[ccp4bb] orthogonal limits of a protein

[Francois Berenger]

Hello,

Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?

Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)

Thanks,
Francois.

Re: [ccp4bb] orthogonal limits of a protein

[Pavel Afonine]

Hi Francois,

a non-ccp4 tool:

if you have PHENIX installed then:

iotbx.pdb.box_around_molecule model.pdb

will do it (if I correctly understood you question).

You can also specify a buffer region around a molecule:

iotbx.pdb.box_around_molecule model.pdb --buffer-layer=5

Pavel.


On 3/24/10 12:18 AM, Francois Berenger wrote:

Hello,

Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?

Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)

Thanks,
Francois.

Re: [ccp4bb] Display x-ray images in windows

[Kay Diederichs]

As I recently learnt from Andy Arvai, the "-nopixmap" is not needed if 
the (free) NX server has

AGENT_EXTRA_OPTIONS_X="-defer 0"
in its node.conf .

I like this a lot because I tend to forget about the -nopixmap option, 
_and_ it does not work for the zoom window.


HTH,

Kay

Am 20:59, schrieb James Holton:

Although the extension *.img is used by more than one detector
manufacturer, you are probably looking at data from an ADSC Inc
detector? Andy Arvai's "adxv" is a popular viewer for this format:

http://www.scripps.edu/~arvai/adxv.html

Run it with the option "-nopixmap" if you are using it inside an NX client.


-James Holton
MAD Scientist

Re: [ccp4bb] orthogonal limits of a protein

[Clemens Vonrhein]

Hi,

On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote:
> Hello,
>
> Is there a ccp4 tool to find automatically the smallest virtual
> orthogonal "box" that contain a given PDB ?

 echo END | pdbset xyzin your.pdb xyzout /dev/null | \
   awk '/Orthogonal Coordinate limits/,/On Z/'

might give you that info.

Cheers

Clemens

-- 

***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--
* BUSTER Development Group  (http://www.globalphasing.com)
***

Re: [ccp4bb] orthogonal limits of a protein

[Eleanor Dodson]

Francois Berenger wrote:

Hello,

Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?

Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)

Thanks,
Francois.

pdbset xyzin thisprotein.pdb
end

This prints out the limits in fractional and othogonal coordinates

Eleanor

Re: [ccp4bb] orthogonal limits of a protein

[Tim Gruene]

Dear Francois,

I don't know if the pdbset command Clemens and Eleanor suggested actually
gives  you the answer you are looking. Take for example this case:

 ---
|  /|
|/  |
 ---

assume the diagonal line is the protein as it is inside the unit cell, the
unit cell dimensions are not the smallest box that contains you diagonal line.
To get the smallest box you have to rotate the line by 45degrees and then
re-measure.

To get this answer I would use moleman2 :
 > read your.pdb
 > xyz align
 > stats
Then that statistics output would give you the mostly correct answer.

As I said, I don't want to blame pdbset, because I simply don't know whether it
takes this into account.

Cheers, Tim

On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote:
> Hello,
>
> Is there a ccp4 tool to find automatically the smallest virtual
> orthogonal "box" that contain a given PDB ?
>
> Even if your favorite tool is not part of ccp4, I would be happy
> to know about it. ;)
>
> Thanks,
> Francois.

-- 
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



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[ccp4bb] Job opportunity in structure-based ligand design in Dundee (UK)

[Ruth Brenk]

Hi,

I have a job opportunity for a highly motivated individual in the area
of structure-based ligand design design in my group.

Check out our University web page for more information about the job and
on how to apply
(http://www.jobs.dundee.ac.uk/vacancies/20100407_1-y.html).

Cheers

Ruth



--
Dr. Ruth Brenk
Biological Chemistry and Drug Discovery
College of Life Sciences
University of Dundee
Dow St.
Dundee, DD1 5EH
U.K.
+44 (0)1382 386230 (phone)
+44 (0)1382 386373 (fax)
http://www.brenkgroup.dundee.ac.uk
http://www.lifesci.dundee.ac.uk/people/ruth_brenk/

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

Re: [ccp4bb] orthogonal limits of a protein

[Ian Tickle]

Strictly speaking even Tim's solution may not give the true 'smallest
box', by which I assume is meant 'minimal volume box'.  I suspect
moleman does this calculation (my apologies to Gerard if I'm wrong!)
by determining the axes of inertia, then rotating the molecule by the
matrix of eigenvectors and finally determining the limits with respect
to this rotated frame of reference.  This will work fine if the
protein is roughly ellipsoidal (including of course spherical as a
special case), but if it has an irregular shape, then it may well not
give the minimal volume box.  To do this properly is not quite as
simple as it looks, it essentially requires a minimisation of the
volume w.r.t. the box parameters (length and orientation of the axes).
 Probably a simplex method would be a good way to do this, starting
from the inertial axes solution as an initial approximation.  So my
answer is that AFAIK there is no program that will do this.

Whether it's worth going to this degree of effort to write a program
of course depends greatly on the purpose to which the results will be
put.  Maybe if you said why you need this, then we can assess how
accurate you need the result to be, and tailor the suggestions
accordingly.

Cheers

-- Ian

On Wed, Mar 24, 2010 at 10:22 AM, Tim Gruene  wrote:
> Dear Francois,
>
> I don't know if the pdbset command Clemens and Eleanor suggested actually
> gives  you the answer you are looking. Take for example this case:
>
>  ---
> |  /|
> |/  |
>  ---
>
> assume the diagonal line is the protein as it is inside the unit cell, the
> unit cell dimensions are not the smallest box that contains you diagonal line.
> To get the smallest box you have to rotate the line by 45degrees and then
> re-measure.
>
> To get this answer I would use moleman2 :
>  > read your.pdb
>  > xyz align
>  > stats
> Then that statistics output would give you the mostly correct answer.
>
> As I said, I don't want to blame pdbset, because I simply don't know whether 
> it
> takes this into account.
>
> Cheers, Tim
>
> On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote:
>> Hello,
>>
>> Is there a ccp4 tool to find automatically the smallest virtual
>> orthogonal "box" that contain a given PDB ?
>>
>> Even if your favorite tool is not part of ccp4, I would be happy
>> to know about it. ;)
>>
>> Thanks,
>> Francois.
>
> --
> --
> Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.9 (GNU/Linux)
>
> iD8DBQFLqefrUxlJ7aRr7hoRAnpYAJ4tj3x96F0DAU4fC8W3P525rajaGwCeJxq7
> 17/s/x4/dQlc1Fh1luo2iPw=
> =X9eu
> -END PGP SIGNATURE-
>
>

[ccp4bb] Butandiol as Cryoprotectant 2.

[Ulrike Demmer]

Dear CCP4BB-users,

thanks so far for sharing your experience with Butanediol. But is it important 
to use a specific enantiomer ? Are you all only using 2R3R-Butanediol which is 
quite expensive ?

Ulrike

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

[W H]

There are three diastereomers, two of which I think work.  The meso
compound, however supposedly does not freeze clear.  Hampton sells two
of these in their kit, but doesn't specify the stereochemistry of one
of them.

http://hamptonresearch.com/product_detail.aspx?cid=30&sid=189&pid=30

William Ho



On Wed, Mar 24, 2010 at 7:31 AM, Ulrike Demmer
 wrote:
> Dear CCP4BB-users,
>
> thanks so far for sharing your experience with Butanediol. But is it 
> important to use a specific enantiomer ? Are you all only using 
> 2R3R-Butanediol which is quite expensive ?
>
> Ulrike
>

Re: [ccp4bb] orthogonal limits of a protein

[Abhinav Kumar]

I have a program that would calculate the limits of the protein along 
it's axes of inertia (besides doing many other things).

If you are interested, please let me know.

Thanks 
Abhinav 


j...@ssrl
Phone: (650) 926-2992 
Fax: (650) 926-3292 




Francois Berenger wrote:

Hello,

Is there a ccp4 tool to find automatically the smallest virtual
orthogonal "box" that contain a given PDB ?

Even if your favorite tool is not part of ccp4, I would be happy
to know about it. ;)

Thanks,
Francois.
  

[ccp4bb] Full B Factor

[Daniel Bonsor]

How do I convert the B-factors from my final structure to full B factors if I 
did not use TLS refinement? I have been refining isotropic B-factors. Do I 
switch to overall B-factor refinement, do something else, or have I missed the 
point altogether? 

It may be a dumb question but best to be safe than sorry.

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

[Leiman Petr]

> 
> thanks so far for sharing your experience with Butanediol. But is it
> important to use a specific enantiomer ? Are you all only using 2R3R-
> Butanediol which is quite expensive ?

Sigma Cat. # 18970 
2,3-Butanediol puriss., mixture of racemic and meso forms, ≥99.0% (GC) (Fluka)  
works well and freezes clear.
And it's cheap!

We've used it recently to collect 1.6 A resolution data from a crystal with 
2000+ residues in the asymmetric unit.

Petr

Re: [ccp4bb] Display x-ray images in windows

[David Waterman]

Dear Paul,
 
You can also use idiffdisp, which might do what you want.
 
See 
http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29
 

 
 
Cheers
David



From: CCP4 bulletin board on behalf of Paul Lindblom
Sent: Tue 23/03/2010 14:51
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Display x-ray images in windows


Hi everybody,

does anybody know a program to display x-ray (.img) data images in windows?

Thanks,

P.

Re: [ccp4bb] Full B Factor

[Pavel Afonine]

Hi Daniel,


How do I convert the B-factors from my final structure to full B factors if I 
did not use TLS refinement?


a non-ccp4 tool:

if you have PHENIX installed then:

1) if your PDB file has TLS matrices in its header and residual 
B-factors in ATOM records, then:


phenix.tls model.pdb combine_tls=true

will combine B-factors from TLS part with the residual B-factors from 
ATOM records and output a PDB file with total B-factors: Btotal = Btls + 
Bresidual.


2) if your PDB file has TLS matrices in its header and total B-factors 
in ATOM records, then:


phenix.tls model.pdb extract_tls=true

will extract TLS contribution from the total B-factor and write out a 
PDB file with residual B-factors in ATOM record.


Note, phenix.tls will recognize both, REFMAC and phenix.refine 
formatting styles of TLS records in PDB file header. For usage 
information type: phenix.tls in the command line and hit Return.


I will be happy to answer your questions should you have any.

Good luck!
Pavel.

[ccp4bb] 2,3-butanediol

[gauri misra]

Dear all,
I would like to know which is the more suitable method of using
2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal
soaking or both can be tried?

Cheers
Gauri

Re: [ccp4bb] Full B Factor

[Eleanor Dodson]

Daniel Bonsor wrote:
How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether? 


It may be a dumb question but best to be safe than sorry.

I think you already have the full B factor.

If you have not done TLS refinement there is no other contributor to the 
tabulated B


Good luck

Eleanor

Re: [ccp4bb] 2,3-butanediol

[Sean Seaver]

Dear all,
I would like to know which is the more suitable method of using 2,3-Butanediol 
as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both 
can be tried?

Cheers
Gauri
--
I am sure both could be tried, but have found quite few papers mentioning brief 
soaking with 2,3-butanediol:

Purification, crystallization and X-ray diffraction analysis of the 
extracellular part of the human Fc receptor for IgA, Fc[alpha]RI (CD89)
http://scripts.iucr.org/cgi-bin/paper?cnor=bw5002
5-10 seconds

Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot 
virus
http://scripts.iucr.org/cgi-bin/paper?cnor=gr2202
described as 'briefly'

Crystallization and preliminary X-ray analysis of recombinant human acid 
[beta]-glucocerebrosidase, a treatment for Gaucher's disease
http://scripts.iucr.org/cgi-bin/paper?cnor=pu0086
described as 'briefly'

Crystallization and preliminary X-ray crystallographic studies of recombinant 
human betaine-homocysteine S-methyltransferase
http://scripts.iucr.org/cgi-bin/paper?cnor=gr2115
'quickly transferred'

Purification, crystallization and X-ray analysis of Hibiscus chlorotic ringspot 
virus
http://scripts.iucr.org/cgi-bin/paper?cnor=pu0115
5% increments from 5 to 30% for 3 min at each step

Hope that helps,

Sean

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

[Tim Gruene]

[nosy]
The one that your crystal likes less. I guess that's the idea of this screen,
isn't it?
[/nosy]

Their product
http://hamptonresearch.com/documents/product/30-000221.pdf
description dedicate a full paragraph to 2,3 Butanediol.

Tim
On Wed, Mar 24, 2010 at 02:27:37PM -0400, Oganesyan, Vaheh wrote:
> Hampton's CryoPro has two 2,3-Butanediols: ## 25 and 26.
> So, which one is not the right one for cryo-preservation?
> 
> 
> 
>  Vaheh  
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Leiman 
> Petr
> Sent: Wednesday, March 24, 2010 12:37 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Butandiol as Cryoprotectant 2.
> 
> > 
> > thanks so far for sharing your experience with Butanediol. But is it
> > important to use a specific enantiomer ? Are you all only using 2R3R-
> > Butanediol which is quite expensive ?
> 
> Sigma Cat. # 18970 
> 2,3-Butanediol puriss., mixture of racemic and meso forms, ≥99.0% (GC) 
> (Fluka)
> works well and freezes clear.
> And it's cheap!
> 
> We've used it recently to collect 1.6 A resolution data from a crystal with 
> 2000+ residues in the asymmetric unit.
> 
> Petr
> 
> 
> 
> 
> 
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary.  This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended.  If you have received this electronic communication in error, 
> please reply to the sender advising of the error in transmission and delete 
> the original message and any accompanying documents from your system 
> immediately, without copying, reviewing or otherwise using them for any 
> purpose.  Thank you for your cooperation.



-- 
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



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Re: [ccp4bb] update on SeMet production

[Zhijie Li]

Hello,

Here is our lab's work with HEK293T in bioreactor:

Pak JE, Rini JM., X-ray crystal structure determination of mammalian 
glycosyltransferases., Methods Enzymol. 2006;416:30-48.


http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4MCC01F-3&_user=994540&_coverDate=12%2F31%2F2006&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C50024&_version=1&_urlVersion=0&_userid=994540&md5=678db69356318fcf86da3f9a4d6f2164


Zhijie Li

[ccp4bb] R merge and R init

[Muhammed bashir Khan]

Dear All;

I have a crystal structure collected on in house X-ray facility from
Bruker using Xprep. I submitted the paper but the reviewer ask for the R
merge. As I can't access to the computer at the moment its crashed out.
But I have the prp file which have the R init values. My question is!!!

1)Can I use the R init value instead of Rmerge?
2)If yes how it has been calculated, I mean the mathematical formula so
that I can write below the table.

Thank you very much for the help in advance

Sincerely

Bashir


-- 
Muhammad Bashir Khan
Department for Biomolecular Structural Chemistry
Max F. Perutz Laboratories
University of Vienna
Campus Vienna Biocenter 5
A-1030 Vienna
Austria

Phone: +43(1)427752224
Fax: +43(1)42779522

[ccp4bb] Positions available: Enzyme Function Initiative

[Steve Almo]

Protein Production Core in the Enzyme Function Initiative
-

We are looking to recruit individuals with extensive experience in 
molecular biology, protein purification, crystallization and automation to 
join the Protein Production Core of the newly established NIH-funded 
Enzyme Function Initiative (EFI). The goal of the EFI is to develop a 
general sequence/structure-based strategy for facilitating the discovery 
of in vitro enzymatic activities and in vivo physiological functions of 
uncharacterized enzymes discovered in genome projects. This goal will be 
accomplished by integrating informatics, structural biology and 
computational chemistry with enzymology, genetics and metabolomics. The 
EFI involves 13 investigators at 8 academic institutions.


The Protein Production Core is located within the Macromolecular 
Therapeutics Development Facility at the Albert Einstein College Medicine 
and is fully equipped to pursue all aspects of state-of-the-art structural 
genomics. The Protein Production Core exploits extensive automation and an 
active program focused on the development of novel protein 
expression/purification strategies, utilizing both prokaryotic and 
eukaryotic hosts.


Interested candidates should provide a CV and arrange for two letters of 
support to be forwarded to Dr. Ron Seidel at rsei...@aecom.yu.edu.

Re: [ccp4bb] Display x-ray images in windows

[Thomas Eriksson]

And in the "paid for" version the keyword is
AgentExtraOptions = "-defer 0"

Thomas

On 03/24/2010 12:39 AM, Kay Diederichs wrote:
> As I recently learnt from Andy Arvai, the "-nopixmap" is not needed if 
> the (free) NX server has
> AGENT_EXTRA_OPTIONS_X="-defer 0"
> in its node.conf .
> 
> I like this a lot because I tend to forget about the -nopixmap option, 
> _and_ it does not work for the zoom window.
> 
> HTH,
> 
> Kay
> 
> Am 20:59, schrieb James Holton:
>> Although the extension *.img is used by more than one detector
>> manufacturer, you are probably looking at data from an ADSC Inc
>> detector? Andy Arvai's "adxv" is a popular viewer for this format:
>>
>> http://www.scripps.edu/~arvai/adxv.html
>>
>> Run it with the option "-nopixmap" if you are using it inside an NX client.
>>
>>
>> -James Holton
>> MAD Scientist

[ccp4bb] looking for people interested in fast (0.8 ms) x-ray shutter

[Jan Kern]

Dear CCP4 community,

please excuse the off topic question. I'm currently looking into buying 
a fast shutter for X-ray use from nmlaser (www.nmlaser.com). They had a 
model LS500, marked as discontinued on their web page. It has a minimum 
opening time of 800 us, an aperture of 2.5 mm and the cross sectional 
path for X-ray use is 1.5 mm steel. They told me that they could make a 
limited custom production of this shutter if I would get a minimum of 10 
orders for these. The price for the shutter would be $695, the 
controller for the shutter would be the CX2250, which is an additional 
$1095. So I was wondering if anyone else would be interested in buying 
this shutter, so we could combine the orders.

Please answer directly to me.

Thanks a lot,

Jan

Dr. Jan Kern
Physical Bioscience Division
LBNL Berkeley
phone: +1-510-486-4330
e-mail: jfk...@lbl.gov or janfk...@gmail.com