Re: [ccp4bb] a new version of XDS

[Sebastiano Pasqualato]

Hi Folmer,
it's just a matter of time, you know, given the short-living license of XDS. ;-)

Anyway, I second the request,
ciao,
s


On May 30, 2013, at 8:50 AM, Folmer Fredslund  wrote:

> Hi all,
> 
> Nice with a new version (I guess that means improvements :-)
> 
> Before I upgrade, I just have one question:
> 
> Does the change in the XPARM.XDS format mean that software such as xia2 will 
> be broken? 
> 
> Thanks,
> Folmer
> 
> 
> 2013/5/29 Kay Diederichs 
> ... is available for academic users at 
> http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
> Please note that there are some incompatibilities; most notably, the new 
> format of XPARM.XDS is different so that the new INTEGRATE does not work with 
> an old XPARM.XDS.
> 
> best,
> 
> Kay
> 
> 
> 
> 
> -- 
> Folmer Fredslund

-- 
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

Re: [ccp4bb] a new version of XDS

[Folmer Fredslund]

Hi all,

Nice with a new version (I guess that means improvements :-)

Before I upgrade, I just have one question:

Does the change in the XPARM.XDS format mean that software such as xia2
will be broken?

Thanks,
Folmer


2013/5/29 Kay Diederichs 

> ... is available for academic users at http://homes.mpimf-heidelberg.**
> mpg.de/~kabsch/xds/ 
> Please note that there are some incompatibilities; most notably, the new
> format of XPARM.XDS is different so that the new INTEGRATE does not work
> with an old XPARM.XDS.
>
> best,
>
> Kay
>
>


-- 
Folmer Fredslund

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

[Bernhard Lechtenberg]

Hi Donghui,

I don't think that is a problem in PyMOL. The cartoon representation is an 
idealized form of the secondary structure and does not strictly follow the 
atomic coordinates of the protein backbone. The strands are flattened and 
that's why you see the gaps between the strand and the side chain. By setting 
'side_chain_helper on' the flatness of the cartoon representation is switched 
off and the strand follows the protein backbone and thus you get the curves. I 
don't think there is a solution to your 'problem'. (Well, I guess you could 
move your side-chains, but that's probably not what you want)

Check the pymol wiki entries 'side-chain helper' and 'cartoon flat cycles' for 
more info:
http://www.pymolwiki.org/index.php/Cartoon_side_chain_helper

Bernhard

On May 29, 2013, at 8:29 PM, wu donghui 
mailto:wdh0...@gmail.com>> wrote:

Dear all,

I found a problem when I use pymol to prepare structure interface. Strand is 
distorted when residue from the strand is connected to the strand by turning on 
"side_chain_helper on". However when side_chain_helper is off, the strand turns 
to normal shape but the residue from it is disconnected to the strand. I 
attached the picture for your help. I know there must be some tricks for this. 
Welcome for any input. Thanks a lot.

Best,

Donghui

Re: [ccp4bb] Screening a protein surface for interaction sites

[Francois Berenger]

On 05/29/2013 04:30 PM, Gang Dong wrote:

Try FTsite: http://ftsite.bu.edu/.


I have seen people using metapocket:

http://projects.biotec.tu-dresden.de/metapocket/


Gang

On Wed, May 29, 2013 09:17, Karsten Niefind wrote:

Dear colleagues,

please allow me to ask crystallography experts for advice in a
bioinformatics issue:

Which methods (programs, servers) would you use and recommend to search
computationally on the surface of a protein/protein complex (> 1100 aa)
for concave and
convex interaction sites with potential ligands of any kind
(preferentially other proteins and
peptides, but also nucleic acids or small metabolites and with emphasis on
"potential", i.e. if
no concrete ligand is known)?

Thanks for any help from

Karsten Niefind


---
Karsten Niefind
University of Cologne
Department of Chemistry
Institute of Biochemistry
Otto-Fischer-Str. 12-14
D-50674 Cologne
Tel.: +49 221 470 6444
Fax: +49 221 470 3244

Re: [ccp4bb] a new version of XDS

[Jacob Keller]

I use Cygwin normally, which seems to work fine for most things...

Jacob


On Wed, May 29, 2013 at 5:08 PM, Jim Fairman  wrote:

> You can always use VMWare player to run a virtual machine of a Linux
> distribution inside Windows.  It's free and it works fairly well.
>
>
> On Wed, May 29, 2013 at 1:29 PM, Jacob Keller <
> j-kell...@fsm.northwestern.edu> wrote:
>
>> Any thoughts of making a Windows executable? Might help a lot of users
>>
>> JPK
>>
>>
>> On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs <
>> kay.diederi...@uni-konstanz.de> wrote:
>>
>>> ... is available for academic users at http://homes.mpimf-heidelberg.**
>>> mpg.de/~kabsch/xds/ 
>>> Please note that there are some incompatibilities; most notably, the new
>>> format of XPARM.XDS is different so that the new INTEGRATE does not work
>>> with an old XPARM.XDS.
>>>
>>> best,
>>>
>>> Kay
>>>
>>>
>>
>>
>> --
>> ***
>>
>> Jacob Pearson Keller, PhD
>>
>> Looger Lab/HHMI Janelia Farms Research Campus
>>
>> 19700 Helix Dr, Ashburn, VA 20147
>>
>> email: kell...@janelia.hhmi.org
>>
>> ***
>>
>
>
>
> --
> Jim Fairman, Ph D.
> Crystal Core Leader I
> Emerald BioStructures 
> Tel: 206-780-8914
> Cell: 240-479-6575
> E-mail: fairman@gmail.com jfair...@embios.com
>



-- 
***

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: kell...@janelia.hhmi.org

***

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)

[Robbie Joosten]

Hi Rachel,

Thanks for clarifying this. Things will be much easier when SPLIT entries are 
consolidated. That is, when all the software is updated as well.

> Entries are split only for reasons of size.  
1apg was, sort of, an example of the contrary (see the, now obsolete, 
reflection file).  I thought there were more examples, but fortunately I 
couldn't find any quickly.

Cheers,
Robbie

> We will continue the practice that any structure deposited as a single
> PDBx/mmCIF file will be divided into SPLIT files and added to the ftp archive
> as usual, in all supported formats (PDB, PDBx/mmCIF, PDBML/XML).
> 
> Entries are split only for reasons of size.  SPLIT entries currently in the 
> archive
> will remain as they are until sometime in 2014 when we plan to consolidate all
> existing and new SPLIT entries into single large files.
> 
> Regards,
> Rachel
> 
> 
> 
> 
> 
> Rachel Kramer Green, Ph.D.
> 
> RCSB PDB
> 
> kra...@rcsb.rutgers.edu
> 
> 
> 
> 
> 
> Twitter: https://twitter.com/#!/buildmodels
> 
> Facebook: http://www.facebook.com/RCSBPDB
> 
> 
> 
> On 5/24/2013 12:41 PM, Robbie Joosten wrote:
> 
> 
> 
>   Perhaps a silly question: will old entries with SPLIT records be
> superseded by consolidated entries? And what about entries split for other
> reasons than size (there are only a few of those, and they are old)?
> 
>   Cheers,
>   Robbie
> 
> 
> 
>   Van: Gerard DVD Kleywegt
>   Verzonden: 24-5-2013 20:21
>   Aan: CCP4BB@JISCMAIL.AC.UK
>   Onderwerp: [ccp4bb] "Formageddon" is upon us... Important news
> from wwPDB!
> 
> 
> 
>   Dear colleagues,
> 
>   I would like to draw your attention to a notification from the wwPDB
> partners
>   about "Deposition and Release of PDB Entries Containing Large
> Structures" -
>   see:
> 
>  http://www.wwpdb.org/news/news_2013.html#22-May-2013
> 
>   There are major changes afoot in the way large structures are
> handled in the
>   PDB, as well as in the deposition and annotation procedures and
> software used
>   by the wwPDB sites. This is of immediate relevance for depositors
> and users of
>   large structures, but also for software developers and anyone who
> routinely
>   processes the entire PDB archive or its weekly releases
> (bioinformatics
>   resources, etc.). From 2014, it will affect essentially everyone who
> deposits,
>   uses or processes PDB entries.
> 
>   If you have any questions about the new deposition system or the
> procedures
>   for handling large structures or any of the other changes, please
> contact:
>   i...@wwpdb.org
> 
>   Please pass on this information to anyone likely to be affected by the
>   upcoming changes. Thanks!
> 
> 
>   On behalf of the Worldwide Protein Data Bank,
> 
>   --Gerard Kleywegt
> 
>   ---
>   Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
>   ger...@ebi.ac.uk . pdbe.org
>   Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk
> 
> 

Re: [ccp4bb] a new version of XDS

[Jim Fairman]

You can always use VMWare player to run a virtual machine of a Linux
distribution inside Windows.  It's free and it works fairly well.


On Wed, May 29, 2013 at 1:29 PM, Jacob Keller <
j-kell...@fsm.northwestern.edu> wrote:

> Any thoughts of making a Windows executable? Might help a lot of users
>
> JPK
>
>
> On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs <
> kay.diederi...@uni-konstanz.de> wrote:
>
>> ... is available for academic users at http://homes.mpimf-heidelberg.**
>> mpg.de/~kabsch/xds/ 
>> Please note that there are some incompatibilities; most notably, the new
>> format of XPARM.XDS is different so that the new INTEGRATE does not work
>> with an old XPARM.XDS.
>>
>> best,
>>
>> Kay
>>
>>
>
>
> --
> ***
>
> Jacob Pearson Keller, PhD
>
> Looger Lab/HHMI Janelia Farms Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
>
> email: kell...@janelia.hhmi.org
>
> ***
>



-- 
Jim Fairman, Ph D.
Crystal Core Leader I
Emerald BioStructures 
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman@gmail.com jfair...@embios.com

[ccp4bb] re big structure

[Kim Henrick]

I have been reprimanded by the PDB as:

"In this instance we could not recommend matrix formulation because of
 the substantial conformational differences between individual
 subunits.  Only with the full set of coordinates released can other
 groups perform independent analyses/evaluation."

both structures have the same split
 zmore 3j3y.cif.gz | grep -i split
 zmore 3j3q.cif.gz | grep -i split

this doesnt make sense ?

all the split files have REMARK   2 RESOLUTION.NULL ANGSTROMS
while each split file doesnt refer to the parent (which one?)
SPLIT  1VUU 1VUV 1VUW 1VUX 1VUY 1VUZ 1VV0 1VV1 1VV2 1VV3 1VV4 1VV5
1VV6 1VV7
SPLIT2 1VV8 1VV9 1VVA 1VVB 1VVF 1VVG 1VVH 1VVI

Only this one has a resolution
 3J34 REMARK   2 RESOLUTION.8.60 ANGSTROMS.

i.e. the large files seem to not have a resolution

zmore 3j3y.cif.gz | grep -i resol
_em_3d_reconstruction.resolution  ?
_em_3d_reconstruction.resolution_method   ?

zmore 3j3q.cif.gz | grep -i resol
_em_3d_reconstruction.resolution  ?
_em_3d_reconstruction.resolution_method   ?

The two structures appear to be
(i) built on a 8.6Ang EM structure
(ii) from a molecular dynamics run(s) with NAMD
 is it a theoretical model

Also at 8.6 Ang one cannot see a 3-10 helix
only in the MD can such a thing come out

The authors cannot have built the EM fitted structure by hand
and found differences - so the EM fitted structure
has to have exact symmetry while the MD structure (why is it in the PDB ?)
may have differences after as they say a 1.5 micro-second MD run
with NAMD

[I am old enough to remember that picoseconds were possible not micro
seconds]

And then how can anyone analyse a normal pdb virus structure which
has incomplete coordinates but symmetry matrices and for the largest
structure in the pdb, i.e.
1m4x1680  3  # well this has 5040 chains in biomolecule

does anyone really believe 8.6Ang data has differences in symmetry

If one does ? then I must be in dreamland


zcat 3j3q.cif.gz | grep _em > 3j3q
zcat 3j3y.cif.gz | grep _em > 3j3y

diff 3j3q 3j3y

there are no differences apart from vitrification category in one
file and pdb idcodes

they both say

;The model was built using hexamer of hexamers (PDB entry 3J34) and
pentamer of hexamers (computer-based MD model available upon request).


OK so the entire PDB ftp/policy is changed over a theoretical model?

Re: [ccp4bb] a new version of XDS

[Kay Diederichs]

Sorry, Wolfgang Kabsch has decided against it.
Kay



Jacob Keller  schrieb:

>Any thoughts of making a Windows executable? Might help a lot of
>users
>
>JPK
>
>
>On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs <
>kay.diederi...@uni-konstanz.de> wrote:
>
>> ... is available for academic users at
>http://homes.mpimf-heidelberg.**
>> mpg.de/~kabsch/xds/
>
>> Please note that there are some incompatibilities; most notably, the
>new
>> format of XPARM.XDS is different so that the new INTEGRATE does not
>work
>> with an old XPARM.XDS.
>>
>> best,
>>
>> Kay
>>
>>
>
>
>-- 
>***
>
>Jacob Pearson Keller, PhD
>
>Looger Lab/HHMI Janelia Farms Research Campus
>
>19700 Helix Dr, Ashburn, VA 20147
>
>email: kell...@janelia.hhmi.org
>
>***

-- 
Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

Re: [ccp4bb] a new version of XDS

[Jacob Keller]

Any thoughts of making a Windows executable? Might help a lot of users

JPK


On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs <
kay.diederi...@uni-konstanz.de> wrote:

> ... is available for academic users at http://homes.mpimf-heidelberg.**
> mpg.de/~kabsch/xds/ 
> Please note that there are some incompatibilities; most notably, the new
> format of XPARM.XDS is different so that the new INTEGRATE does not work
> with an old XPARM.XDS.
>
> best,
>
> Kay
>
>


-- 
***

Jacob Pearson Keller, PhD

Looger Lab/HHMI Janelia Farms Research Campus

19700 Helix Dr, Ashburn, VA 20147

email: kell...@janelia.hhmi.org

***

[ccp4bb] a new version of XDS

[Kay Diederichs]

... is available for academic users at 
http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
Please note that there are some incompatibilities; most notably, the new 
format of XPARM.XDS is different so that the new INTEGRATE does not work 
with an old XPARM.XDS.


best,

Kay



smime.p7s
Description: S/MIME Kryptografische Unterschrift

Re: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB! (help-4246)

[Rachel Kramer Green]

Dear Robbie,

We will continue the practice that any structure deposited as a single 
PDBx/mmCIF file will be
divided into SPLIT files and added to the ftp archive as usual, in all 
supported formats (PDB,

PDBx/mmCIF, PDBML/XML).

Entries are split only for reasons of size.  SPLIT entries currently in 
the archive will remain as
they are until sometime in 2014 when we plan to consolidate all existing 
and new SPLIT entries into

single large files.

Regards,
Rachel



Rachel Kramer Green, Ph.D.

RCSB PDB

kra...@rcsb.rutgers.edu

Twitter: https://twitter.com/#!/buildmodels

Facebook: http://www.facebook.com/RCSBPDB

On 5/24/2013 12:41 PM, Robbie Joosten wrote:


Perhaps a silly question: will old entries with SPLIT records be 
superseded by consolidated entries? And what about entries split for 
other reasons than size (there are only a few of those, and they are old)?


Cheers,
Robbie

Van: Gerard DVD Kleywegt
Verzonden: 24-5-2013 20:21
Aan: CCP4BB@JISCMAIL.AC.UK
Onderwerp: [ccp4bb] "Formageddon" is upon us... Important news from wwPDB!

Dear colleagues,

I would like to draw your attention to a notification from the wwPDB 
partners
about "Deposition and Release of PDB Entries Containing Large 
Structures" -

see:

http://www.wwpdb.org/news/news_2013.html#22-May-2013

There are major changes afoot in the way large structures are handled 
in the
PDB, as well as in the deposition and annotation procedures and 
software used
by the wwPDB sites. This is of immediate relevance for depositors and 
users of
large structures, but also for software developers and anyone who 
routinely

processes the entire PDB archive or its weekly releases (bioinformatics
resources, etc.). From 2014, it will affect essentially everyone who 
deposits,

uses or processes PDB entries.

If you have any questions about the new deposition system or the 
procedures
for handling large structures or any of the other changes, please 
contact:

i...@wwpdb.org

Please pass on this information to anyone likely to be affected by the
upcoming changes. Thanks!


On behalf of the Worldwide Protein Data Bank,

--Gerard Kleywegt

---
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
ger...@ebi.ac.uk . pdbe.org
Secretary: Pauline Haslam  pdbe_ad...@ebi.ac.uk

[ccp4bb] the large structure now in the pdb

[Kim Henrick]

I am surprised that the fuss about the structure 3J3Q

the pdb documentation states
"For all structures deposited as complex assemblies, we will archive
 symmetry information as appropriate in _pdbx_point_symmetry or
 _pdbx_helical_symmetry records."

For the cone shaped viral capsid discussed in 1999:
 Assembly and Analysis of Conical Models for the HIV-1 Core
 Science 1 January 1999: Vol. 283 no. 5398 pp. 80-83
 DOI: 10.1126/science.283.5398.80
 Barbie K. Ganser, Su Li, Victor Y. Klishko, John T. Finch, Wesley I.
 Sundquist

and the symmetry properties explained in

 Elasticity Theory and Shape Transitions of Viral Shells
 T. T. Nguyen, R. F. Bruinsma, W. M. Gelbart
 Phys. Rev. E 72, 051923 (2005)
 DOI:10.1103/PhysRevE.72.051923
 this paper describes the cone shape and the symmetry, i.e.
"In contrast, an example where continuum theory really is expected to
 be applicable are core particles of the HIV-1 virus. The immature HIV
 capsid is spherical, though not icosahedral, with diameters in the
 range of 120 to 260 nm39. After cleavage of the Gag capsid protein
 into CA ("capsid") and NC ("nucleocapsid") proteins – plus a matrix
 protein – the core reforms into a conical shell with a size of about
 100 nm (majority case) plus a smaller fraction of tubular particles.
 The FvK number of the (mature) cone is of the order of 20,000, well
 above the buckling threshold. According to our results, conical
 capsids with FvK numbers in this range do constitute a well-defined
 local minimum of the elastic energy with m/n ratios between 1.5 and 2
 and spontaneous curvatures about twice the critical value (see
 Fig.15)."

These 2 papers on symmetry of cones must be known to all concerned
isnt it possible to use this symmetry as NCS in the structure just
released that causes the fuss about large structures?

Simply cat the split*.pdb and rasmol clearly shows the symmetry of the
cone from the apex radiating out and recombining back to the other
end, of note is that rasmol colours chains at a TER record and the
colours are based on the order in the file so the split of this
molecule is very random.

Surely the authors and the PDB staff should have known about the
symmetry description  or is everyone
stuck on the idea of Viral Capsid T-numbers which only cover basically
spherical shapes? At the resolution (actually not stated on the EMDB page)
http://www.ebi.ac.uk/pdbe/entry/EMD-5639/visualization
and using the volume viewer, it is unlikely that the authors could
have built the chains without the use of the cone symmetry and
at the map details shown there could not be any detectable break in the
use of symmetry. (The title page figure shown is
  "simulated density of all-atom HIV-1 capsid model (3J3Y)
   overlaid with a slice of HIV-1 core tomogram." so appears
   not an experimental observation.


Actually just what is the difference between 3j3q and 3j3y
as there is no obvious difference on display and the mmcif titles
are no help.

_struct.entry_id 3J3Y
_struct.title'Atomic-level structure of the entire HIV-1 capsid (186
hexamers
  + 12 pentamers)'
_struct.entry_id 3J3Q
_struct.title'Atomic-level structure of the entire HIV-1 capsid'

And why is what was a part of the old pqs o/p for a virus showing
the 5fold and the 23fold being issued as yet another PDB idcode
as PDB  3J34 unspecified 'Hexameric unit obtained by MDFF and cryo-EM'
- which shows a core fragment, is this a theoretical model ?

The structure would have made less fuss if issued with BIOMOLECULE
matrices and been generated in full by software.

If the author can over ride PDB stated processing policy then what is
the use of the documentation? under
"Processing Procedures Version 2.6 as of December 2012"
on  http://www.wwpdb.org/docs.html#format
as it is obviously not in use.

Re: [ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

[Ed Pozharski]

> I am wondering whether there is a function I could use to build the
> missing bases in one strand of the DNA to base pair with the other
> strand of DNA which is complete...

Calculate->Other modeling tools-> Base pair...

-- 
Coot verendus est

[ccp4bb] To build ssDNA to base pair with the other strand of DNA in coot

[Wei Shi]

Hi all,
I am working on solving the crystal structure of a protein-DNA complex. I
could complete one strand of the DNA to fit the electron density using
Coot, but for the other strand, the density for several bases at each end
of the DNA is not clear and it's missing several bases at each end of the
DNA. I am wondering whether there is a function I could use to build the
missing bases in one strand of the DNA to base pair with the other strand
of DNA which is complete and without the need to fit the density (since the
density for those several bases are not very clear). Thank you so much!

Best,
Wei

Re: [ccp4bb] use only companies that you know to purchase chemicals

[Jeremy Stevenson]

> Just curious - why registration date indicates unsavory nature of "Jieke"?

>From what I have seen people set up fake companies and use them as a front to 
>scam as many people as possible until they are discovered and someone posts 
>that it is a scam. Once they are found out they establish the next fake 
>website and continue.

If you look at this company's about us page the pictures and the description of 
the scale of the company it doesn't match with a company that would only have 
had a website for 1 year.

The scammers definitely take advantage of the language and cultural difference. 
If you see something that is odd you dismiss it as just a language barrier 
issue instead of an actual problem. That's one of the big things that got me.

-Jeremy

-Original Message-
From: Ed Pozharski [mailto:epozh...@umaryland.edu] 
Sent: Wednesday, May 29, 2013 12:37 PM
To: Jeremy Stevenson
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] use only companies that you know to purchase chemicals

On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote:
> In this particular case you can see the website was registered in 
> September of 2012, which is a good indication that it was set up just 
> to scam people.

Just curious - why registration date indicates unsavory nature of "Jieke"?

--
After much deep and profound brain things inside my head, I have decided to 
thank you for bringing peace to our home.
Julian, King of Lemurs

Re: [ccp4bb] use only companies that you know to purchase chemicals

[Ed Pozharski]

On Wed, 2013-05-29 at 12:30 -0400, Jeremy Stevenson wrote:
> In this particular case you can see the website was registered in
> September of 2012, which is a good indication that it was set up just
> to scam people.

Just curious - why registration date indicates unsavory nature of
"Jieke"?

-- 
After much deep and profound brain things inside my head, 
I have decided to thank you for bringing peace to our home.
Julian, King of Lemurs

Re: [ccp4bb] use only companies that you know to purchase chemicals

[Jeremy Stevenson]

Jackie,

My heart goes out to you. I got scammed much worse than you. Someone posing as 
a distributor said they had several customers in China that wanted to place 
orders for our equipment. They got me to fly out to China and asked me to buy 
gifts for the president of their company. It turned out to be a scam just to 
get the gifts - but they were VERY, VERY good at it. When I called the police 
they came to my hotel room and tried to help but couldn't. They were very nice 
but also had a good laughed at me. I wasn't laughing at the time, but I can 
look back now and see that that it was a relatively cheap lesson. 

Having said that, we are now doing great business in China and we have lots of 
good customers. So, because of a few bad apples, don't assume that everyone in 
China is out to get you. There are reputable companies that supply quality 
products. Unfortunately, there are also a disproportionate number of scammers 
looking to make a quick buck.

You did the right thing trying to retrieve the wire - that worked for us in 
another case with a vendor. However, if that didn't work I would say that 
anything else will require a lot of effort and will likely be fruitless. But, 
you did the right thing, you posted and made everyone aware of this problem.

In the future one thing to do is to check the DNS registration of the website. 
Go to http://www.networksolutions.com/whois/index.jsp and type in the website 
address (without the HTTP). In this particular case you can see the website was 
registered in September of 2012, which is a good indication that it was set up 
just to scam people. Likely all of the names and addresses associated with the 
registration are fake.

-Jeremy

Jeremy Stevenson, President, Formulatrix, Inc.

-
Date:Tue, 28 May 2013 12:47:04 -0400
From:Jacqueline Vitali 
Subject: use only companies that you know to purchase chemicals

Dear all,

I used the guidechem chemical network to obtain a compound that is not sold in 
US.  Many people responded and I was persuaded to try to buy it from

SHANGHAI JIEKE BIOTECHNOLOGY LIMITED COMPANY

Adress：NO.1008 Qigangroad,FengXianZone,ShangHai,China

Tel  ：+86-031-97265503
Fax  ：+86-031-97265320
Site  ： http://www.jiekechem.com/


 My University send the money as they requested the money to be paid in 
advance.  I saw no compound and the person disappeared when she obtained the 
information of my University.  My university requested the wire back but the 
recipients "cannot be reached" and the bank in China closed the request to 
return the funds because it could not reach the recipients.  Yet the recipients 
still have an account in this bank.


I reported to guidechem and they ignored me.


(1) Do not trust companies that you do not know especially in other countries.  
There are many unreliable places.  Do not take a chance like I did.


(2) Is there any way to get the money back?


The bank information and account are
This is our bank information:
COMPANY NAME :  SHIJIAZHUANG DUNAO CHEMICAL CO., LTD
Name: BANK OF CHINA SHIJIAZHUANG ,ZHONGSHAN BR.
Address:NO.83WEST  ZHONGSHAN  ROAD,
SHIJIAZHUANG,  HEBEI,  CHINA
Account No.: 100391967084
Swift Code : BKCHCNBJ220

I feel very bad about the whole thing.

Can anyone advise how to get the money back?

Jackie

[ccp4bb] CSHL X-ray Methods in Structural Biology Course Oct 14-29, 2013: Application deadline June 15th

[Jim Pflugrath]

Hey Everybody,

I wanted to draw your attention again to the upcoming application deadline on 
June 15, 2013 for the
CSHL X-ray Methods in Structural Biology Course to be held October 14-29, 2013.

Also please also pass this on to any colleagues, friends, professors, research 
associates, grad students, and I suppose relatives who would benefit from 
attending the course.

Here's a link to the announcement:  
http://meetings.cshl.edu/courses/2013/c-crys13.shtml
The course is supported by a grant from the National Institute of General 
Medical Sciences

Some financial assistance is also available, see the course announcement on the 
details of that.

I think the course is an outstanding place to learn both the theoretical and 
practical aspects of Macromolecular Crystallography because of the extensive 
lectures from world-renowned teachers and the hands-on experiments. An  entire 
"always open" wet lab is devoted to the Course and we rent 18 iMacs for all the 
computational work, so everyone has simultaneous access for any and all 
computational work. But the real plus of this course is the interactions of the 
participants and the instructors --- just ask any former student.

This year's course will once again see the return of the long-time instruction 
team of Alex McPherson, Gary Gilliland, Bill Furey and myself along with many 
talented experts to help us give the participants an experience in 
Macromolecular Crystallography learning that cannot be found anywhere else.  
(The student:teacher ratio ends up to be about 1:1).  We expect to have the 
participants crystallize several proteins and determine their structures all in 
about two weeks.  In 2012, participants also crystallized a membrane protein, 
collected diffraction data, and solved the structure by molecular replacement.  
We intend to expand on that in 2013.

The course is limited to 16 participants due to the very hands-on nature of the 
experiments and the intimate seminar room.  Please check the above web site for 
more details.

If anyone has any questions, please send me e-mail, I will be happy to answer 
all queries.

Jim

Re: [ccp4bb] Dimple on windows?

[Marcin Wojdyr]

On Tue, May 28, 2013 at 11:44:55AM +, Björn Kauppi wrote:
> Is there any way to install the dimple script on my windows CCP4i 
> installation?
> 

It will be included in the next version of the ccp4 suite.
For now you can try command-line version from:
http://devtools.fg.oisin.rc-harwell.ac.uk/files/dimple-1.3.zip
(that's a version for windows prepared today).
Requires installed CCP4 6.3 and WinCoot (coot is only for making images).
It also uses Raster3d which is included in the zip.

Basic usage:
dimple.bat input.mtz input.pdb output_dir

But first try running tests/test.bat to check if it works.
It's not much tested yet.

Regards
Marcin
-- 
Scanned by iCritical.

Re: [ccp4bb] how to make the crystal thicker

[Xiaohu Guo]

Dear Yan:

I had a similar problem with the crystal(thin, thread diffraction in one 
direction ). Many try with the crystal optimization failed. However using 
micro-focus beamline with a small oscillation angel (0.1- 0.2 degree) I could 
collect a full data set and successfully processed with XDS. 

Best
Xiaohu


On May 29, 2013, at 3:18 AM, 姜艳 wrote:

> Dear professors,
> I get my crystal in 0.1M Tris, PH7.5, 200mM (NH4)2SO4, and 20% PEG3350, 
> however, it is very thin. From one side, the diffraction is perfect, about 
> 2.2A, but from the other side, diffraction is too bad, the spots look like a 
> thread! Process cannot be done by HKL2000.
> As top guns of this field, could you  give me some suggestion to make the 
> crystal thicker? I will be grateful for your kind help.
> Best,
> Jiang Yan
> 
> Institute of Biophysics, Chinese Academy of Sciences
> Beijing, Chaoyang District
> 
> 

---
Xiaohu Guo, Ph.D student
Department of Cell and Molecular Biology, Uppsala University
Uppsala Biomedical Center (BMC)
Box 596
S-751 24 Uppsala
Sweden
Phone: +46 765826578

Re: [ccp4bb] how to make the crystal thicker

[Yong Wang]

There are many variables you can adjust, not sure how many you have tried.  
Here are a few that pop up first for me:

Seeding (if growth is not well controlled)
Changing drop ratio or vapor diffusion set up (sitting vs hanging vs under oil) 
to control the kinetic process as well as the final point in the phase diagram
Changing growth temperature
Additive screen
The above are the easy stuff without changing the well composition.  If they 
don’t work, you can optimize the well composition.  I will start with the salt 
concentration, then buffer type, then other components.  Good luck.


---
Yong Wang, Ph.D.   Research Advisor, 
Discovery Chemistry Research
Eli Lilly & Company   Phone:  
317-655-9145
Lilly Corporate Center  DC 0403  Fax:  317-651-6333
Indianapolis, IN  46285   wang_y...@lilly.com

CONFIDENTIALITY NOTICE:  This e-mail message from Eli Lilly and Company 
(including all attachments) is for the sole use of the intended recipient(s) 
and may contain confidential and privileged information.  Any unauthorized 
review, use, disclosure, copying or distribution is strictly prohibited.  If 
you are not the intended recipient, please contact the sender by reply e-mail 
and destroy all copies of the original message.




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??
Sent: Tuesday, May 28, 2013 9:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] how to make the crystal thicker

Dear professors,
I get my crystal in 0.1M Tris, PH7.5, 200mM (NH4)2SO4, and 20% PEG3350, 
however, it is very thin. From one side, the diffraction is perfect, about 
2.2A, but from the other side, diffraction is too bad, the spots look like a 
thread! Process cannot be done by HKL2000.
As top guns of this field, could you  give me some suggestion to make the 
crystal thicker? I will be grateful for your kind help.
Best,
Jiang Yan

Institute of Biophysics, Chinese Academy of Sciences
Beijing, Chaoyang District

Re: [ccp4bb] Screening a protein surface for interaction sites

[Gang Dong]

Try FTsite: http://ftsite.bu.edu/.

Gang

On Wed, May 29, 2013 09:17, Karsten Niefind wrote:
> Dear colleagues,
>
> please allow me to ask crystallography experts for advice in a
> bioinformatics issue:
>
> Which methods (programs, servers) would you use and recommend to search
> computationally on the surface of a protein/protein complex (> 1100 aa)
> for concave and
> convex interaction sites with potential ligands of any kind
> (preferentially other proteins and
> peptides, but also nucleic acids or small metabolites and with emphasis on
> "potential", i.e. if
> no concrete ligand is known)?
>
> Thanks for any help from
>
> Karsten Niefind
>
>
> ---
> Karsten Niefind
> University of Cologne
> Department of Chemistry
> Institute of Biochemistry
> Otto-Fischer-Str. 12-14
> D-50674 Cologne
> Tel.: +49 221 470 6444
> Fax: +49 221 470 3244
>

[ccp4bb] Screening a protein surface for interaction sites

[Karsten Niefind]

Dear colleagues,  

please allow me to ask crystallography experts for advice in a bioinformatics 
issue:

Which methods (programs, servers) would you use and recommend to search 
computationally on the surface of a protein/protein complex (> 1100 aa) for 
concave and 
convex interaction sites with potential ligands of any kind (preferentially 
other proteins and 
peptides, but also nucleic acids or small metabolites and with emphasis on 
"potential", i.e. if 
no concrete ligand is known)?

Thanks for any help from

Karsten Niefind


---
Karsten Niefind
University of Cologne
Department of Chemistry
Institute of Biochemistry
Otto-Fischer-Str. 12-14
D-50674 Cologne
Tel.: +49 221 470 6444
Fax: +49 221 470 3244