Re: [ccp4bb] protein quasicrystals?

2018-02-16 Thread Harry Powell
Just to add to the list, Mosflm can handle multiple crystals without prior 
knowledge and is distributed as part of  CCP4 

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 




On 15 Feb 2018, at 22:03, Richard Staples wrote:

> I agree with Joe CrysAlisPro works very well.
>  
>  
>  
> Dr. Richard J. Staples
> Crystallographer
> Department of Chemistry
> 578 S. Shaw Lane
> Michigan State University
> East Lansing, MI 48824
> stap...@chemistry.msu.edu
> 517-353-1074
> Lab: 517-353-1079
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joseph 
> Ferrara
> Sent: Thursday, February 15, 2018 4:57 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] protein quasicrystals?
>  
> Nakane-san,
>  
> There is also CrysAlisPro, which can handle multiple crystals and may already 
> support your detector. If you send me the data, offline, I would be happy to 
> pass it onto the CrysAlisPro development team for testing.
>  
> Joseph D. Ferrara, Ph.D.
> CSO
> Deputy Director, X-ray Research Laboratory
> Vice President, American Crystallographic Association
>  
> Rigaku Corporation
> 9009 New Trails Drive
> The Woodlands, TX 77381
> Tel: 281-362-2300 x 168
> Skype: xrayjoe
> url: www.rigaku.com
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
> Phillips
> Sent: Tuesday, February 13, 2018 2:03 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] protein quasicrystals?
>  
> There are programs which are good at indexing patterns from multiply twinned 
> crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
> suggest you try that first before you invoke a quasicrystal explanation.
>  
>  
>  
>  
> James Phillips
>  
> On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane <tnak...@mrc-lmb.cam.ac.uk> 
> wrote:
> Hi,
> 
> "dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
> For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
> useful.
> 
> Best regards,
> 
> Takanori Nakane
> 
> > Have you tried microseeding of these sphere crystals? It may help to get
> > better crystals.
> >
> >
> > Burak
> >
> > 
> > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Yu Qiu
> > <yu@sanofi.com>
> > Sent: 13 February 2018 15:09:43
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] protein quasicrystals?
> >
> >
> > Hi,
> >
> >
> >
> > I have been trying to crystallize a protein complex and keep getting
> > sphere shape crystals. The diffraction is around 3 angstrom, but looks
> > like multiple lattices. I am wondering if it could be a quasi crystal? Is
> > there anyone has such experience?
> >
> >
> >
> > Thanks,
> >
> > Yu
> >
>  



Re: [ccp4bb] protein quasicrystals?

2018-02-15 Thread Richard Staples
I agree with Joe CrysAlisPro works very well.



Dr. Richard J. Staples
Crystallographer
Department of Chemistry
578 S. Shaw Lane
Michigan State University
East Lansing, MI 48824
stap...@chemistry.msu.edu<mailto:stap...@chemistry.msu.edu>
517-353-1074
Lab: 517-353-1079



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joseph 
Ferrara
Sent: Thursday, February 15, 2018 4:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

Nakane-san,

There is also CrysAlisPro, which can handle multiple crystals and may already 
support your detector. If you send me the data, offline, I would be happy to 
pass it onto the CrysAlisPro development team for testing.

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com<http://www.rigaku.com>



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
<tnak...@mrc-lmb.cam.ac.uk<mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> <yu@sanofi.com<mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



Re: [ccp4bb] protein quasicrystals?

2018-02-15 Thread Joseph Ferrara
Nakane-san,

There is also CrysAlisPro, which can handle multiple crystals and may already 
support your detector. If you send me the data, offline, I would be happy to 
pass it onto the CrysAlisPro development team for testing.

Joseph D. Ferrara, Ph.D.
CSO
Deputy Director, X-ray Research Laboratory
Vice President, American Crystallographic Association

Rigaku Corporation
9009 New Trails Drive
The Woodlands, TX 77381
Tel: 281-362-2300 x 168
Skype: xrayjoe
url: www.rigaku.com



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
<tnak...@mrc-lmb.cam.ac.uk<mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> <yu@sanofi.com<mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



Re: [ccp4bb] protein quasicrystals?

2018-02-15 Thread Satya
Hello Yu,

As every one knows, this is major crystallization problem for large
difficult protein targets, specially  proteins with large moving loops
and/or domains may be responsible for this unique crystals/diffraction
pattern. If you think your protein has large moving loop/domain in
presence/absence of ligands, adding specific substrate/additives or
removing loop/domain through site directed mutagenesis or making different
construct of your protein domains (if you are interested in only unique
protein structure)  may be another option to obtained better crystals
depends on the method, which you are going to solve the crystal structure.

This is another way of obtaining better crystals in addition to above
mentioned useful comments.

Wish you good luck for better crystals,
Satya



On Wed, Feb 14, 2018 at 12:33 PM, Kevin Jin <kevin...@gmail.com> wrote:

> Hi Yu,
>
> I did not see your images before I sent my previous email. I had a same
> case like this long time ago. However, the diffraction image was much worse
> than your. After I modified the condition, I got a single crystal with
> clear edges and reasonable resolution (not diffraction to 2.7 Ang). I have
> no idea which kind of protein you are working on. Membrane protein?
>
> Here is my understanding for your laughing,
>
> 1. According to your diffraction image, those spots (with red circles,
> image attached) may not be diffractions from ice and organic salt. Did you
> use your mouse to check the distance between these spot manually? It may
> give you clues for size of the unit cell, if you can not index it. It will
> be helpful If there was another image with 90 degree offset.
>
> 2. For your first image, folk discussed before here. It is a phase
> separation. In this case, you need to change the ratio between the
> hydrophobic portion (may be a little bit high here?) and hydrophilic
> portion. For instance,
> (1) if you used 20% PEG8K, then you may try 20% PGE 6K or 20% PGE 3300.
> (2) Sometimes, the combination of 2-5% 2-propanol with < 5mM ZnCl2 could
> also give some surprising results.
> (3). Change your salt concentration, and try different anions for
> comparison, Cl vs SO4.
>
> The whole idea above is to fine shuffle the surface charge for better
> packing.
>
> 3. Change your buffer salt with the same pH.
> 4.  You may try some surface detergent.
> 5. Decrease the concentration of your protein sample.
>
> However, each protein has its unique characteristics for crystallization.
>
>  Best Regards,
>
> Kevin
>
> On Tue, Feb 13, 2018 at 1:03 PM, Yu Qiu <yu@sanofi.com> wrote:
>
>> As asked by a few people, here are the images of crystals and diffraction.
>>
>>
>>
>> Thanks,
>>
>> Yu
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Keller, Jacob
>> *Sent:* Tuesday, February 13, 2018 4:00 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [EXTERNAL] Re: [ccp4bb] protein quasicrystals?
>>
>>
>>
>> I also would love to see an image….
>>
>>
>>
>> JPK
>>
>>
>>
>> +
>>
>> Jacob Pearson Keller
>>
>> Research Scientist / Looger Lab
>>
>> HHMI Janelia Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>> <https://maps.google.com/?q=19700+Helix+Dr,+Ashburn,+VA+20147=gmail=g>
>>
>> Desk: (571)209-4000 x3159 <(571)%20209-4000>
>>
>> Cell: (301)592-7004 <(301)%20592-7004>
>>
>> +
>>
>>
>>
>> The content of this email is confidential and intended for the recipient
>> specified in message only. It is strictly forbidden to share any part of
>> this message with any third party, without a written consent of the sender.
>> If you received this message by mistake, please reply to this message and
>> follow with its deletion, so that we can ensure such a mistake does not
>> occur in the future.
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>> <CCP4BB@JISCMAIL.AC.UK>] *On Behalf Of *James Phillips
>> *Sent:* Tuesday, February 13, 2018 3:03 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] protein quasicrystals?
>>
>>
>>
>> There are programs which are good at indexing patterns from multiply
>> twinned crystals. Bruker AXS has one, to my knowledge. There may be other
>> sources. I suggest you try that first before you invoke a quasicrystal
>> explanation.
>>
>>
>>
>>
>>
>>
>>
>>
>>

Re: [ccp4bb] protein quasicrystals?

2018-02-14 Thread Prem Prakash
Hi Yu,

Microseeding along with additive screening could give a better result,
because I encountered a situation once like this. Try higher concentration
of protein with bigger drop volume during crystallisation.

Good luck

Prem

On Wed, Feb 14, 2018 at 4:16 PM, Huyton, Trevor  wrote:

> Dear Yu,
>
>
>
> If the crystals are grown from salt then put the drop over water for a few
> hours and dissolve them, then put it back over the reservoir solution and
> recrystallize.
>
> Sometimes you can get better crystals this way.
>
> You could also try melting them with temperature and recrystallizing
>
>
>
> Best
>
>
>
> Trevor
>
>
>
> *From: *CCP4 bulletin board  on behalf of Yu Qiu <
> yu@sanofi.com>
> *Reply-To: *"yu@sanofi.com" 
> *Date: *Tuesday 13 February 2018 at 16:11
> *To: *"CCP4BB@JISCMAIL.AC.UK" 
> *Subject: *[ccp4bb] protein quasicrystals?
>
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I am wondering if it could be a quasi crystal? Is there
> anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



-- 
With kind regards,

Prem Prakash
PhD Research Scholar
Protein Crystallography Lab
Biosciences and Bioengineering
IIT Bombay


Re: [ccp4bb] protein quasicrystals?

2018-02-14 Thread Huyton, Trevor
Dear Yu,

If the crystals are grown from salt then put the drop over water for a few 
hours and dissolve them, then put it back over the reservoir solution and 
recrystallize.
Sometimes you can get better crystals this way.
You could also try melting them with temperature and recrystallizing

Best

Trevor

From: CCP4 bulletin board  on behalf of Yu Qiu 

Reply-To: "yu@sanofi.com" 
Date: Tuesday 13 February 2018 at 16:11
To: "CCP4BB@JISCMAIL.AC.UK" 
Subject: [ccp4bb] protein quasicrystals?

Hi,

I have been trying to crystallize a protein complex and keep getting sphere 
shape crystals. The diffraction is around 3 angstrom, but looks like multiple 
lattices. I am wondering if it could be a quasi crystal? Is there anyone has 
such experience?

Thanks,
Yu


Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Gyanendra Kumar
Hi Yu,

Have you tried using the Additive Screen (e.g. from Hampton Research) on
top of your crystallization condition, and varying the ratio between
protein complex and crystallization solution? From the diffraction pattern,
it looks you are almost there. Salt crystals don't show spots close to the
beam stop usually, so the chance of them being salt crystals is negligible.
A little bit of tweaking in crystallization conditions should do the trick.
If all this fails, probably, you will have to remove any floppy ends from
the proteins in the new constructs.
I had a similar experience where the protein with His-tag showed crystals
in a lot of conditions but all spherical and cylindrical crystals
diffracting to 3.5 A. The protein after removing the His-tag gave crystals
that diffracted to 2.4 A.

Good luck!
-Gyan

On Tue, Feb 13, 2018 at 9:09 AM, Yu Qiu  wrote:

> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I am wondering if it could be a quasi crystal? Is there
> anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



-- 
Gyanendra Kumar, PhD
Associate Scientist,
St. Jude Children's Research Hospital,
Department of Structural Biology,
262, Danny Thomas Place, MS-311
Memphis, TN 38105
Cell: 631-875-9189
https://www.linkedin.com/in/gyanendrakumar
https://scholar.google.com/gyanendrakumar

https://www.researchgate.net/profile/Gyanendra_Kumar3
http://stjude.academia.edu/GyanendraKumar
---


Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Diana Tomchick
Some of the high intensity, high resolution spots are possibly from ice.

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<mailto:diana.tomch...@utsouthwestern.edu>
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Feb 13, 2018, at 3:09 PM, Keller, Jacob 
<kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> wrote:

I would say definitely not a quasicrystal, just multiple crystals, but the 
spots look like salt spots to me, being very sharp and intense. The puzzling 
thing is that the low-resolution zone is so populated, which would argue a bit 
against salt.

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 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: yu@sanofi.com<mailto:yu@sanofi.com> [mailto:yu@sanofi.com]
Sent: Tuesday, February 13, 2018 4:03 PM
To: Keller, Jacob <kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>>; 
CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: RE: [ccp4bb] protein quasicrystals?

As asked by a few people, here are the images of crystals and diffraction.

Thanks,
Yu

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, February 13, 2018 4:00 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [EXTERNAL] Re: [ccp4bb] protein quasicrystals?

I also would love to see an image….

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 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
<tnak...@mrc-lmb.cam.ac.uk<mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> <yu@sanofi.com<mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>




UT Southwestern


Medical Center



The future of medicine, today.



Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Keller, Jacob
I would say definitely not a quasicrystal, just multiple crystals, but the 
spots look like salt spots to me, being very sharp and intense. The puzzling 
thing is that the low-resolution zone is so populated, which would argue a bit 
against salt.

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 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: yu@sanofi.com [mailto:yu@sanofi.com]
Sent: Tuesday, February 13, 2018 4:03 PM
To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK
Subject: RE: [ccp4bb] protein quasicrystals?

As asked by a few people, here are the images of crystals and diffraction.

Thanks,
Yu

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, February 13, 2018 4:00 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: [EXTERNAL] Re: [ccp4bb] protein quasicrystals?

I also would love to see an image….

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 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
<tnak...@mrc-lmb.cam.ac.uk<mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> <yu@sanofi.com<mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Keller, Jacob
I also would love to see an image….

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
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From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
Phillips
Sent: Tuesday, February 13, 2018 3:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] protein quasicrystals?

There are programs which are good at indexing patterns from multiply twinned 
crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
suggest you try that first before you invoke a quasicrystal explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane 
<tnak...@mrc-lmb.cam.ac.uk<mailto:tnak...@mrc-lmb.cam.ac.uk>> wrote:
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board 
> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Yu Qiu
> <yu@sanofi.com<mailto:yu@sanofi.com>>
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>



Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread James Phillips
There are programs which are good at indexing patterns from multiply
twinned crystals. Bruker AXS has one, to my knowledge. There may be other
sources. I suggest you try that first before you invoke a quasicrystal
explanation.




James Phillips

On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane  wrote:

> Hi,
>
> "dials.reciprocal_space_viewer" is very useful to identify multiple
> lattices.
> For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
> useful.
>
> Best regards,
>
> Takanori Nakane
>
> > Have you tried microseeding of these sphere crystals? It may help to get
> > better crystals.
> >
> >
> > Burak
> >
> > 
> > From: CCP4 bulletin board  on behalf of Yu Qiu
> > 
> > Sent: 13 February 2018 15:09:43
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] protein quasicrystals?
> >
> >
> > Hi,
> >
> >
> >
> > I have been trying to crystallize a protein complex and keep getting
> > sphere shape crystals. The diffraction is around 3 angstrom, but looks
> > like multiple lattices. I am wondering if it could be a quasi crystal? Is
> > there anyone has such experience?
> >
> >
> >
> > Thanks,
> >
> > Yu
> >
>


Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Takanori Nakane
Hi,

"dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
useful.

Best regards,

Takanori Nakane

> Have you tried microseeding of these sphere crystals? It may help to get
> better crystals.
>
>
> Burak
>
> 
> From: CCP4 bulletin board  on behalf of Yu Qiu
> 
> Sent: 13 February 2018 15:09:43
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] protein quasicrystals?
>
>
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting
> sphere shape crystals. The diffraction is around 3 angstrom, but looks
> like multiple lattices. I am wondering if it could be a quasi crystal? Is
> there anyone has such experience?
>
>
>
> Thanks,
>
> Yu
>


Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Kabasakal, Burak V
Have you tried microseeding of these sphere crystals? It may help to get better 
crystals.


Burak


From: CCP4 bulletin board  on behalf of Yu Qiu 

Sent: 13 February 2018 15:09:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] protein quasicrystals?


Hi,



I have been trying to crystallize a protein complex and keep getting sphere 
shape crystals. The diffraction is around 3 angstrom, but looks like multiple 
lattices. I am wondering if it could be a quasi crystal? Is there anyone has 
such experience?



Thanks,

Yu


Re: [ccp4bb] protein quasicrystals?

2018-02-13 Thread Gloria Borgstahl
I am very interested in this topic, and have found incommensurately
modulated crystals and few examples of possible protein quasicrystals.
Do you have any images you could share?

On Tue, Feb 13, 2018 at 9:09 AM, Yu Qiu  wrote:
> Hi,
>
>
>
> I have been trying to crystallize a protein complex and keep getting sphere
> shape crystals. The diffraction is around 3 angstrom, but looks like
> multiple lattices. I am wondering if it could be a quasi crystal? Is there
> anyone has such experience?
>
>
>
> Thanks,
>
> Yu