Re: [ccp4bb] coot fragment translation for nucleic acids

[chenzhonghao...@163.com]

Dear Schulze-Gahmen,
 
  Which version of coot did you use?

For me, Coot 0.8.4 works well in windows 8.1 system. It does not have a 
question in optimizing nucleic acids.

best,

Zhonghao



chenzhonghao...@163.com
 
From: Ursula Schulze-Gahmen
Date: 2017-03-25 04:35
To: CCP4BB
Subject: [ccp4bb] coot fragment translation for nucleic acids
Although I have used Coot a lot for modeling protein structures, I have little 
experience using it for nucleic acids. I am trying to translate fragments of 
nucleic acid using the rotate/translate zone option in Coot. But I am unable to 
select a zone; instead the whole chain is selected when I am clicking on 2 
atoms in the chain. Any suggestion how to get around this would be appreciated.

Ursula

-- 
Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220
(510) 643 9491

Re: [ccp4bb] CCP4BB Digest - 23 Mar 2017 to 24 Mar 2017 (#2017-83)

[Dusan Turk]

Dear Alex,

try MAIN "http://www-bmb.ijs.si/";

it has a two way interface to Ramachandran plot, you can either display 
“HIS_RAMA” of individual clicked residues in displayed 3D  model and also the 
other way around, you can click on residues in Ramachandran plot and center on 
the residue in 3D model.

If you need some help to on how this works  do not hesitate to contact me.

regards,
dusan
 
> On 25 Mar 2017, at 01:00, CCP4BB automatic digest system 
>  wrote:
> 
> Date:Thu, 23 Mar 2017 20:39:46 -0700
> From:Alex Lee 
> Subject: software or tool for Individual residue in a Ramachandran plot graph?
> 
> Dear All,
> 
> Is there a tool or software which can give Ramachandran information of
> individual residues in a plot?
> 
> I used Coot to check for Ramachandran plots, but it shows all the residues
> in a coordinate I put in Coot, not individual one. I also use "residue
> info" in coot, it tells Ramachandran "phi psi" angles of individual
> residue, but it does not show it in a plot, only numbers.
> 
> Thanks ahead for any input.
> 

Re: [ccp4bb] Antibody modelling software

[Degano Massimo]

Try also the LYRA server
http://www.cbs.dtu.dk/services/LYRA/
In my experience, most programs do an excellent job with the canonical CDR 
loops, but care must be taken when looking at the CDR3s.
Hope this helps,

Massimo

Sent from my iPhone

On 24 Mar 2017, at 20:18, Hugh Morgan 
<1103e90ebb53-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Hi all, can anyone recommend some user friendly software for modelling 
antibodies. Commercial or academic is fine. Thanks in advance for the help.
Hugh


Rispetta l’ambiente: non stampare questa mail se non è necessario.
Respect the environment: if it's not necessary, don't print this mail.

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Edward A. Berry]

On 03/23/2017 11:39 PM, Alex Lee wrote:

Dear All,

Is there a tool or software which can give Ramachandran information of 
individual residues in a plot?

I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in 
Coot, not individual one. I also use "residue info" in coot, it tells Ramachandran 
"phi psi" angles of individual residue, but it does not show it in a plot, only numbers.

Thanks ahead for any input.


Well, you can always AWK out 3 residues and run procheck on them,
something like:

  awk '$1~/ATOM/ && $5~/B/ && $6~/^6[567]/' /a/pdb/pdb2h88.ent >w.pdb
  procheck w.pdb 1.8
followed by:
  gs w_01.ps
or:
  ps2pdf w_01.ps
  acroread !$

(The AWK command will have to be tweaked if fields run together in the
  pdb due to large numbers or alt. conformations for these three residues)

I agree such a feature would be useful in coot. Sometimes you want to
know if an outlier is just outside or way outside, or if it is halfway
between two allowed regions, and with large, low-quality structures it is
 hard to find the residue in the crowded rama plot.
Clickable points in the R plot fills the bill going one way, now highlighting
points corresponding to selected residue would be the other half.
eab


w_01.pdf
Description: Adobe PDF document

Re: [ccp4bb] Antibody modelling software

[Frank Von Delft]

My Oxford colleague Charlotte Deane develops SAbPred:

   
http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/WelcomeSAbPred.php


Sent from tiny silly touch screen

From: Hugh Morgan <1103e90ebb53-dmarc-requ...@jiscmail.ac.uk>
Sent: 24 Mar 2017 7:18 p.m.
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Antibody modelling software


Hi all, can anyone recommend some user friendly software for modelling 
antibodies. Commercial or academic is fine. Thanks in advance for the help.
Hugh

[ccp4bb] coot fragment translation for nucleic acids

[Ursula Schulze-Gahmen]

Although I have used Coot a lot for modeling protein structures, I have
little experience using it for nucleic acids. I am trying to translate
fragments of nucleic acid using the rotate/translate zone option in Coot.
But I am unable to select a zone; instead the whole chain is selected when
I am clicking on 2 atoms in the chain. Any suggestion how to get around
this would be appreciated.

Ursula

-- 
Ursula Schulze-Gahmen, Ph.D.
Project Scientist
UC Berkeley, QB3
360 Stanley Hall #3220
Berkeley, CA 94720-3220
(510) 643 9491

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Pavel Afonine]

May be not exactly what you want, but should be close:

phenix.secondary_structure_restraints 1yjp.pdb

then here you have options

- for output format:

format = *phenix phenix_refine phenix_bonds pymol pdb refmac kinemage

- for search  (annotation method):

search_method = *ksdssp mmtbx_dssp from_ca cablam
I suggest you please with them and see which one suits you most.

Pavel



On Fri, Mar 24, 2017 at 1:18 PM, Xiao Lei  wrote:

> Thanks Pavel,  is there a command that can tell secondary structure
> assignment based on Rama plot of each residue beside phi and psi? for
> example :
>  A   2  ASN:56.93:-60.58:141.19:Favored:General   alpha helix
>  A   3  ASN:48.44:-119.25:125.15:Favored:General  alpha helix
>
> On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine  wrote:
>
>> Trivial using command line. Example:
>>
>> - get a file from PDB:
>>
>> phenix.fetch_pdb 1yjp
>>
>> - get all phi/psi for all residues:
>>
>> phenix.ramalyze 1yjp.pdb
>> residue:score%:phi:psi:evaluation:type
>>  A   2  ASN:56.93:-60.58:141.19:Favored:General
>>  A   3  ASN:48.44:-119.25:125.15:Favored:General
>>  A   4  GLN:16.23:-126.16:112.81:Favored:General
>>  A   5  GLN:55.13:-114.98:126.76:Favored:General
>>  A   6  ASN:6.17:-116.42:97.69:Favored:General
>> SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A
>> where applicable)
>> SUMMARY: 0.00% outliers (Goal: < 0.2%)
>> SUMMARY: 100.00% favored (Goal: > 98%)
>>
>> Pavel
>>
>>
>> On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty 
>> wrote:
>>
>>> Alex
>>>
>>> It seems that nobody has answered your question. I'm not sure what you
>>> can do in CCP4, but if I understand your question correctly, you can
>>> perform a comprehensive validation in Phenix complete with Ramachandran
>>> plot including clickable points relating to your residues which allow you
>>> to see the residues in Coot.
>>>
>>> Happen to help further on the PHENIXBB or off-line.
>>>
>>> Cheers
>>>
>>> Nigel
>>>
>>> ---
>>> Nigel W. Moriarty
>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>> Lawrence Berkeley National Laboratory
>>> Berkeley, CA 94720-8235
>>> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>>
>>> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee 
>>> wrote:
>>>
 Dear All,

 Is there a tool or software which can give Ramachandran information of
 individual residues in a plot?

 I used Coot to check for Ramachandran plots, but it shows all the
 residues in a coordinate I put in Coot, not individual one. I also use
 "residue info" in coot, it tells Ramachandran "phi psi" angles of
 individual residue, but it does not show it in a plot, only numbers.

 Thanks ahead for any input.


>>>
>>
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Xiao Lei]

Thanks Pavel,  is there a command that can tell secondary structure
assignment based on Rama plot of each residue beside phi and psi? for
example :
 A   2  ASN:56.93:-60.58:141.19:Favored:General   alpha helix
 A   3  ASN:48.44:-119.25:125.15:Favored:General  alpha helix

On Fri, Mar 24, 2017 at 1:09 PM, Pavel Afonine  wrote:

> Trivial using command line. Example:
>
> - get a file from PDB:
>
> phenix.fetch_pdb 1yjp
>
> - get all phi/psi for all residues:
>
> phenix.ramalyze 1yjp.pdb
> residue:score%:phi:psi:evaluation:type
>  A   2  ASN:56.93:-60.58:141.19:Favored:General
>  A   3  ASN:48.44:-119.25:125.15:Favored:General
>  A   4  GLN:16.23:-126.16:112.81:Favored:General
>  A   5  GLN:55.13:-114.98:126.76:Favored:General
>  A   6  ASN:6.17:-116.42:97.69:Favored:General
> SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A where
> applicable)
> SUMMARY: 0.00% outliers (Goal: < 0.2%)
> SUMMARY: 100.00% favored (Goal: > 98%)
>
> Pavel
>
>
> On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty 
> wrote:
>
>> Alex
>>
>> It seems that nobody has answered your question. I'm not sure what you
>> can do in CCP4, but if I understand your question correctly, you can
>> perform a comprehensive validation in Phenix complete with Ramachandran
>> plot including clickable points relating to your residues which allow you
>> to see the residues in Coot.
>>
>> Happen to help further on the PHENIXBB or off-line.
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov
>> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>>
>> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee 
>> wrote:
>>
>>> Dear All,
>>>
>>> Is there a tool or software which can give Ramachandran information of
>>> individual residues in a plot?
>>>
>>> I used Coot to check for Ramachandran plots, but it shows all the
>>> residues in a coordinate I put in Coot, not individual one. I also use
>>> "residue info" in coot, it tells Ramachandran "phi psi" angles of
>>> individual residue, but it does not show it in a plot, only numbers.
>>>
>>> Thanks ahead for any input.
>>>
>>>
>>
>

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Pavel Afonine]

Trivial using command line. Example:

- get a file from PDB:

phenix.fetch_pdb 1yjp

- get all phi/psi for all residues:

phenix.ramalyze 1yjp.pdb
residue:score%:phi:psi:evaluation:type
 A   2  ASN:56.93:-60.58:141.19:Favored:General
 A   3  ASN:48.44:-119.25:125.15:Favored:General
 A   4  GLN:16.23:-126.16:112.81:Favored:General
 A   5  GLN:55.13:-114.98:126.76:Favored:General
 A   6  ASN:6.17:-116.42:97.69:Favored:General
SUMMARY: 5 Favored, 0 Allowed, 0 Outlier out of 5 residues (altloc A where
applicable)
SUMMARY: 0.00% outliers (Goal: < 0.2%)
SUMMARY: 100.00% favored (Goal: > 98%)

Pavel


On Fri, Mar 24, 2017 at 10:37 AM, Nigel Moriarty  wrote:

> Alex
>
> It seems that nobody has answered your question. I'm not sure what you can
> do in CCP4, but if I understand your question correctly, you can perform a
> comprehensive validation in Phenix complete with Ramachandran plot
> including clickable points relating to your residues which allow you to see
> the residues in Coot.
>
> Happen to help further on the PHENIXBB or off-line.
>
> Cheers
>
> Nigel
>
> ---
> Nigel W. Moriarty
> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709 <(510)%20486-5709> Email : nwmoria...@lbl.gov
> Fax   : 510-486-5909 <(510)%20486-5909>   Web  : CCI.LBL.gov
>
> On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee  wrote:
>
>> Dear All,
>>
>> Is there a tool or software which can give Ramachandran information of
>> individual residues in a plot?
>>
>> I used Coot to check for Ramachandran plots, but it shows all the
>> residues in a coordinate I put in Coot, not individual one. I also use
>> "residue info" in coot, it tells Ramachandran "phi psi" angles of
>> individual residue, but it does not show it in a plot, only numbers.
>>
>> Thanks ahead for any input.
>>
>>
>

[ccp4bb] Antibody modelling software

[Hugh Morgan]

Hi all, can anyone recommend some user friendly software for modelling 
antibodies. Commercial or academic is fine. Thanks in advance for the help.
Hugh

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

[Nigel Moriarty]

Alex

It seems that nobody has answered your question. I'm not sure what you can
do in CCP4, but if I understand your question correctly, you can perform a
comprehensive validation in Phenix complete with Ramachandran plot
including clickable points relating to your residues which allow you to see
the residues in Coot.

Happen to help further on the PHENIXBB or off-line.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

On Thu, Mar 23, 2017 at 8:39 PM, Alex Lee  wrote:

> Dear All,
>
> Is there a tool or software which can give Ramachandran information of
> individual residues in a plot?
>
> I used Coot to check for Ramachandran plots, but it shows all the residues
> in a coordinate I put in Coot, not individual one. I also use "residue
> info" in coot, it tells Ramachandran "phi psi" angles of individual
> residue, but it does not show it in a plot, only numbers.
>
> Thanks ahead for any input.
>
>

Re: [ccp4bb] Coot and pymol 3D on Mac Pro with NVIDIA Quadro FX4500

[Chris Ulens]

Dear ccp4 members,
I am looking for a recommendation from users who still have older generations 
of a Mac Pro with the NVIDIA Quadro FX 4500 stereo card. My question is which 
generation of the Mac Pro... 
http://www.ebay.com/sch/Apple-Mac-Pro/111418/bn_649847/i.html
.. is still compatible with the Quadro FX 4500 stereo and Nuvision emitter? We 
have the 2008 version which still is the stereo workhorse in the lab, but was 
wondering if the 2012 version still has the compatibility?

Thank you and best regards
Chris

[ccp4bb] Call reminder: XChem fragment screening at Diamond (and iNEXT)

[Frank von Delft]

Dear Protein Crystallographers

This is a second reminder for proposals for performing crystal-based 
fragment screening at Diamond's XChem facility at beamline I04-1, for 
the next allocation period (Oct 2017 to April 2018).


   *The deadline for proposals is NEXT SATURDAY:  1st APRIL 5PM.*

   *Details of how to submit at this page
   .

   *

Full details of the facility are available here 
.  It 
supports the full crystal-to-structure experiment, and since opening for 
users in 2015, it has hosted over 40 users from academia and industry, 
with over 30 experiments (>40,000 crystals) consistently yielding 
credible, high quality fragment hits.  With the right crystals, it'll 
keep you busy for less than a few weeks; and you get lots of support and 
advice.


The previous call (Sept 2016) was heavily (3x) oversubscribed, and 
though we ought to have increased our capacity by next October, please 
pay close attention to the instructions and guidelines.


Access for EU users is now funded via iNEXT  
(if you follow the instructions!);  however we welcome all international 
proposals.




--
Prof Frank von Delft
Associate Professor

Principal Beamline Scientist: I04-1
Diamond Light Source
+44 1235 778997

Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583

Visiting Professor
Department of Biochemistry
University of Johannesburg
South Africa

[ccp4bb] PhD position at IGBMC, Strasbourg, France

[Helgo Schmidt]

Dear all,

just a reminder that the deadline for applications is in one week.

Best regards,
Helgo



On 23 January 2017 at 15:36, Helgo Schmidt <
0eb5ac628ee4-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear all,



I’m looking for an enthusiastic and highly motivated PhD student to
join my newly established group at IGBMC, Strasbourg, France. We are
studying the structure and function of the dynein motor protein through an
integrated structural biology approach combining x-ray crystallography and
high-resolution cryoEM. The dynein motor is a complex and fascinating
molecular machine involved in essential cellular processes like mitosis,
organelle positioning and the beating of cilia (
https://www.ncbi.nlm.nih.gov/pubmed/24064538).

Applicants should possess a Master’s or Bachelor’s degree in the life
sciences, or a related discipline. The applicant should have experience in
molecular biology as well as protein expression and purification.
Experience in protein expression in yeast and/or insect cells would be
considered an advantage. Training in x-ray crystallography and cryoEM will
be provided. English language skills, the ability to work in a team,
initiative, flexibility as well as good organizational and learning skills
are required.

The IGBMC (http://www.igbmc.fr/) is one of the leading biomedical
research institutions in Europe and provides regular synchrotron access as
well as cutting-edge cryo-EM facilities like a Titan Krios electron
microscope equipped with a Cs corrector, a GIF energy filter, a phase plate
and a Gatan summit K2 direct electron detector. An ion beam scanning
electron microscope (cryo-FIB/SEM) and super-resolution fluorescence
microscopy for cellular tomography studies are also available.

Applicants should send a CV, a one-page summary of their research
experience and contact details for two referees till 31st of March to
helgoschmi...@gmail.com. The starting date is flexible.


Selected publications:

Schmidt H (2015) “Dynein motors: How AAA+ ring opening and closing
coordinates microtubule binding and linker movement.” Bioessays: 37:
532-543.

Schmidt H, Zalyte R, Urnavicius L, Carter AP (2015) “Structure of human
cytoplasmic dynein-2 primed for its power stroke.” Nature 518: 435-438.

Schmidt H, Gleave ES, Carter AP (2012) “Insights into dynein motor
domain function from a 3.3-Å crystal structure” Nat Struct Mol Biol.
19:492-7.

Re: [ccp4bb] Correct reading of HDF5 (meta)data

[Herbert J. Bernstein]

Dear Colleagues,

  The information Graeme is requesting would be very helpful in making
accurate NeXus/HDF5, minicbf, and full cbf beamline templates.  We would be
happy to host the beamline photographs on the HDRMX web site (
www.medsbio.org/hdrmx).  These photographs would be even more useful if you
added markings for all axes showing the direction of increasing translation
for each translation axis  and a curled arrow showing the direction of
increasing rotation for each rotation axis.

  Thank you.

Regards,
  Herbert

On Fri, Mar 24, 2017 at 4:18 AM, Graeme Winter 
wrote:

> Dear All,
>
> There has been much discussion of XDS efficiently reading HDF5 data - this
> is of course highly desirable though not sufficient for the correct
> processing of the data.
>
> One thing which I think could very much help the community would be to
> have data published from beamlines where Eiger detectors are in use,
> including the following:
>
>  - a *photograph* of the beamline showing the orientation of the detector
> and principle rotation axis
>  - a single rotation scan e.g. of thermolysin or some other
> easy-to-solve-by-SAD structure
>
> Between these there is sufficient information to ensure that the geometry
> of the experiment described in the headers (master file) is correct.
>
> While XDS does not use this, and many beamline systems generate an XDS.INP
> file, in the future this record of the experiment in the master file may be
> all that remains and so ensuring that this is correct seems like a very
> good idea.
>
> So - beamline people - how do you feel about the above? Clearly this will
> also help with software people making sure data from your beamline process
> correctly!
>
> Thanks & best wishes Graeme
>
>
> --
> 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
>
>

[ccp4bb] Correct reading of HDF5 (meta)data

[Graeme Winter]

Dear All,

There has been much discussion of XDS efficiently reading HDF5 data - this is 
of course highly desirable though not sufficient for the correct processing of 
the data.

One thing which I think could very much help the community would be to have 
data published from beamlines where Eiger detectors are in use, including the 
following:

 - a *photograph* of the beamline showing the orientation of the detector and 
principle rotation axis
 - a single rotation scan e.g. of thermolysin or some other 
easy-to-solve-by-SAD structure 

Between these there is sufficient information to ensure that the geometry of 
the experiment described in the headers (master file) is correct.

While XDS does not use this, and many beamline systems generate an XDS.INP 
file, in the future this record of the experiment in the master file may be all 
that remains and so ensuring that this is correct seems like a very good idea.

So - beamline people - how do you feel about the above? Clearly this will also 
help with software people making sure data from your beamline process correctly!

Thanks & best wishes Graeme


-- 
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

[ccp4bb] Cryo-EM positions at EMBL

[Carsten Sachse]

Dear all,

We invite applications for postdoc and support scientist positions in the 
Sachse laboratory at EMBL:
Postdoctoral Fellow – Structural membrane biology cryo-EM
http://s.embl.org/HD01058 

Research Technician – Support scientist structural biology
http://s.embl.org/HD01057 

EMBL hosts a unique and vibrant 3D-EM/structural biology community and houses 
outstanding microscopy and computational facilities.

Best wishes,


Carsten

Carsten Sachse 
Group Leader
European Molecular Biology Laboratory 
Germany
http://www.embl.de/research/units/scb/sachse/ 

http://www.sachse.embl.de 

Re: [ccp4bb] Possibility of Quasi-crystal formation of heterodimeric protein complex

[Vivoli, Mirella]

Dear Debiasish,
it looks like you got spherulites.
You might try to optimize the conditions or use these spherulites for 
microseeding. It worked for me once.
Good luck!

Mirella

Sent from my iPhone

On 24 Mar 2017, at 08:29, Camillo Rosano 
mailto:camillo.ros...@gmail.com>> wrote:

Dear Debiasish,
   more than "quasicrystals" (crystal in which molecules 
adopt an ordered but aperiodic structure), to me the one in your photo looks 
like spherulites. You shouldn't be far for finding the right crystallization 
conditions: maybe change the pH of your precipitant and try lower concentration 
of protein or precipitant or both at the same time.
Camillo

On Fri, Mar 24, 2017 at 12:10 AM, Debasish Kumar Ghosh 
mailto:dkgh...@cdfd.org.in>> wrote:
Dear All,

I have a small doubt regarding possibility of formation of quasi-crystal of 
protein complex. I am trying to co-crystallize a heterodimeric protein complex 
of two small proteins (14KDa and 16KDa, both are human origin). One of them is 
a membrane protein. we have extensively characterized their qualitative and 
quantitative binding properties (with IP/IB, Confocal microscopy, ITC etc.). We 
are quite certain of their strong 1:1 binding stochiometry.
In some crystallizing conditions, we are getting some structures which appears 
to me as quasi-crystals (Image attached). However, I am not coming across ample 
examples of quasi-crystals of protein complexes.
I will be very keen to know if anyone had this (similar) kind of experience(s). 
And of course it would be wonderful to know if they are diffractable and, if 
yes, what are the odds of having good diffraction.


Best !!

Debasish

CSIR- Senior Research Fellow
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Re: [ccp4bb] Possibility of Quasi-crystal formation of heterodimeric protein complex

[Camillo Rosano]

Dear Debiasish,
   more than "quasicrystals" (crystal in which
molecules adopt an ordered but aperiodic structure), to me the one in your
photo looks like spherulites. You shouldn't be far for finding the right
crystallization conditions: maybe change the pH of your precipitant and try
lower concentration of protein or precipitant or both at the same time.
Camillo

On Fri, Mar 24, 2017 at 12:10 AM, Debasish Kumar Ghosh 
wrote:

> Dear All,
>
> I have a small doubt regarding possibility of formation of quasi-crystal
> of protein complex. I am trying to co-crystallize a heterodimeric protein
> complex of two small proteins (14KDa and 16KDa, both are human origin). One
> of them is a membrane protein. we have extensively characterized their
> qualitative and quantitative binding properties (with IP/IB, Confocal
> microscopy, ITC etc.). We are quite certain of their strong 1:1 binding
> stochiometry.
> In some crystallizing conditions, we are getting some structures which
> appears to me as quasi-crystals (Image attached). However, I am not coming
> across ample examples of quasi-crystals of protein complexes.
> I will be very keen to know if anyone had this (similar) kind of
> experience(s). And of course it would be wonderful to know if they are
> diffractable and, if yes, what are the odds of having good diffraction.
>
>
> Best !!
>
> Debasish
>
> CSIR- Senior Research Fellow
> Computational and Functional Genomics Group
> Centre for DNA Fingerprinting and Diagnostics
> Hyderabad, INDIA
>
>