[ccp4bb] Phaser: tNCS present but correction not applied

2016-11-25 Thread KAUSHIK H.S. 
Hello,
I have a crystal in C2 spacegroup (94.2073 148.003 72.9967 90 97.6686 90) and 
Xtriage predicts 923 residues in ASU.  My protein could be anywhere between 95 
to 110 residues long (assuming the terminals could be cleaved).  Using a 
homolog, Phaser gives me a solution with LLG=1072 and TFZ=45.  Molrep placed 4 
protomers in the ASU however, the crystal packing is poor.
I understand from Phaser that the tNCS is not accounted for (because the 
structure is linear?).  Is there a way the exact location of the tNCS related 
protomers be predicted using information from SfCheck and Xtriage?  

Xtriage information:Fraqc. coord. : 0.500 0.000 0.000Distance to origin: 
47.104Height relative to origin: 79.688%p_value(height) : 5.283e-07
SFCHECK:
Pseudo-translation is detected: 62.6%Pseudo-translation vector: 0.500 0.000 
0.000
Sorry if my question is too naive.
Thanks in advance,Kaushik Hatti,Molecular Biophysics Unit,Indian Institute of 
Science,India.

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Vivian Saridakis 
The conversation is continuing but very positive.
Remarkable.
Vivian

> On Nov 25, 2016, at 4:55 PM, Jenny Martin (IMB) UQ  
> wrote:
> 
> A starting point would be to adopt a policy and stick to it - 
> as the ACA has done: http://www.amercrystalassn.org/speaker-policy
> Similarly SCANZ: http://www.crystal29.com/conference-policy/
> 
> For more information on how to achieve gender balance at 
> conferences/symposia/seminar series see:
> http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003903
> 
> Jenny

[ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Jenny Martin (IMB) UQ 
A starting point would be to adopt a policy and stick to it - 
as the ACA has done: http://www.amercrystalassn.org/speaker-policy 

Similarly SCANZ: http://www.crystal29.com/conference-policy/ 


For more information on how to achieve gender balance at 
conferences/symposia/seminar series see:
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003903 


Jenny

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Gerlind Sulzenbacher 

Hi Carlos and friends,

somewhere I understood that this discussion was about women in SCIENCE, 
and not about politics in general. But being a woman myself, maybe I 
understood wrongly.
Thanks Eddie and all the other sensitive people of male gender for 
bringing up and sustaining this discussion.

Happy to see what follows.
all the best,
Gerlind


Le 25/11/16 à 21:05, Carlos Pla Prats a écrit :


Like it happened when Trump won the election, someone with a slightly 
different view will reply and then we will agree to use this board 
only for science.





--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@afmb.univ-mrs.fr

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Carlos Pla Prats 
Like it happened when Trump won the election, someone with a slightly
different view will reply and then we will agree to use this board only for
science.

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Jurgen Bosch 

Just because we have modern technology doesn't mean we have socially made 
progress or for that matter made mental progress regarding women in science, 
which in my opinion is a huge mistake . Despite many efforts, many fields are 
still very male dominated.

Eddie, I like you stirring up the pot. You were already nominated recently on 
this board for president :-)

Jürgen

On Nov 25, 2016, at 12:35, Gerd Rosenbaum 
> wrote:

Very good point, Eddie.

The exclusion of females starts already with the Program Committee.

Gerd Rosenbaum

On 25.11.2016 10:48, Edward Snell wrote:

​This looks like a very interesting scientific meeting but I would just like to 
point out an observation based on the current invited speakers and program 
committee - there are also  scientists who are women in this field.


Gentleman, a little bit of effort would go a long way.


Apologies for my observation but I think this is important.




From: CCP4 bulletin board  
on behalf of Kleine, Irmtraud 

Sent: Friday, November 25, 2016 10:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 
22nd February 2017

Dear all,

This is to remind you of the 5th Banff Meeting on Structural Dynamics 
https://banff2017.desy.de/  which will take place 18/19th February – 22nd 
February 2017.
Please register now for and benefit from early-bird registration fee.

Best regards,


Irmtraud Kleine
Assistant to Professor Chapman
Deutsches Elektronen-Synchrotron DESY
Ein Forschungszentrum der Helmholtz-Gemeinschaft
Center for Free-Electron Laser Science (FS-CFEL-1)
Notkestr. 85
22607 Hamburg
Germany

Phone:  +49 40 8998 5798
Fax:+49 40 8994 5798
E-mail:   irmtraud.kle...@desy.de

Re: [ccp4bb] diffraction images simulator

2016-11-25 Thread Bernhard Rupp (Hofkristallrat a.D.) 
Contact James Holton, he has MLFSOM and other goodies.

James Holton (jmhol...@lbl.gov)

 

Best, BR

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Daniele 
de Sanctis
Sent: Friday, November 25, 2016 8:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] diffraction images simulator

 

Hi all,

I need to simulate some diffraction images and play with different parameters 
(divergence, flux, bandwitdh, beamsize, crystal size, ...), and I was wondering 
what are the most up-to-date available software . 

Thanks for your help

Daniele

-- 

ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869

Re: [ccp4bb] programmatically get mtz files from PDB_REDO

2016-11-25 Thread Robbie Joosten 
Hi Rob,

You are right that the two characters are the middle two of the PDBid. The 
server that generates the list of entries is being fixed.

Cheers,
Robbie

Verzonden vanaf mijn Windows 10-telefoon

Van: R.D. Oeffner
Verzonden: vrijdag 25 november 2016 18:52
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] programmatically get mtz files from PDB_REDO

Hi,

I would like to get mtz files via a script from the PDB_REDO server. The
documentation on http://www.cmbi.ru.nl/pdb_redo/downloads.html suggests
that the way to get the refined file, 1xhb_final.mtz, for the structure
1XHB is to run the command:

wget www.cmbi.ru.nl/pdb_redo/xh/1xhb/1xhb_final.mtz > 1xhb_final.mtz

My question is, can assume that in the URL the two characters aftethe
string, "www.cmbi.ru.nl/pdb_redo/" will always be the middle characters
of the PDB id I'm interested in?

On a separate note, the list of databank entries,
http://www.cmbi.ru.nl/WHY_NOT2/resources/list/PDB_REDO_PRESENT appears
to be dead.

Many thanks,


Rob

--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234
mobile: +44(0)7712 887162

[ccp4bb] programmatically get mtz files from PDB_REDO

2016-11-25 Thread R.D. Oeffner 

Hi,

I would like to get mtz files via a script from the PDB_REDO server. The 
documentation on http://www.cmbi.ru.nl/pdb_redo/downloads.html suggests 
that the way to get the refined file, 1xhb_final.mtz, for the structure 
1XHB is to run the command:


wget www.cmbi.ru.nl/pdb_redo/xh/1xhb/1xhb_final.mtz > 1xhb_final.mtz

My question is, can assume that in the URL the two characters after the 
string, "www.cmbi.ru.nl/pdb_redo/" will always be the middle characters 
of the PDB id I'm interested in?


On a separate note, the list of databank entries, 
http://www.cmbi.ru.nl/WHY_NOT2/resources/list/PDB_REDO_PRESENT appears 
to be dead.


Many thanks,


Rob

--
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html
tel: +44(0)1223 763234
mobile: +44(0)7712 887162

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Gerd Rosenbaum 

Very good point, Eddie.

The exclusion of females starts already with the Program Committee.

Gerd Rosenbaum

On 25.11.2016 10:48, Edward Snell wrote:


​This looks like a very interesting scientific meeting but I would 
just like to point out an observation based on the current invited 
speakers and program committee - there are also  scientists who are 
women in this field.



Gentleman, a little bit of effort would go a long way.


Apologies for my observation but I think this is important.




*From:* CCP4 bulletin board  on behalf of 
Kleine, Irmtraud 

*Sent:* Friday, November 25, 2016 10:52 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th 
Febr. - 22nd February 2017


Dear all,

This is to remind you of the 5th Banff Meeting on Structural Dynamics 
https://banff2017.desy.de/  which will take place 18/19^th February – 
22^nd February 2017.


Please register now for and benefit from early-bird registration fee.

Best regards,

Irmtraud Kleine

Assistant to Professor Chapman

Deutsches Elektronen-Synchrotron DESY

Ein Forschungszentrum der Helmholtz-Gemeinschaft

Center for Free-Electron Laser Science (FS-CFEL-1)

Notkestr. 85

22607 Hamburg

Germany

Phone:  +49 40 8998 5798

Fax:+49 40 8994 5798

E-mail: irmtraud.kle...@desy.de

Re: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Edward Snell 
?This looks like a very interesting scientific meeting but I would just like to 
point out an observation based on the current invited speakers and program 
committee - there are also  scientists who are women in this field.


Gentleman, a little bit of effort would go a long way.


Apologies for my observation but I think this is important.




From: CCP4 bulletin board  on behalf of Kleine, Irmtraud 

Sent: Friday, November 25, 2016 10:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 
22nd February 2017

Dear all,

This is to remind you of the 5th Banff Meeting on Structural Dynamics 
https://banff2017.desy.de/  which will take place 18/19th February - 22nd 
February 2017.
Please register now for and benefit from early-bird registration fee.

Best regards,


Irmtraud Kleine
Assistant to Professor Chapman
Deutsches Elektronen-Synchrotron DESY
Ein Forschungszentrum der Helmholtz-Gemeinschaft
Center for Free-Electron Laser Science (FS-CFEL-1)
Notkestr. 85
22607 Hamburg
Germany

Phone:  +49 40 8998 5798
Fax:+49 40 8994 5798
E-mail:   irmtraud.kle...@desy.de

[ccp4bb] diffraction images simulator

2016-11-25 Thread Daniele de Sanctis 
Hi all,

I need to simulate some diffraction images and play with different
parameters (divergence, flux, bandwitdh, beamsize, crystal size, ...), and
I was wondering what are the most up-to-date available software .

Thanks for your help

Daniele

-- 
ἀρετή
---
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869

[ccp4bb] 5th Banff Meeting on Structural Dynamics, 18/19th Febr. - 22nd February 2017

2016-11-25 Thread Kleine, Irmtraud 
Dear all,

 

This is to remind you of the 5th Banff Meeting on Structural Dynamics
https://banff2017.desy.de/  which will take place 18/19th February - 22nd
February 2017.

Please register now for and benefit from early-bird registration fee.

 

Best regards,

 

 

Irmtraud Kleine

Assistant to Professor Chapman

Deutsches Elektronen-Synchrotron DESY

Ein Forschungszentrum der Helmholtz-Gemeinschaft

Center for Free-Electron Laser Science (FS-CFEL-1)

Notkestr. 85

22607 Hamburg

Germany

 

Phone:  +49 40 8998 5798

Fax:+49 40 8994 5798   

E-mail: irmtraud.kle...@desy.de

Re: [ccp4bb] Unsubcribed

2016-11-25 Thread Ekiert, Damian 
Ting and CCP4ers,

I want to apologize for my unkind words, which were completely out if line.  In 
a moment of frustration, I sent this and immediately regretted it.  And with a 
twist if irony, I sent it to the entire list instead of just one user, 
precisely what I was complaining about!  I did not mean to publicly shame 
anyone, and I wish I had followed Marilyn's example and instead kindly directed 
them to instructions for unsubscribing.

I am very sorry about this!

Sincerely,

Damian

On Nov 24, 2016, at 8:29 PM, Pavel Afonine 
> wrote:

I guess I've just seen two extreme-opposite versions of something (etiquette, 
politeness?). Regardless, RM part of Damian's message is a fine idea -;) 
Everything else can be filtered out!


On Thu, Nov 24, 2016 at 7:50 PM, Yoder, Marilyn 
> wrote:
Hi Ting,

What D. Ekiert was so ungraciously saying, is that instructions to unsubscribe 
from the bulletin board can be found here: http://www.ccp4.ac.uk/ccp4/ccp4bb.php

Regards, Marilyn Yoder


Marilyn D. Yoder
School of Biological Sciences
University of Missouri-Kansas City
Kansas City, MO  64110-2499
phone: 816-235-1986


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
on behalf of Ekiert, Damian 
[damian.eki...@ucsf.edu]
Sent: Thursday, November 24, 2016 9:23 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Unsubcribed

RTFM.  Your email just spammed thousands of people...
> On Nov 24, 2016, at 3:20 PM, Ting Yi Tian 
> > wrote:
>
> Hi
>
> Please unsubscribed me from the mailing list.
>
> Thanks
>
> Ting

[ccp4bb] Bent crystal integration

2016-11-25 Thread Eugene Osipov 
Dear community,
I've collected dataset from thin protein crystal which was obviously bent
during manipulations.
Magnified spots  shape from images 90 degrees apart:
http://imgur.com/a/8nI1k
Is it possible to correctly integrate such wide spots? Does XDS correctly
detects integration box for them?
P.S.: I am trying to produce better crystals but this dataset is still the
best one I have.

-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com

[ccp4bb] Another problem after last CCP4 update...

2016-11-25 Thread Rafal Dolot 

Dear CCP4 users,

I observed problems with "Real space refine zone" in Coot after CCP4 
package last update, which revealed a complete disaster in phosphate 
groups of nucleotides...


Windows 8.1 system

Best regards,

Rafal
--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Department of Bioorganic Chemistry|
|Macromolecular Crystallography Team   |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803215 |
|Cell:  +48 502897781  |
|--|