[ccp4bb] FW: Stanford-SLAC Cryo-EM Center (S2C2) Image Processing Workshop for Cryo-Electron Microscopy

[Polizzi, JoAnn]

We are pleased to announce the upcoming 2023 Image Processing Workshop for 
Cryo-Electron 
Microscopy
 at Stanford-SLAC Cryo-EM Center (S2C2) on May 17-19, 2023.  The workshop will 
alternate theoretical discussions with practical examples using experimental 
data with a main focus on Single Particle Analysis (SPA).  We will demonstrate 
simultaneously how to apply different software packages at different stages of 
the image processing pipeline (like Relion, Xmipp, CryoSPARC, among others), a 
task that we will achieve transparently using the software integration 
framework Scipion.  We will also address some advanced topics in Tomography in 
which an extra degree of robustness can be introduced along similar lines as 
those introduced in SPA with the help of Scipion running iMod, EMAN, Relion, 
Dynamo, and Xmipp. Attendees are expected to be familiar with standard image 
processing pipelines in Single Particle Analysis. On the last day the talks on 
theory and practices will focus on advanced image processing topics, as well as 
their connection with molecular motion, 3D visualization, atomic modeling, 
structure validation, and drug design.

This will be a hybrid workshop.  Due to available resources, we will have only 
50 spots for onsite hands-on practical participation with all others attending 
via Zoom.

We welcome all to register at the following link: 2023 Image Processing 
Workshop for Cryo-Electron Microscopy | S2C2 |Stanford-SLAC Cryo-EM 
Center.
  You will also need to fill out an online conference access form  Conference 
Attendee | Coming to SLAC 
(stanford.edu),
 required by SLAC guidelines. These steps must be completed in order to be 
considered for both "Practical" and "Zoom" participation.

The registration deadline for in-person participation is April 10, 2023.  
Notification of acceptance to the first-round of "Practical" participants will 
be sent out on April 14, all others will receive notice beginning April 17.  
The deadline for virtual participation is May 5, 2023.  Zoom details for this 
workshop will be sent with notifications of acceptance.
The S2C2 is supported by the National Institutes of Health Common Fund 
Transformative High Resolution Cryo-Electron 
Microscopy
 program.




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Eleanor Dodson]

I am asked to test ZANADU which is meant to sort out spacegroup anomalies!
Maybe your example can be the test case..
Eleanor

On Fri, 24 Mar 2023 at 14:21, Gianluca Cioci  wrote:

> Hi Eleanor, Hi All,
>
> As suggested by Andrew (thanks!), I've switched off the NCS in Phaser and
> this gave a solution in C2 (a=66.2 b=83.9  c=66.2   90  98.7  90) that
> refines much better than the others (R=0.32/0.39).
>
> Still, I am not 100% convinced this is the correct cell/spacegroup... but
> it's a good starting point to continue the investigation.
>
> Thanks to all for your help !
>
> GIA
>
>
>
>
> Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :
>
> You have tried all spacegroups within point groups? P2 p21 c222 c2221?.
>
> On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:
>
>> If data processing to be ok and all possible monoclinic and orthorombic
>> SG gave unreasonable high Rs, maybe good to give a try with p1 space group?
>>  Since the p-lattice indexing gave same a and  b also very close alpha
>> and beta, it could not exclude the possibility of p1 then twinned (also
>> together with ncs and tNCS) to show higher symmetry?
>>
>> Sent from my iPhone
>>
>> On Mar 21, 2023, at 1:25 PM, Jessica Bruhn 
>> wrote:
>>
>> 
>>
>> Hi Gianluca,
>>
>> Have you checked for diffraction anisotropy problems? It might be worth
>> running it through the STARANISO webserver:
>> https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi. Anisotropy
>> can make your data look twinned and elliptical truncation can help improve
>> maps.
>>
>> Good luck!
>>
>> Best,
>> Jessica
>>
>> On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper <
>> 488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Hello, can you give us a screenshot of a diffraction image, with the
>>> caveat that they never look all that good with fine-slicing, still it might
>>> help ;-0 Also, an idea of the R-merge, R-meas, CC-half in some of those
>>> space groups.
>>>
>>> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>>>
>>> Sent from Proton Mail mobile
>>>
>>>
>>>
>>>  Original Message 
>>> On 21 Mar 2023, 16:43, Gianluca Cioci <
>>> 8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:
>>>
>>>
>>> Dear All,
>>>
>>> I have collected a dataset from a small protein diffracting at 2.7A
>>> resolution, here is the space-group determination from XDS:
>>>
>>>  *  44aP  0.0  66.3   66.3   83.9  90.2  90.1  98.7
>>>  *  31aP  1.2  66.3   66.3   83.9  89.8  90.1  81.3
>>>  *  14mC 1.3  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  34mP 2.9  66.3   83.9   66.3  90.2  98.7  90.1
>>>  *  13oC  3.7  86.4  100.6   83.9  90.0  90.2  90.0
>>>  *  10mC 4.9 100.6   86.4   83.9  89.8  90.0  90.0
>>>
>>> Clearly, something weird is going on...
>>>
>>> The structure can be solved in C2/P21/C2221 with different number of
>>> molecules in the AU, with Phaser complaining about strong tNCS modulation.
>>>
>>> However the maps look bad and the structure is impossible to refine
>>> (Rfact > 0.5) in all the space-groups that I have tried so far...
>>>
>>> Thanks in advance for any advice on how to rescue these data !
>>>
>>> Cheers,
>>>
>>> GIA
>>>
>>>
>>> [image: Click to zoom the image]
>>>
>>>
>>> --
>>> Dr. Gianluca CIOCI
>>> Toulouse Biotechnology Institute 
>>> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
>>> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr/
>>>
>>> Tel: +33 (0)5 61 55 97 68
>>> E-mail: ci...@insa-toulouse.fr
>>>
>>> TBI - INSA Toulouse135 avenue de Rangueil 
>>> 
>>> 31077 Toulouse CEDEX 04http://www.toulouse-biotechnology-institute.fr
>>>
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>>
>>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> --
> Dr. Gianluca CIOCI
> Toulouse Biotechnology Institute 
> (TBI)http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
> PICT - Plateforme Intégrée de Criblage de Toulousehttp://www.pict.ipbs.fr

Re: [ccp4bb] twin, pseudosymmetry and NCS in P2/C2 ?

[Gianluca Cioci]

Hi Eleanor, Hi All,

As suggested by Andrew (thanks!), I've switched off the NCS in Phaser 
and this gave a solution in C2 (a=66.2 b=83.9  c=66.2   90 98.7  90) 
that refines much better than the others (R=0.32/0.39).


Still, I am not 100% convinced this is the correct cell/spacegroup... 
but it's a good starting point to continue the investigation.


Thanks to all for your help !

GIA




Le 22/03/2023 à 07:10, Eleanor Dodson a écrit :

You have tried all spacegroups within point groups? P2 p21 c222 c2221?.

On Wed, 22 Mar 2023 at 03:01, Lijun Liu  wrote:

If data processing to be ok and all possible monoclinic and
orthorombic SG gave unreasonable high Rs, maybe good to give a try
with p1 space group? Since the p-lattice indexing gave same a and
 b also very close alpha and beta, it could not exclude the
possibility of p1 then twinned (also together with ncs and tNCS)
to show higher symmetry?

Sent from my iPhone


On Mar 21, 2023, at 1:25 PM, Jessica Bruhn
 wrote:


Hi Gianluca,

Have you checked for diffraction anisotropy problems? It might be
worth running it through the STARANISO webserver:
https://staraniso.globalphasing.org/cgi-bin/staraniso.cgi.
Anisotropy can make your data look twinned and elliptical
truncation can help improve maps.

Good luck!

Best,
Jessica

On Tue, Mar 21, 2023 at 11:17 AM Jon Cooper
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello, can you give us a screenshot of a diffraction image,
with the caveat that they never look all that good with
fine-slicing, still it might help ;-0 Also, an idea of the
R-merge, R-meas, CC-half in some of those space groups.

Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Sent from Proton Mail mobile



 Original Message 
On 21 Mar 2023, 16:43, Gianluca Cioci <
8d6e5314cb4c-dmarc-requ...@jiscmail.ac.uk> wrote:


Dear All,

I have collected a dataset from a small protein
diffracting at 2.7A resolution, here is the space-group
determination from XDS:

 *  44    aP  0.0  66.3 66.3   83.9 
90.2  90.1  98.7
 *  31    aP  1.2  66.3 66.3   83.9 
89.8  90.1  81.3
 *  14    mC 1.3  86.4 100.6   83.9 
90.0  90.2  90.0
 *  34    mP 2.9  66.3 83.9   66.3  90.2 
98.7  90.1
 *  13    oC  3.7  86.4 100.6   83.9 
90.0  90.2  90.0
 *  10    mC 4.9 100.6 86.4   83.9  89.8 
90.0  90.0

Clearly, something weird is going on...

The structure can be solved in C2/P21/C2221 with
different number of molecules in the AU, with Phaser
complaining about strong tNCS modulation.

However the maps look bad and the structure is impossible
to refine (Rfact > 0.5) in all the space-groups that I
have tried so far...

Thanks in advance for any advice on how to rescue these
data !

Cheers,

GIA


Click to zoom the image


--
Dr. Gianluca CIOCI
Toulouse Biotechnology Institute (TBI)

http://www.toulouse-biotechnology-institute.fr/en/research/enzyme-molecular-engineering-and-catalysis/cimes.html
PICT - Plateforme Intégrée de Criblage de Toulouse
http://www.pict.ipbs.fr/

Tel: +33 (0)5 61 55 97 68
E-mail:ci...@insa-toulouse.fr

TBI - INSA Toulouse
135 avenue de Rangueil  

31077 Toulouse CEDEX 04
http://www.toulouse-biotechnology-institute.fr





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







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






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




---

[ccp4bb] Final Registration - 9th CCP-EM Spring Symposium 25-27th April 2023

[Tom Burnley - STFC UKRI]

Dear all,

Final reminder that registration for the CCP-EM Symposium closes today (Friday 
24th March).

Registration link and more conference details here…

https://www.ccpem.ac.uk/training/spring_symposium_2023/spring_symposium_2023.php

* Applying for a talk
As in previous years we are seeking a number of additional talks selected from 
submitted abstracts.
If interested, please submit a proposed title and abstract during registration 
for consideration by the scientific organisers or submit a talk title and 
abstract (up to 500 words) directly by email to:

ccpemeve...@stfc.ac.uk.

Please also include your name, position, group and institute.  We are 
particularly interested in abstracts with a computational focus e.g. new 
algorithms or methods for the spring symposium. For the BCI user meeting we 
welcome new results that have been made possible by use of eBIC in the last 
12-18 months.  Deadline for abstract submission is Friday 31st March.

* BCI User Survey
Please can all Diamond users of BCI facilities complete the survey by 11th 
April (see link below).  During the user meeting representatives from eBIC, B24 
and the Membrane Protein Lab (MPL) will discuss topics raised in the User 
Survey and welcome your feedback and support:

https://forms.office.com/pages/responsepage.aspx?id=dLonnQABDU2B_x1yja6N9k2iEV9rkoVBsESt7IZg17BUMk9XVzdDTUoyMTJERUg1N1JZUURFRzZKSy4u

All the best from CCP-EM & DLS BCI




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

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/