75015 Paris FRANCE
>
>
>
> *Dr. Chiara Rapisarda*
>
> *Tel : +33 (0)1.40.61.35.31*
> *Fax :**+33 (0)1.45.68.88.36*
>
> *Email: chiara.rapisarda*@pasteur.fr
>
>
>
>
>
>
>
>

[ccp4bb] OFF TOPIC: Cooling system for columns

[Chiara Rapisarda]

Hello,

we have an AKTA Avant that we keep at room temperature. We would like to be 
able to use it for preps at 4 degrees, so we would like to keep the FPLC 
columns (type 10/30 from GE) in the cold. We were thinking of buying a 
circulating water bath and connect it somehow to the columns through a jacket. 
Has anybody had any experience with that? We looked also into buying the hot 
pocket from Fisher Scientific but it is a bit out of our budget.
Any suggestions are very welcome.

Chiara



POSTDOC
Structural Biology of 
Bacterial secretion
Department of Structural Biology and Chemistry

INSTITUT PASTEUR

25 rue du Docteur Roux
75015 Paris FRANCE
 
 

Dr. Chiara Rapisarda

Tel : +33 (0)1.40.61.35.31
Fax :+33 (0)1.45.68.88.36

Email: chiara.rapisa...@pasteur.fr