[ccp4bb] Post-doctoral position in Amsterdam

[Titia K. Sixma]

A post-doctoral position is available in the Netherlands Cancer Institute in 
the group of Titia Sixma

The Netherlands Cancer Institute is a center of excellence with a high standard 
of biological research and an interactive atmosphere. It is located in 
Amsterdam, with all its cultural amenities, close to Schiphol airport.

The group has an interest in structural studies coupled to functional analysis. 
We share meetings and lab-space with the group of Tassos Perrakis, who amongst 
other things has an interest in method development for structural biology. 
Equipment includes high throughput crystallization, in-house X-ray facility, 
excellent biophysics (SPR, stopped-flow, ITC, thermophoresis, MALLS, Optim etc).

The project focuses ubiquitin conjugation in cholesterol homeostasis and has 
mechanistic and clinically relevant aims. We are looking for an enthusiastic 
researcher with experience in protein crystallo­gra­phy, molecular biology 
and/or biochemistry. Applicants should write an e-mail with CV and names of 
three references to t.si...@nki.nl by Feb 2nd.

[ccp4bb] PhD positions-Structural Biology (IRB Barcelona)

[Esther Fernandez]

*PhD positions-Structural Biology*

The "*La Caixa- Severo Ochoa/IRB Barcelona International PhD Programme*"
call has been opened.

· A total of *9 doctoral fellowships in several fields, including
Structural Biology, * are available for the academic year *2014-2015*,
under the auspices of "la Caixa", the third largest Spanish financial
institution.

· Open to students in the *last year of their undergraduate studies*.

·  *Deadline *for applications: *Wednesday, February 18, 2015*

· More information and application forms can be found at:

 
*http://www.irbbarcelona.org/en/phd-and-postdocs/predoctoral-programme/opportunities/la-caixa-severo-ochoa-irb-barcelona
*


*IRB Barcelona* is an independent, non-profit research institution engaged
in basic and applied biomedical sciences, located at the *Parc Científic de
Barcelona* on the *University of Barcelona campus. *We provide students in
the life sciences from across the world with the opportunity to do training
and research toward their degree in a unique international and
multidisciplinary scientific environment.



Thank you.
Best regards,
*Esther Fernández*
*Structural & Computational Biology Programme*
* Institute for Research in Biomedicine (IRB Barcelona) *
Parc Científic de Barcelona (PCB)
C/ Baldiri Reixac 10,  08028 Barcelona - Spain

Re: [ccp4bb] chloride or water

[Oliviero Carugo]

Hi Rohit,

you might be interested in the following paper:

Buried chloride stereochemistry in the Protein Data Bank
BMC Structural Biology 2014, 14:19
doi:10.1186/s12900-014-0019-8
http://www.biomedcentral.com/1472-6807/14/19

Best,

Oliviero



On Tue, January 20, 2015 10:53, Eleanor Dodson wrote:
> Also it just might be useful to do an anomalous Fourier - Cl has a weak
> signal, but may be visible if the phases are good. cf any peaks to ones
> over the S atoms to get a measure of what you might expect- Eleanor
>
>
>
> On 20 January 2015 at 07:17, Robbie Joosten  wrote:
>
>> Hi Rohit,
>>
>> The pictures you sent are not that informative. There are a few things
>> you
>> can use to distinguish chloride from water. Chloride prefers nitrogens
>> over
>> oxygens as ligands. Also the coordination lengths are higher than those
>> of
>> water, typically between 3 and 3.5Å. Usually, the coordination is not as
>> pretty as that of cations.
>>
>> HTH,
>> Robbie
>> --
>> Van: rohit kumar 
>> Verzonden: ‎20-‎1-‎2015 08:05
>> Aan: CCP4BB@JISCMAIL.AC.UK
>> Onderwerp: [ccp4bb] chloride or water
>>
>>
>> Dear all,
>>
>> I am solving a data of 3.0 Å resolution. In the active site we found an
>> unidentified blob. The crystallization condition is (PEG 3350-25%,
>> Naformate-200mM, MES (100mM)-6.5pH, and Nacl-200mM).
>> Can anyone suggest what it could be? If I suppose that, it is chloride,
>> how could someone differentiate between a chloride moiety and water.
>> below I am showing the coot figure in two different orientations.
>>
>> Thanks in advance...
>>
>>
>> [image: Inline image 1]
>>
>>
>>
>> [image: Inline image 2]
>>
>>
>>
>>
>>
>> --
>> WITH REGARDS
>> Rohit Kumar Singh
>> Lab. no. 430,
>> P.I. Dr. S. Gourinath,
>> School of Life Sciences,
>> Jawaharlal Nehru University
>> New Delhi -110067
>>
>

[ccp4bb] Three assistant-professorships within tenure track system available

[Rik Van Deun]

To whom it may concern:

there are currently three assistant professorships available at Ghent 
University (Belgium), among which one in the field of "Single crystal X-ray 
Analysis of Bio-inorganic Materials for Life Science Applications”.
Interested people can find more information using the following link:

http://www.ugent.be/en/work/vacancies/professorial-staff/3-assistant-professors-within-the-tenure-track-system-predominantly-undertaking-research-against-the-account-of-the-special-research-fund

Kind regards,

**
Prof. dr. Rik Van Deun
L3 - Luminescent Lanthanide Lab
f-element coordination chemistry
Ghent University
Department of Inorganic and Physical Chemistry (WE06)
Krijgslaan 281 – building S3
9000 Gent
Belgium
Phone: +32 9 264 44 20
Fax: +32 9 264 49 83
E-mail: rik.vand...@ugent.be
URL: www.L3.ugent.be
**

[ccp4bb] Configuring updates through a firewall

[Guenter Fritz]

Hi,
I am using CCP4 on Sci Linux machines  and running now into some trouble 
with update manager and our firewall.

I connect through a proxy and defined the proxy in the ccp4-setup.sh.
Running update-manager gives me an error message; a new window pops up 
telling me "Downloaded data is corrupt, try again."


The proxy is as well as defined in the  ./config/CCP4/ccp4pm.conf file 
produced by the package manager. However, I had a forced passwd change 
here  and  the usrid  "Ppxu=" and the passwd "pxw=" for the proxy are 
not given in clear text, so I cannot edit those.


 I also tried simply to run the new package manager, but I cannot get 
through the firewall.


Can somebody point me how to get updates once more  running through the 
proxy?
Or, can somebody give me a hint how to edit the ccp4pm.conf file? That 
could resolve the issue as well.


Thanks, Guenter

Re: [ccp4bb] active 3D monitors: successor of Asus VG278HR?

[Kay Diederichs]

Having configured my CentOS-7 workstation for Stereo today, I have also updated 
the Stereo article in the CCP4 wiki ( 
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo ). It turns 
out that there seem to be 8 active monitors (i.e. built-in emitter) that can be 
bought in Germany (EU), at the moment. 

If anything in the article is incorrect, pls fix it (or tell me what's wrong).

Performance of the Quadro K420 that I have: loading the "tutorial" data into 
coot and doing "spin view", it does about 1 revolution per 2-3 seconds, very 
smoothly (120 Hz update frequency). The speed is the same when labels are on 
the screen, and with/without stereo.

best,

Kay

On Thu, 8 Jan 2015 21:11:54 -0800, Jens Kaiser  wrote:

>In addition to what others have -- correctly -- stated I want to add one
>more thing:
>
>Yes, you are right, if you do not get your hands on a monitor with
>built-in emitter, you'll need ad least a K4000 and in many cases the
>VESA din bracket (~$50). You do not have to buy the expensive ($800+) 3D
>Vision pro emitter, though, for about $150 you can get the 3D Vision 2
>(the "2" is important!) kit, that includes the DIN-to-Phone jack cable
>(officially for connection to DLP) you'll need to connect the graphics
>card to the emitter. Don't use the DP-DVI adapter, there's not enough
>bandwidth - go straight out of the DVI and you'll be fine (this
>realization cost me a day).
>
>HTH,
>
>Jens
>
>
>On Thu, 2015-01-08 at 15:08 +0100, Tobias Beck wrote:
>> Dear all,
>>
>>
>> I am looking again at 3D monitors. Last year I bought for my old lab
>> the VG278HR and the PNY K600, as advised by the CCP4BB. (The 3D test
>> images from Nvidia were running fine under Windows, but I did not get
>> around to finish the set up with pymol and coot under linux.)
>>
>>
>> Now at a new place, I looked at available monitors again (that have
>> the built-in emitter since I want to use the K600 graphics card) and
>> noticed that the VG278HR is out of stock. The VG278H, which seems to
>> be a very similar model, is also out of stock.
>>
>>
>> This page
>>
>> http://www.nvidia.com/object/3d-vision-displays.html
>>
>> also lists the Acer HN274H as a 27'' monitor with built-in emitter,
>> but that seems to be out of stock as well (I would prefer not to buy a
>> refurbished or used one). The monitors mentioned above are also listed
>> here:
>>
>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
>>
>>
>> (The smaller BenQ XL2420TX listed there is also out of stock).
>>
>>
>>
>> Has anybody ordered a 3D monitor with built-in emitter recently or
>> could provide me with a current list of 27'' monitors with built-in
>> emitters? I checked with Nvidia via their chat support, but they did
>> not have an updated list, just provided links to the manufacturers'
>> homepages.
>>
>>
>> If monitors with built-in emitters are not available anymore, I need
>> to buy a different graphics card in order for the setup to work with
>> linux, right?
>>
>>
>>
>> Thank you and best wishes, Tobias.
>>
>>
>> --
>> ___
>>
>> Dr. Tobias Beck
>> - group leader -
>> RWTH Aachen University
>> Institute of Inorganic Chemistry
>> Landoltweg 1, office: 304N
>> 52056 Aachen, Germany
>> phone:  +49-241-80-90057
>> fax:   +49-241-80-99003
>> ___
>>
>>

[ccp4bb] fitting peptide with non-standard and standard amino acids

[ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ]

Dear All,

I wonder if you could help me with this. I am trying to do some 
regularisation/real space refinement of a ligand with Coot. The ligand is a 
pseudopeptide with two non-standard aminoacids, followed by several standard 
ones. I assume that to do this correctly, I would need a cif file that 
specifies the two non-standard aa's plus the links between these two and 
between second and third (which is a standard one). When trying to generate a 
cif with a program such as eLBOW (using a pdb as the starting reference), each 
of the non-standard aa's gets a cif of its own, and the third, standard one, is 
ignored, meaning that there are no specified links between the first two 
(non-standard) and even less between second (non-standard) and third 
(standard). Coot of course keeps each aa as it should be, but breaks up the 
peptide chain completely.

Could you direct me how to built a cif that includes such bond specifications, 
starting from a reference pdb or otherwise? Is there an altogether different 
way of getting Coot to do what I want?

Many thanks,

Emmanuel



Dr. Emmanuel Saridakis
Researcher C
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

[Horrell, Sam]

Hi Emmanuel, 

I've never tried something quite as complex as a pseudopeptide but if you can 
build your lingand in the coot ligand builder coot will generate a cif file for 
you. Previously I have built my ligand, used real space refinement to get it 
into position, merged the protein and ligand and saved the model. Your coot may 
be different but my cif file always ended up in 
wincoot/new/examples/coot-ccp4/prodrg-out.cif. Make sure you rename this cif 
and move it to a new directory as I believe coot will just save over this when 
you make your next ligand.

Good luck, 

Sam

Sam Horrell BSc (Hons)
Research Student
School of Life Sciences
Life Sciences Building
University of Liverpool
Crown Street
Liverpool L69 7ZB
United Kingdom


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of ΕΜΜΑΝΟΥΗΛ 
ΣΑΡΕΙΔΑΚΗΣ [e.sarida...@inn.demokritos.gr]
Sent: 20 January 2015 15:32
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] fitting peptide with non-standard and standard amino acids

Dear All,

I wonder if you could help me with this. I am trying to do some 
regularisation/real space refinement of a ligand with Coot. The ligand is a 
pseudopeptide with two non-standard aminoacids, followed by several standard 
ones. I assume that to do this correctly, I would need a cif file that 
specifies the two non-standard aa's plus the links between these two and 
between second and third (which is a standard one). When trying to generate a 
cif with a program such as eLBOW (using a pdb as the starting reference), each 
of the non-standard aa's gets a cif of its own, and the third, standard one, is 
ignored, meaning that there are no specified links between the first two 
(non-standard) and even less between second (non-standard) and third 
(standard). Coot of course keeps each aa as it should be, but breaks up the 
peptide chain completely.

Could you direct me how to built a cif that includes such bond specifications, 
starting from a reference pdb or otherwise? Is there an altogether different 
way of getting Coot to do what I want?

Many thanks,

Emmanuel



Dr. Emmanuel Saridakis
Researcher C
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

[Robbie Joosten]

Dear Emmanuel,

Is the modified residues are really new, you can make restraint files with 
jligand or acedrug (both in CCP4). Make sure the backbone atoms have the same 
names as in standard amino acids. Now open de cif-file(s) in a text editor and 
set the residue type to 'peptide' (you can use ALA.cif from ccp4 as an 
example). If your residues are sequentially numbered, then Refmac should detect 
the LINKs automatically. Coot may do that as well.

HTH,
Robbie

-Oorspronkelijk bericht-
Van: "ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ" 
Verzonden: ‎20-‎1-‎2015 16:55
Aan: "CCP4BB@JISCMAIL.AC.UK" 
Onderwerp: [ccp4bb] fitting peptide with non-standard and standard amino acids

Dear All,

I wonder if you could help me with this. I am trying to do some 
regularisation/real space refinement of a ligand with Coot. The ligand is a 
pseudopeptide with two non-standard aminoacids, followed by several standard 
ones. I assume that to do this correctly, I would need a cif file that 
specifies the two non-standard aa's plus the links between these two and 
between second and third (which is a standard one). When trying to generate a 
cif with a program such as eLBOW (using a pdb as the starting reference), each 
of the non-standard aa's gets a cif of its own, and the third, standard one, is 
ignored, meaning that there are no specified links between the first two 
(non-standard) and even less between second (non-standard) and third 
(standard). Coot of course keeps each aa as it should be, but breaks up the 
peptide chain completely.

Could you direct me how to built a cif that includes such bond specifications, 
starting from a reference pdb or otherwise? Is there an altogether different 
way of getting Coot to do what I want?

Many thanks,

Emmanuel



Dr. Emmanuel Saridakis
Researcher C
Institute of Nanoscience and Nanotechnology
National Centre for Scientific Research "DEMOKRITOS"
15310 Athens
GREECE

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

[Paul Emsley]

On 20/01/15 15:32, ΕΜΜΑΝΟΥΗΛ ΣΑΡΕΙΔΑΚΗΣ wrote:

Dear All,

I wonder if you could help me with this. I am trying to do some 
regularisation/real space refinement of a ligand with Coot. The ligand is a 
pseudopeptide with two non-standard aminoacids, followed by several standard 
ones. I assume that to do this correctly, I would need a cif file that 
specifies the two non-standard aa's plus the links between these two and 
between second and third (which is a standard one).


What's the group?  You need 'peptide'.


When trying to generate a cif with a program such as eLBOW (using a pdb as the 
starting reference), each of the non-standard aa's gets a cif of its own, and 
the third, standard one, is ignored, meaning that there are no specified links 
between the first two (non-standard) and even less between second 
(non-standard) and third (standard).


Have you read the JLigand tutorial?



Coot of course keeps each aa as it should be, but breaks up the peptide chain 
completely.


When you try to do what?




Could you direct me how to built a cif that includes such bond specifications, 
starting from a reference pdb or otherwise? Is there an altogether different 
way of getting Coot to do what I want?


You can use Prodrg (via Prodrgify in Coot) but that is not recommended 
(because it requires chemistry perception)


I have no reason to doubt that Elbow restraints for modified amino acids 
would be just fine.  I wouldn't do it that way, of course though.


Paul.

Re: [ccp4bb] fitting peptide with non-standard and standard amino acids

[Karim Rafie (PG Research)]

Hi Emmanuel,

Additionally you can also use the PRODRG server straight away and just
pipe in the coordinates for your peptide and it will give you one cif file
for it.

Cheers,
Karim
##
Karim Rafie; M.Sc.
PhD research studentDaan van Aalten lab
MRC Protein Phosphorylation and Ubiquitylation Unit
College of Life Sciences
University of Dundee
Scotland / UK






On 20/01/2015 16:12, "Horrell, Sam"  wrote:

>Hi Emmanuel,
>
>I've never tried something quite as complex as a pseudopeptide but if you
>can build your lingand in the coot ligand builder coot will generate a
>cif file for you. Previously I have built my ligand, used real space
>refinement to get it into position, merged the protein and ligand and
>saved the model. Your coot may be different but my cif file always ended
>up in wincoot/new/examples/coot-ccp4/prodrg-out.cif. Make sure you rename
>this cif and move it to a new directory as I believe coot will just save
>over this when you make your next ligand.
>
>Good luck,
>
>Sam
>
>Sam Horrell BSc (Hons)
>Research Student
>School of Life Sciences
>Life Sciences Building
>University of Liverpool
>Crown Street
>Liverpool L69 7ZB
>United Kingdom
>
>
>From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of ΕΜΜΑΝΟΥΗΛ
>ΣΑΡΕΙΔΑΚΗΣ [e.sarida...@inn.demokritos.gr]
>Sent: 20 January 2015 15:32
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] fitting peptide with non-standard and standard amino
>acids
>
>Dear All,
>
>I wonder if you could help me with this. I am trying to do some
>regularisation/real space refinement of a ligand with Coot. The ligand is
>a pseudopeptide with two non-standard aminoacids, followed by several
>standard ones. I assume that to do this correctly, I would need a cif
>file that specifies the two non-standard aa's plus the links between
>these two and between second and third (which is a standard one). When
>trying to generate a cif with a program such as eLBOW (using a pdb as the
>starting reference), each of the non-standard aa's gets a cif of its own,
>and the third, standard one, is ignored, meaning that there are no
>specified links between the first two (non-standard) and even less
>between second (non-standard) and third (standard). Coot of course keeps
>each aa as it should be, but breaks up the peptide chain completely.
>
>Could you direct me how to built a cif that includes such bond
>specifications, starting from a reference pdb or otherwise? Is there an
>altogether different way of getting Coot to do what I want?
>
>Many thanks,
>
>Emmanuel
>
>
>
>Dr. Emmanuel Saridakis
>Researcher C
>Institute of Nanoscience and Nanotechnology
>National Centre for Scientific Research "DEMOKRITOS"
>15310 Athens
>GREECE


The University of Dundee is a registered Scottish Charity, No: SC015096

Re: [ccp4bb] chloride or water

[Zhijie Li]

Hi Rohit,

If it is of some significance you may consider replacing NaCl with KI or NaI in 
your crystallization condition and collect a dataset at 1.5-2 Angstrom. The 
Iodide anomalous signal might be of some help for identifying Chloride binding 
sites. 
Without further evidence for a Cl ion, unless the environment strongly suggests 
an anion binding site (as what Robbie said) my personal view is that it is more 
proper to put a water there. 

Zhijie



From: rohit kumar 
Sent: Tuesday, January 20, 2015 1:59 AM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] chloride or water


Dear all,

I am solving a data of 3.0 Å resolution. In the active site we found an 
unidentified blob. The crystallization condition is (PEG 3350-25%, 
Naformate-200mM, MES (100mM)-6.5pH, and Nacl-200mM). 
Can anyone suggest what it could be? If I suppose that, it is chloride, how 
could someone differentiate between a chloride moiety and water.
below I am showing the coot figure in two different orientations.

Thanks in advance...



 




 





-- 

WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

Re: [ccp4bb] chloride or water

[Keller, Jacob]

Try each one, refine, compare resulting b-factors and bond lengths to 
surrounding atoms. It’s a chloride though.

JPK

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
Sent: Tuesday, January 20, 2015 2:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] chloride or water

Hi Rohit,

If it is of some significance you may consider replacing NaCl with KI or NaI in 
your crystallization condition and collect a dataset at 1.5-2 Angstrom. The 
Iodide anomalous signal might be of some help for identifying Chloride binding 
sites.
Without further evidence for a Cl ion, unless the environment strongly suggests 
an anion binding site (as what Robbie said) my personal view is that it is more 
proper to put a water there.

Zhijie



From: rohit kumar
Sent: Tuesday, January 20, 2015 1:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] chloride or water


Dear all,

I am solving a data of 3.0 Å resolution. In the active site we found an 
unidentified blob. The crystallization condition is (PEG 3350-25%, 
Naformate-200mM, MES (100mM)-6.5pH, and Nacl-200mM).
Can anyone suggest what it could be? If I suppose that, it is chloride, how 
could someone differentiate between a chloride moiety and water.
below I am showing the coot figure in two different orientations.

Thanks in advance...














--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067

[ccp4bb] A basic question about Fourier Transform

[Chen Zhao]

Dear all,

I am sorry about this slightly off-topic question. I am now a graduate TA
for crystallography course and one student asked me a question that I
didn't ask myself before. I don't have enough knowledge to precisely answer
this question, so I am seeking for help here.

The question is, as I rephrased it, assuming we are able to measure the
diffraction pattern of a single molecule with acceptable accuracy and
precision (comparable to what we have now for the common crystals), is it
better than we measure the diffraction spots from a crystal, given that the
spots are just a sampling of the continuous pattern from a single molecule
and there is loss of information in the space between the spots that are
not sampled by the lattice? Of course this is more of a thought experiment,
so we don't need to consider that all measurement is discrete in nature
owing to the limitation of the pixel size. I kinda agree with him and I
have a feeling that this is related to the sampling theorem. I do
appreciate your valuable comments. If this is not true, why? If this is
true, what is its effect on electron density?

Thank you so much for your attention and your help in advance!

Best,
Chen

Re: [ccp4bb] A basic question about Fourier Transform

[Keller, Jacob]

>The question is, as I rephrased it, assuming we are able to measure the 
>diffraction pattern of a single molecule with acceptable accuracy and 
>precision (comparable to what we have now for the common crystals), is it 
>better than we measure the diffraction spots from a crystal, given that the 
>spots are just a sampling of the continuous pattern from a single molecule and 
>there is loss of information in the space between the spots that are not 
>sampled by the lattice? Of course this is more of a thought experiment, so we 
>don't need to consider that all measurement is discrete in nature owing to the 
>limitation of the pixel size. I kinda agree with him and I have a feeling that 
>this is related to the sampling theorem. I do appreciate your valuable 
>comments. If this is not true, why? If this is true, what is its effect on 
>electron density?

This question depends on how you set your criteria for the goodness of the 
single-molecule data; in a way by saying the data quality is comparable to 
crystals, the question is tautological, since the cases would by stipulation be 
the same. If you mean the resolution would be equal, and all amplitudes would 
be of SNR similar to crystal data, of course the continuously-sampled version 
would be far better. There would be no phase problem (sampling theorem), and 
maps would be outstanding.

This type of thing was, I think, the original vision of the XFEL projects—you 
could check out those early papers for more details.

JPK

Re: [ccp4bb] A basic question about Fourier Transform

[Chen Zhao]

Hi Jacob,

Thanks a lot for your reply! Yes, by comparable data quality I did mean the
comparable resolution and SNR. I now understand the original question and
kinda confirm what I thought. But I am also learning myself and I don't
quite get why the continuous sampling would get rid of the phase problem.
My first thought would be that mathematically speaking, the difference
between solving the structure from a crystal diffraction pattern and
solving the structure from a single molecule diffraction pattern only means
the transition from a discrete Fourier summation to a continuous Fourier
integral, but the phase term is always there. I am sorry for my lack of
knowledge and I only knew the very basics in the sampling theorem many
years ago.

Another related question is, do different crystal lattices sample the
reciprocal space equally well (or lose the same amount of information)? My
intuition is yes because of the symmetry in the real space stays in the
reciprocal space, but maybe I am wrong.

Sorry for keeping bothering,
Chen

On Tue, Jan 20, 2015 at 10:41 PM, Keller, Jacob 
wrote:

>   >The question is, as I rephrased it, assuming we are able to measure
> the diffraction pattern of a single molecule with acceptable accuracy and
> precision (comparable to what we have now for the common crystals), is it
> better than we measure the diffraction spots from a crystal, given that the
> spots are just a sampling of the continuous pattern from a single molecule
> and there is loss of information in the space between the spots that are
> not sampled by the lattice? Of course this is more of a thought experiment,
> so we don't need to consider that all measurement is discrete in nature
> owing to the limitation of the pixel size. I kinda agree with him and I
> have a feeling that this is related to the sampling theorem. I do
> appreciate your valuable comments. If this is not true, why? If this is
> true, what is its effect on electron density?
>
>  This question depends on how you set your criteria for the goodness of
> the single-molecule data; in a way by saying the data quality is comparable
> to crystals, the question is tautological, since the cases would by
> stipulation be the same. If you mean the resolution would be equal, and all
> amplitudes would be of SNR similar to crystal data, of course the
> continuously-sampled version would be far better. There would be no phase
> problem (sampling theorem), and maps would be outstanding.
>
>
>
> This type of thing was, I think, the original vision of the XFEL
> projects—you could check out those early papers for more details.
>
>
>
> JPK
>
>
>
>
>

Re: [ccp4bb] A basic question about Fourier Transform

[Steven Chou]

I would say you cannot measure the diffraction pattern of a single
biological molecule accurately thus far, because biological molecules are
not strong scatters and can be damaged easily. For other molecules,
actually you can!

In high-resolution electron microscopy, the diffraction pattern in the back
focal plane is actually the diffraction pattern of a projection of your
sample, which is usually composed of one to several hundred biological
molecules. For biological molecules, this pattern usually is dampened to
almost zero at a resolution between 30A-4A (actual resolution, not
theoretical); for some metal compounds, the resolution can reach up to 1 A,
or even better.

The diffraction pattern in the back focal plane is the Fourier transform
(achieved by a convex lens) of the a 2D projection of your sample. If you
apply another Fourier transform (using another convex lens) to the
diffraction pattern, you can get the 2D image of your sample (which
contains both amplitude and phase). That is, in single particle EM (imaging
mode), people don't have the phase problem. In diffraction mode (2D
electron crystallography), only the diffraction pattern (intensity) is
recorded, so they also have the phase problem.


HTH,

Steven

On Tue, Jan 20, 2015 at 10:18 PM, Chen Zhao  wrote:

> Dear all,
>
> I am sorry about this slightly off-topic question. I am now a graduate TA
> for crystallography course and one student asked me a question that I
> didn't ask myself before. I don't have enough knowledge to precisely answer
> this question, so I am seeking for help here.
>
> The question is, as I rephrased it, assuming we are able to measure the
> diffraction pattern of a single molecule with acceptable accuracy and
> precision (comparable to what we have now for the common crystals), is it
> better than we measure the diffraction spots from a crystal, given that the
> spots are just a sampling of the continuous pattern from a single molecule
> and there is loss of information in the space between the spots that are
> not sampled by the lattice? Of course this is more of a thought experiment,
> so we don't need to consider that all measurement is discrete in nature
> owing to the limitation of the pixel size. I kinda agree with him and I
> have a feeling that this is related to the sampling theorem. I do
> appreciate your valuable comments. If this is not true, why? If this is
> true, what is its effect on electron density?
>
> Thank you so much for your attention and your help in advance!
>
> Best,
> Chen
>



-- 
Steven Chou

Re: [ccp4bb] A basic question about Fourier Transform

[Chen Zhao]

Dear Steven,

Thank you for your reply! I understand that it is nearly impossible to
measure the diffraction of a single molecule, and I am just bringing this
up as a thought experiment to help understand the basics in
crystallography. But I never thought that some molecules actually allow
such measurement because you can burn it over and over again without severe
damage. Thanks a lot for this piece of information.

But for the phase problem, the difference is that, you can have magnetic
lens for the electrons in EM, but you cannot have any lenses for X-ray
beam. This is why I am still confused about this point.

Thanks a lot again,
Chen

On Tue, Jan 20, 2015 at 11:21 PM, Steven Chou  wrote:

> I would say you cannot measure the diffraction pattern of a single
> biological molecule accurately thus far, because biological molecules are
> not strong scatters and can be damaged easily. For other molecules,
> actually you can!
>
> In high-resolution electron microscopy, the diffraction pattern in the
> back focal plane is actually the diffraction pattern of a projection of
> your sample, which is usually composed of one to several hundred biological
> molecules. For biological molecules, this pattern usually is dampened to
> almost zero at a resolution between 30A-4A (actual resolution, not
> theoretical); for some metal compounds, the resolution can reach up to 1 A,
> or even better.
>
> The diffraction pattern in the back focal plane is the Fourier transform
> (achieved by a convex lens) of the a 2D projection of your sample. If you
> apply another Fourier transform (using another convex lens) to the
> diffraction pattern, you can get the 2D image of your sample (which
> contains both amplitude and phase). That is, in single particle EM (imaging
> mode), people don't have the phase problem. In diffraction mode (2D
> electron crystallography), only the diffraction pattern (intensity) is
> recorded, so they also have the phase problem.
>
>
> HTH,
>
> Steven
>
> On Tue, Jan 20, 2015 at 10:18 PM, Chen Zhao  wrote:
>
>> Dear all,
>>
>> I am sorry about this slightly off-topic question. I am now a graduate TA
>> for crystallography course and one student asked me a question that I
>> didn't ask myself before. I don't have enough knowledge to precisely answer
>> this question, so I am seeking for help here.
>>
>> The question is, as I rephrased it, assuming we are able to measure the
>> diffraction pattern of a single molecule with acceptable accuracy and
>> precision (comparable to what we have now for the common crystals), is it
>> better than we measure the diffraction spots from a crystal, given that the
>> spots are just a sampling of the continuous pattern from a single molecule
>> and there is loss of information in the space between the spots that are
>> not sampled by the lattice? Of course this is more of a thought experiment,
>> so we don't need to consider that all measurement is discrete in nature
>> owing to the limitation of the pixel size. I kinda agree with him and I
>> have a feeling that this is related to the sampling theorem. I do
>> appreciate your valuable comments. If this is not true, why? If this is
>> true, what is its effect on electron density?
>>
>> Thank you so much for your attention and your help in advance!
>>
>> Best,
>> Chen
>>
>
>
>
> --
> Steven Chou
>
>
>

[ccp4bb] Ramachandran outlier

[Dialing Pretty]

Dear All,
Real space refinement in COOT is one important strategy to reduce Ramachandran 
outlier, right?
Dialing

Re: [ccp4bb] A basic question about Fourier Transform

[Ethan Merritt]

On Tuesday, 20 January 2015 10:18:35 PM Chen Zhao wrote:
> Dear all,
> 
> I am sorry about this slightly off-topic question. I am now a graduate TA
> for crystallography course and one student asked me a question that I
> didn't ask myself before. I don't have enough knowledge to precisely answer
> this question, so I am seeking for help here.
> 
> The question is, as I rephrased it, assuming we are able to measure the
> diffraction pattern of a single molecule with acceptable accuracy and
> precision (comparable to what we have now for the common crystals), is it
> better than we measure the diffraction spots from a crystal, given that the
> spots are just a sampling of the continuous pattern from a single molecule
> and there is loss of information in the space between the spots that are
> not sampled by the lattice?

While it is true that there is a loss of information because of the space
between the Bragg reflections, this is not as bad as you might think.
The Nyquist theorem tells us that we can reconstruct a Fourier term exactly
if we can sample at one half the period of that term.
So for any given resolution of Bragg spots, the continuous transform
to half that resolution can be reconstructed.  Here "can be reconstructed"
implicitly includes "... if we know the phase".  So it comes back to the
phase problem.  If we could measure the phase, it would only matter to a
factor of 2 in resolution that we are not measuring the continuous transform.

By the way, as Jacob Keller alluded to earlier, XFEL diffraction from 
nanocrystals introduces a situation half way between the two cases.
Because there are only a small number of unit cells in each direction,
the observed diffraction pattern indeed contains information in between
the Bragg peaks. One approach to interpreting this data is to treat the
measured diffraction pattern as a continuous transform of a single particle,
where that single particle just happens to be a nanocrystal containing
a small number of identical unit cells.

Ethan  

> Of course this is more of a thought experiment,
> so we don't need to consider that all measurement is discrete in nature
> owing to the limitation of the pixel size. I kinda agree with him and I
> have a feeling that this is related to the sampling theorem. I do
> appreciate your valuable comments. If this is not true, why? If this is
> true, what is its effect on electron density?
> 
> Thank you so much for your attention and your help in advance!
> 
> Best,
> Chen

-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742