[ccp4bb] Les Houches/TSRC Workshop on Protein Dynamics, Chamonix Valley, May 27-June 1, 2018

[martin weik]

Dear colleague,

A few participant slots remain for the *Les Houches/TSRC Workshop on 
Protein Dynamics*, to be held in *Les Houches, close to Chamonix * at 
the heart of the French Alps, from *May 27 to June 1, 2018.*


This international workshop is a forum for presenting and discussing 
results from state-of-the-art experimental approaches (including optical 
spectroscopy, NMR spectroscopy, X-ray crystallography, XFELs, electron 
microscopy, atomic-force microscopy and scattering methods), and 
theoretical and computational methods to studying protein dynamics.


The Les Houches – TSRC Protein Dynamics Workshop complements the 
long-standing TSRC Protein Dynamics Workshop, held every other year in 
the odd calendar years at the Telluride Science Research Center 
 in Telluride, Colorado. In Les 
Houches, about 30 invited speakers will give oral presentations that 
comprise a pedagogic introduction to the methodology employed, followed 
by applications from their own work. Each 30-minute presentation will be 
followed by 15 minutes of discussion. In addition to the 30 invited 
speakers, there will be space for 30 student/postdoctoral participants 
that can present posters.Itsrelatively small number of 
participantsfavorsexchangeof ideasacross disciplines and 
fosteringofcollaborations.A few slots for oral presentations are still 
available.


The Ecole de Physique des Houches can be conveniently reached from 
Geneva Airport(including the train station at the airport with direct 
connections to Zurich)by shuttle-bus service within 80 minutes .


Please find details of the program at :
https://www.sites.google.com/site/houches2018/

With best regards,

Martin Weik


--
Martin Weik
Structural Protein Dynamics Research Team
Institut de Biologie Structurale
CAMPUS EPN
71 avenue des Martyrs
CS10090
38044 Grenoble Cedex 9; France  

Phone:(33) 4 57 42 85 80


email:  w...@ibs.fr
http://www.ibs.fr/groups/dynamics-and-kinetics-of-molecular/structural-protein-dynamics/?lang=en

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Eleanor Dodson]

Use words!!!

Eleanor

On 14 March 2018 at 00:56, Paul Emsley  wrote:

> On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote:
>
>> You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side
>> menu). Just click Fix Atom and then click the atom(s) you wish to fix. It
>> won’t move in real space refinement or in regularisation.
>>
>
>
> That's right, Ana Luísa.
>
> And for the record, it's often useful to move fixed atoms. Use Ctrl
> Left-mouse click and drag. So Fixed Atoms move when nothing else moves and
> stay still when everything else refines. Paradoxical maybe, but useful. I
> use it when I have to assert my authority over recalcitrant atoms.
>
> Paul.
>

Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?

[Eleanor Dodson]

No problem with GUI2..

Eleanor

On 13 March 2018 at 22:38, Edward A. Berry  wrote:

> Thanks- that works!
> pdb-redo/tools/cif2cif in.cif out.cif
> eab
>
>
> On 03/13/2018 05:47 PM, Robbie Joosten wrote:
>
>> Hi Ed,
>>
>> The pdb-redo program cif2cif does that. I implemented this feature
>> because there was no obvious CCP4 program that did this. You have to have
>> your data in mmCIF format though.
>>
>> Cheers,
>>
>> Robbie
>>
>> Sent from my Windows 10 phone
>>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> --
>> *From:* CCP4 bulletin board  on behalf of Edward
>> A. Berry 
>> *Sent:* Tuesday, March 13, 2018 10:25:25 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] How to get Imean/SIGImean from separated anomalous
>> data?
>>
>> I want to work with an mmcif file that has I+,sigI+,I-,SigI-;
>>in different columns for each reflection (no Imean).
>> cif2mtz gives those same columns in the output mtz, with or without
>> ANOMALOUS keyword.
>> cif2mtz and truncate seem to need the anomalous data as separate
>> reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is
>> the best way to do this?
>> Thanks,
>> eab
>>
>

Re: [ccp4bb] Is it possible to fix the position of an atom during real space fitting in Coot?

[Paul Emsley]

On 14/03/2018 10:40, Eleanor Dodson wrote:

Use words!!!



I am nonplussed.

Is that what you meant?

Paul.



On 14 March 2018 at 00:56, Paul Emsley mailto:pems...@mrc-lmb.cam.ac.uk>> wrote:

On 13/03/2018 20:12, Ana Luísa Moreira de Carvalho wrote:

You can find the tool “Fixed Atoms” in the Refinement Toolbar (the side 
menu). Just click Fix Atom
and then click the atom(s) you wish to fix. It won’t move in real space 
refinement or in regularisation.



That's right, Ana Luísa.

And for the record, it's often useful to move fixed atoms. Use Ctrl 
Left-mouse click and drag. So Fixed
Atoms move when nothing else moves and stay still when everything else 
refines. Paradoxical maybe, but
useful. I use it when I have to assert my authority over recalcitrant atoms.

Paul.

Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?

[Edward A. Berry]

Thanks, that seems to work also, and with lots of nice graphical analysis.
With Task "Import merged data", or all in one go with "convert intensities to amplitudes" 
selecting the .cif file as input and option "output Imean for anomalous data", to run ctruncate on 
the result.

But I have a long way to go to get used to I2. It was disconcerting not being 
able to set the output filenames, or even find the output files except by 
listing files in the project directory.  I guess it's a new paradigm, where you 
don't need to worry about details like file names and you identify datasets by 
internal labels within the gui. And going back to the finished job, looking at 
input and options, there was very little information about exactly what had 
been done (compared to the detailed forms in ccp4i). But now I am motivated to 
learn the new system!
eab

On 03/14/2018 06:42 AM, Eleanor Dodson wrote:

No problem with GUI2..

Eleanor

On 13 March 2018 at 22:38, Edward A. Berry mailto:ber...@upstate.edu>> wrote:

Thanks- that works!
pdb-redo/tools/cif2cif in.cif out.cif
eab


On 03/13/2018 05:47 PM, Robbie Joosten wrote:

Hi Ed,

The pdb-redo program cif2cif does that. I implemented this feature 
because there was no obvious CCP4 program that did this. You have to have your 
data in mmCIF format though.

Cheers,

Robbie

Sent from my Windows 10 phone




-
-

*From:* CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
on behalf of Edward A. Berry mailto:ber...@upstate.edu>>
*Sent:* Tuesday, March 13, 2018 10:25:25 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] How to get Imean/SIGImean from separated anomalous 
data?

I want to work with an mmcif file that has I+,sigI+,I-,SigI-;
in different columns for each reflection (no Imean).
cif2mtz gives those same columns in the output mtz, with or without 
ANOMALOUS keyword.
cif2mtz and truncate seem to need the anomalous data as separate 
reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is the 
best way to do this?
Thanks,
eab

Re: [ccp4bb] How to get Imean/SIGImean from separated anomalous data?

[Christian Roth]

It's quite a change compared to i1, but worth to learn it.

On Wed, Mar 14, 2018 at 5:33 PM, Edward A. Berry  wrote:

> Thanks, that seems to work also, and with lots of nice graphical analysis.
> With Task "Import merged data", or all in one go with "convert intensities
> to amplitudes" selecting the .cif file as input and option "output Imean
> for anomalous data", to run ctruncate on the result.
>
> But I have a long way to go to get used to I2. It was disconcerting not
> being able to set the output filenames, or even find the output files
> except by listing files in the project directory.  I guess it's a new
> paradigm, where you don't need to worry about details like file names and
> you identify datasets by internal labels within the gui. And going back to
> the finished job, looking at input and options, there was very little
> information about exactly what had been done (compared to the detailed
> forms in ccp4i). But now I am motivated to learn the new system!
> eab
>
> On 03/14/2018 06:42 AM, Eleanor Dodson wrote:
>
>> No problem with GUI2..
>>
>> Eleanor
>>
>> On 13 March 2018 at 22:38, Edward A. Berry > ber...@upstate.edu>> wrote:
>>
>> Thanks- that works!
>> pdb-redo/tools/cif2cif in.cif out.cif
>> eab
>>
>>
>> On 03/13/2018 05:47 PM, Robbie Joosten wrote:
>>
>> Hi Ed,
>>
>> The pdb-redo program cif2cif does that. I implemented this
>> feature because there was no obvious CCP4 program that did this. You have
>> to have your data in mmCIF format though.
>>
>> Cheers,
>>
>> Robbie
>>
>> Sent from my Windows 10 phone
>>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>
> -
> -
>
>> *From:* CCP4 bulletin board > CCP4BB@JISCMAIL.AC.UK>> on behalf of Edward A. Berry > >
>> *Sent:* Tuesday, March 13, 2018 10:25:25 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK 
>> *Subject:* [ccp4bb] How to get Imean/SIGImean from separated
>> anomalous data?
>>
>> I want to work with an mmcif file that has I+,sigI+,I-,SigI-;
>> in different columns for each reflection (no Imean).
>> cif2mtz gives those same columns in the output mtz, with or
>> without ANOMALOUS keyword.
>> cif2mtz and truncate seem to need the anomalous data as separate
>> reflections hkl and -h-k-l in order to calculate Imean or Fmean. What is
>> the best way to do this?
>> Thanks,
>> eab
>>
>>
>>