[ccp4bb] Rfree going up after refinement

[张士军]

Dear all

I have got my se-phase structure with ccp4-CRANK2-SAD, and its Rfree is 0.26 
when CRANK2 output, but the Rfree is higher to 0.36 when I refine it with 
refmac or phenix-refinement. does it mean I got a wrong phase, or I didn't got 
the right parameters when refinement.BTW, the resolution is 2.1A.THANKS A LOT

Best Regards

shijun

Re: [ccp4bb] determining the point group and the space group

[Gihan Ketawala]

Thanks a lot for your input

Best,
Gihan

> On Apr 19, 2018, at 9:56 AM, Rezaul Karim  wrote:
> 
> 
> 
> 
> On Thu, Apr 19, 2018 at 11:32 AM, Rezaul Karim
>  wrote:
> I think Graeme's point is right. This is the work expert crystallographer. By 
> the way, DIALS could be used for XFEL data, as the program page & recent 
> publication indicates. NB: I have no experience in XFEL data.
> 
> Thanks,
> Rezaul
> 
> Sent from Yahoo Mail on Android 
> 
> On Wed, Apr 18, 2018 at 9:13 PM, Gihan Ketawala
>  wrote:
> Hi,
> my question is;
> how should one determine a point group and the space group of an unknown 
> crystal?
> 
> I have a protein crystal with know unit-cell parameters. (these are XFEL data 
> so indexing wouldn't give the point and space groups). I checked the PDB, but 
> no luck the PDB structures have the different space group assigned, no 
> definitive answer 
> hopefully, somebody can point me in the right direction 
> 
> Best,
> Gihan

Re: [ccp4bb] According correct space group assignment...

[Diana Tomchick]

Several years ago I solved a small RNA structure by direct methods using the 
CCP4 program ACORN, and built the model using Nautilus. This was with data to 
only 1.25 Å resolution, collected at the Se edge, so there was no significant 
anomalous signal.

I think that this worked like a charm because the crystal probably diffracted 
to around 1 Å resolution, but due to beam line hardware issues, I decided it 
wasn’t worth it to try to collect the higher resolution data.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
University of Texas Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Apr 20, 2018, at 2:35 PM, Randy Read  wrote:

I think that starting with a direct methods program like shelxt would be fun.  
If that doesn’t work, it could be interesting to try to solve it by molecular 
replacement with fragments varying from a tetraplex, a base pair or even just 
single bases.  (Assuming that Phoebe’s concern about twinning does not turn out 
to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +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

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
>
> Dear Rafal,
>
> shelxt does not require the space group, it only needs the Laue group. If it
> finds a decent solution, it'll find also the space group for you.
>
> Best,
> Tim
>
> On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
>> Dear CCP4BB,
>>
>> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
>> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
>> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this
>> size of the molecule. 11mer is rich in G, so we expect the G-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>>
>> Best regards,
>>
>> Rafal
>
> --
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A




UT Southwestern


Medical Center



The future of medicine, today.

Re: [ccp4bb] According correct space group assignment...

[Randy Read]

I think that starting with a direct methods program like shelxt would be fun.  
If that doesn’t work, it could be interesting to try to solve it by molecular 
replacement with fragments varying from a tetraplex, a base pair or even just 
single bases.  (Assuming that Phoebe’s concern about twinning does not turn out 
to be correct…)

Best wishes,

Randy Read

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +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

> On 20 Apr 2018, at 20:09, Tim Gruene  wrote:
> 
> Dear Rafal,
> 
> shelxt does not require the space group, it only needs the Laue group. If it 
> finds a decent solution, it'll find also the space group for you.
> 
> Best,
> Tim
> 
> On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
>> Dear CCP4BB,
>> 
>> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
>> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
>> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this
>> size of the molecule. 11mer is rich in G, so we expect the G-tetraplex
>> formation. Data were collected to almost 1 A, so it should be enough for
>> trials with direct methods/ab initio solution. What I should do first to
>> find correct SG and/or cell parameters?
>> 
>> Best regards,
>> 
>> Rafal
> 
> -- 
> --
> Paul Scherrer Institut
> Tim Gruene
> - persoenlich -
> OSUA/204
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
> 
> GPG Key ID = A46BEE1A

Re: [ccp4bb] According correct space group assignment...

[Tim Gruene]

Dear Rafal,

shelxt does not require the space group, it only needs the Laue group. If it 
finds a decent solution, it'll find also the space group for you.

Best,
Tim

On Friday, April 20, 2018 3:30:36 PM CEST Rafal Dolot wrote:
> Dear CCP4BB,
> 
> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this
> size of the molecule. 11mer is rich in G, so we expect the G-tetraplex
> formation. Data were collected to almost 1 A, so it should be enough for
> trials with direct methods/ab initio solution. What I should do first to
> find correct SG and/or cell parameters?
> 
> Best regards,
> 
> Rafal

-- 
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OSUA/204
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A


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[ccp4bb] Postdoctoral Position at the University of Chicago Araç Lab

[Demet Araç]

Postdoctoral Position in Cellular Communication
Applications are invited for an immediate opening at the Cellular Communication 
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Highly motivated candidates with a strong track record of publications should 
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Thank you,
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Re: [ccp4bb] According correct space group assignment...

[Phoebe A. Rice]

How do your twinning statistics look?  It could be that the real space group 
has lower symmetry (and thus more space for your G4 DNA).

~~~
Phoebe A. Rice
Dept. of Biochem & Mol. Biol. and
  Committee on Microbiology
https://voices.uchicago.edu/phoebericelab/
 
 
On 4/20/18, 8:31 AM, "CCP4 bulletin board on behalf of Rafal Dolot" 
 wrote:

Dear CCP4BB,

I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and 
DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell 
dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this 
size of the molecule. 11mer is rich in G, so we expect the G-tetraplex 
formation. Data were collected to almost 1 A, so it should be enough for 
trials with direct methods/ab initio solution. What I should do first to 
find correct SG and/or cell parameters?

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  |
|--|

Re: [ccp4bb] N-linked glycans

[Paul Emsley]

On 20/04/2018 16:57, F.Xavier Gomis-Rüth wrote:
Thanks a lot, Jon. The resolution is very low (3.1Å) and the density is confusing, I was trying to rule out 
things.


FWIW, 3.1Å is not very low for modelling N-linked glycans these days.



I am not an expert in glycoproteins, if a boat GlcNAc is this extremely 
unlikely, I will try other things....


Allow me to suggest that one of those things be

Extensions -> Modelling -> Modules -> Carbohydrate -> Glyco -> N-Linked Glycan 
Addition...

(if you use Coot, that is).

Paul

Re: [ccp4bb] N-linked glycans

[F.Xavier Gomis-Rüth]

Thanks a lot, Jon. The resolution is very low (3.1Å) and the density is 
confusing, I was trying to rule out things.


I am not an expert in glycoproteins, if a boat GlcNAc is this extremely 
unlikely, I will try other things....



On 20/4/18 17:25, Jon Agirre wrote:
I would be very, very surprised to find such a thing in a crystal 
structure of a glycoprotein. What's the resolution of the data?


On Fri, 20 Apr 2018 at 16:21 F.Xavier Gomis-Rüth > wrote:


Dear all,

has anybody ever seen a GlcNAc in boat conformation attached to an
asparagine and, if so, is there any reference for it?

Thanks a lot in advance,

Xavier

-- 


--
Dr Jon Agirre
Royal Society University Research Fellow
York Structural Biology Laboratory / Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @alwaysonthejazz


--

[ccp4bb] N-linked glycans

[F.Xavier Gomis-Rüth]

Dear all,

has anybody ever seen a GlcNAc in boat conformation attached to an 
asparagine and, if so, is there any reference for it?


Thanks a lot in advance,

Xavier

--

Re: [ccp4bb] According correct space group assignment...

[Keller, Jacob]

Why not try direct methods on both SG options, and maybe P1 as well? Depending 
on the wavelength and multiplicity, you might also have some good anomalous 
signal from the P's.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
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-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rafal 
Dolot
Sent: Friday, April 20, 2018 9:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] According correct space group assignment...

Dear CCP4BB,

I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and DIALS 
gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell dimension 
20.65, 22.96, 43.37, 90, 90, 90, what is too small for this size of the 
molecule. 11mer is rich in G, so we expect the G-tetraplex formation. Data were 
collected to almost 1 A, so it should be enough for trials with direct 
methods/ab initio solution. What I should do first to find correct SG and/or 
cell parameters?

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  |
|--|

Re: [ccp4bb] According correct space group assignment...

[graeme.win...@diamond.ac.uk]

Rafal,

Unit cell parameters: if you look at the images, and all the reflections are 
integrated, you should see little blue boxes & no missed reflections - if this 
is correct then the P1 unit cell is probably correct

Regarding the space group: for this case you may find NCS confusing the 
symmetry determination routines so I would take the outcome with a pinch of 
salt, but it could be that you have something different to what you expect. 
With this resolution you could probably solve it in P1 and work out the 
symmetry a posteri. I have solved structures of DNA in the past with SHELXT but 
this was (i) small and (ii) made the computer sweat. 

Re: I222/I212121 you cannot tell the difference from systematic absences i.e. 
what POINTLESS does. 

If XSD and DIALS give a similar solution and the reflections are all 
integrated, then on the balance of probability I would guess the answer is 
correct i.e. PG 222 and body centred, but only probably - some one will always 
come up with exceptions

As someone said earlier this week - you only know the symmetry once you’ve 
refined the structure

Best wishes Graeme

> On 20 Apr 2018, at 14:30, Rafal Dolot  wrote:
> 
> Dear CCP4BB,
> 
> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and 
> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell 
> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this size of 
> the molecule. 11mer is rich in G, so we expect the G-tetraplex formation. 
> Data were collected to almost 1 A, so it should be enough for trials with 
> direct methods/ab initio solution. What I should do first to find correct SG 
> and/or cell parameters?
> 
> 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  |
> |--|


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Re: [ccp4bb] According correct space group assignment...

[Eleanor Dodson]

I guess do molecular replacement in both spacegroups?
Presumably the crystallographic 2-fold will create a dimer?
Eleanor

On 20 April 2018 at 14:30, Rafal Dolot  wrote:

> Dear CCP4BB,
>
> I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and
> DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell
> dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this size
> of the molecule. 11mer is rich in G, so we expect the G-tetraplex
> formation. Data were collected to almost 1 A, so it should be enough for
> trials with direct methods/ab initio solution. What I should do first to
> find correct SG and/or cell parameters?
>
> 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  |
> |--|
>

[ccp4bb] According correct space group assignment...

[Rafal Dolot]

Dear CCP4BB,

I've recently collected data for 11mer build of DNA (9xG, 2xT). XDS, and 
DIALS gave me similar solution - SG: I2(1)2(1)2(1) or I222, with cell 
dimension 20.65, 22.96, 43.37, 90, 90, 90, what is too small for this 
size of the molecule. 11mer is rich in G, so we expect the G-tetraplex 
formation. Data were collected to almost 1 A, so it should be enough for 
trials with direct methods/ab initio solution. What I should do first to 
find correct SG and/or cell parameters?


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  |
|--|

Re: [ccp4bb] xds_par licence expired error

[Nishant Varshney]

Thank you Graeme and Mark,

I have downloaded the newest version and If I am not wrong I have to
install it again following the Installation instructions on XDSWiki.

Cheers

Nishant

On Fri, Apr 20, 2018 at 2:10 PM, graeme.win...@diamond.ac.uk <
graeme.win...@diamond.ac.uk> wrote:

> Dear Nishant
>
> XDS always has an expiry date - you download a new version from
> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html to replace
> the old version.
>
> I do not know if XDSGUI also has an expiry date
>
> This should not be a surprise - when you run XDS you will see something
> like
>
> [gw56@cs03r-sc-serv-16 ~]$ xds
>
>  * XDS * (VERSION Nov 11, 2017  BUILT=2017)  20-Apr-2018
>  Author: Wolfgang Kabsch
>  Copy licensed until 30-Jun-2018 to
>   academic users for non-commercial applications
>  No redistribution.
>
> best wishes Graeme
>
> On 20 Apr 2018, at 09:36, Nishant Varshney  a...@gmail.com>> wrote:
>
> Dear All,
>
> I am sure I have done it before but do not remember/finding the solution
> online for this now.
>
> My XDSGUI returns with the error of xds_par  "Licence Expired on 31st Mar
> 2018".
>
> Before Reinstalling XDS and XDSGUI on my iMac I would like to ask the
> experts if there is an easy solution to start XDS to work again?
>
> Looking forward to your expert solutions
>
> Regards
>
> Nishant
>
> --
> Dr. Nishant Kumar Varshney,
> Research Associate,
> C/O Dr. Sameena Khan,
> Drug Discovery Research Center,
> Translational Health Science and Technology Institute (THSTI)
> NCR Biotech Science Cluster,
> 3rd Milestone, Faridabad – Gurgaon Expressway,
> Faridabad – 121001 (HARYANA), India
> Ph: +91- 0129-2876477
> Mob: 8390564690
>
>
> --
> 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
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with 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
>



-- 
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690

Re: [ccp4bb] xds_par licence expired error

[graeme.win...@diamond.ac.uk]

Dear Nishant

XDS always has an expiry date - you download a new version from 
http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html to replace the old 
version.

I do not know if XDSGUI also has an expiry date

This should not be a surprise - when you run XDS you will see something like

[gw56@cs03r-sc-serv-16 ~]$ xds

 * XDS * (VERSION Nov 11, 2017  BUILT=2017)  20-Apr-2018
 Author: Wolfgang Kabsch
 Copy licensed until 30-Jun-2018 to
  academic users for non-commercial applications
 No redistribution.

best wishes Graeme

On 20 Apr 2018, at 09:36, Nishant Varshney 
> wrote:

Dear All,

I am sure I have done it before but do not remember/finding the solution online 
for this now.

My XDSGUI returns with the error of xds_par  "Licence Expired on 31st Mar 2018".

Before Reinstalling XDS and XDSGUI on my iMac I would like to ask the experts 
if there is an easy solution to start XDS to work again?

Looking forward to your expert solutions

Regards

Nishant

--
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690


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please notify us of receipt by returning the e-mail and do not use, copy, 
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Any opinions expressed within this e-mail are those of the individual and not 
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Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
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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] xds_par licence expired error

[Nishant Varshney]

Dear All,

I am sure I have done it before but do not remember/finding the solution
 online for this now.

My XDSGUI returns with the error of xds_par  "Licence Expired on 31st Mar
2018".

Before Reinstalling XDS and XDSGUI on my iMac I would like to ask the
experts if there is an easy solution to start XDS to work again?

Looking forward to your expert solutions

Regards

Nishant

-- 
Dr. Nishant Kumar Varshney,
Research Associate,
C/O Dr. Sameena Khan,
Drug Discovery Research Center,
Translational Health Science and Technology Institute (THSTI)
NCR Biotech Science Cluster,
3rd Milestone, Faridabad – Gurgaon Expressway,
Faridabad – 121001 (HARYANA), India
Ph: +91- 0129-2876477
Mob: 8390564690