Re: [ccp4bb] MSE

[Charlie Bond]

Kim Henrick wrote:

A standard amino acid is a gene product
with a specific t-RNA.


Isn't it arguable that Met-tRNA is no more specific for S-Met than for 
Se-Met, it's just a matter of what the organism has been eating?


Cheers,
Charlie
--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406

Re: [ccp4bb] MSE

[Kim Henrick]

The PDB is not an isolated database and one of our tasks is
to allow mapping and integration activities with other databases.

The PDB has closely matched GENBANK and UniProt/SwissProt over the
definitions of standard groups. A standard amino acid is a gene product
with a specific t-RNA. The number of possible post translational
modifications is very large see the UniProtKB/Swiss-Prot list
on http://www.expasy.org/cgi-bin/ptmlist.pl these are listed as
either cross_link or mod_res and the latter group include the suggestions
  Phosphoserine
  Phosphothreonine
  Phosphotyrosine

 but dont include selenomethioine

We all follow as ATOM
  http://www.chem.qmul.ac.uk/iupac/AminoAcid/AA1n2.html

We have tried to get 3-letter codes to match for HETATM
  http://www.chem.qmul.ac.uk/iupac/AminoAcid/A1416.html
  sections AA17 to Addenda


 The mapping to sequence databases such as PFam and to fasta/blast
functions would be become un-manageable depending on where one
draws the line - e.g. taking the chromophore modifications such as
 L-serine 5-imidazolinone glycine
 or
 2-imino-methionine 5-imidazolinone glycine

These are a cross-link of the peptide backbone from the alpha-carboxyl
carbon of residue N, a serine (or methionine), to the alpha-amino nitrogen
of residue N+2, a glycine, coupled with the formation of a double bond
to the alpha-amino nitrogen of residue N+1 which loses one hydrogen,
and the loss of a molecule of water. These cross-links are accompanied
by modification of residue N+1. These then dont have a 1-to-1 mapping
back to the original sequence as the product can come from several
3 residues parents.

The same is true of the many modified RNA residues in
  http://library.med.utah.edu/RNAmods/
and the exhaustive list of natural modified amino acids in
  http://www.ebi.ac.uk/RESID/

The PDB includes synthetic modified amino acids which still
have a peptide bond and in most of these cases refinement programs
treat then as patches in the topology files. In a similar manner
the PDB no longer uses the old 3-letter designations for cis-PRO
and CYS in a SS-bond.

The main problem with MSE is that many comon programs do not
treat this as an amino acid in secondary structure determination
(e.g. dssp which treats it as a chain break) whereas most of the
 ~500 modified amino acids are annotated in the PDB by software (such as
the EBI modified promotif, doss) as part of the chains and appear
in helix & sheet records if they appear as a peptide bond in a
polymeric chain.

We will be out of step with Genbank & UniProt from Jan 2008
when the Natural amino acids, PYL and SEC will become standard.
These are scheduled to be used in UniProt with one letter codes
O and U respectively from Jan 2008. Both selenocysteine and pyrrolysine
are encoded by what are otherwise termination codons using their
own special tRNA's.

As in other issues faced by the PDB this will be put to the wwPDB
SAC and the individual partner SAC's for advice and will we
will request advise from the recently formed invited wwPDB software forum
discussion group.

Treat yourself lucky that both the sequence world and the PDB dont
actually follow the t-RNA rule exactly as some primative bacteria
which lack  t-RNA for GLN and ASN - these make only ASP and GLU
but post-translationaly to produce ASN & GLN so in the PDB
you would have to use HETATM for these modified residues.

kim

[ccp4bb] CDC position available

[Stevens, James (CDC/CCID/NCIRD)]

Job Title:  Molecular Virologist
Employer: Centers for Disease Control and Prevention (CDC), Molecular Virology 
and Vaccines Branch, Influenza Division; Atlanta, GA  
Date:  30 August 2007
Job Description:  
The Molecular Virology and Vaccines Branch is recruiting outstanding scientists 
to join the Influenza Division of the CDC. Candidates will be appointed at the 
GS11/12 level. Applications will be considered from individuals with a solid 
publication record and demonstrated expertise in Structural Biology, although 
applications with experience in Virology and Molecular Biology/Biochemistry 
will also be considered. Candidates must possess a Ph.D. or equivalent degree. 
Successful candidates will be expected to integrate within a team studying the 
molecular mechanisms and markers of virulence among influenza viruses to assess 
pandemic and public health threat and develop preventive or therapeutic 
intervention strategies. The CDC offers excellent infrastructure for whole 
organism, cellular, and molecular research approaches, including 
state-of-the-art proteomics, protein interactions, microarray, confocal 
microscopy, bioinformatics, and flow cytometry facilities as well as 
BLS-3-enhanced laboratory and animal facilities. The CDC campus is contiguous 
with Emory University and provides a highly interactive health sciences 
research environment in Atlanta, a vibrant metropolitan area offering abundant 
professional, cultural, family and leisure options. Email questions about the 
position to [EMAIL PROTECTED] Applicants should email a single PDF file 
including curriculum vitae, statement of research interests, career goals, and 
the names of three references to the e-mail address above by September 30th, 
2007. CDC is an Equal Opportunity Provider and Employer.  

[ccp4bb] Pre - announcement for Study Weekend, 3 - 5 January 2008

[Howard, ME (Maeri)]

This is a pre-announcement for the annual CCP4 Study Weekend meeting to be held 
the 3rd, 4th and 5th of January 2008 at The University of Leeds, Leeds UK. 
Registration will start on the 10th of September via the Study Weekend website 
- the website is not yet live but the link will be included in the registration 
announcement on the CCP4 Bulletin Board on September 10h.
The topic of the meeting will be "Low Resolution Structure Determination and 
Validation", and speakers will include: 
Tom Steitz   (Yale 
University, USA)
Piet Gros   (Utrecht University, The 
Netherlands)
Simon Jenni   (ETH 
Zurich, Switzerland)
Florian Bruckner   
(Ludwig-Maximilians-Universität Munich, Germany)
Manfred Weiss   (EMBL Hamburg, 
Germany) 
Axel Brunger   (Stanford University, 
USA)
Nick Furnham   (Cambridge University, 
UK)
Rhiju Das   (University of Washington, 
USA)
Alwyn Jones   (Uppsala University, 
Sweden)
Jane Richardson   (Duke University, USA) 
Ton Spek   (Utrecht University, The 
Netherlands) 
Alexander Schuettelkopf 
  (Dundee 
University, UK)
Gert Vriend   (Radboud 
University Nijmegen, The Netherlands)
Thomas Luetteke   (Utrecht 
University, The Netherlands) 
Phil Jeffrey   (Princeton University, 
USA)
Chris Tate   (Cambridge University, UK) 
You can also look forward to the conference dinner to be held on the Friday 
evening at the Refectory, which is located on the campus, and is included in 
the cost of your registration fee.
The registration fee for Study Weekend will include a reduced rate for 
registering early. The rates (and dates) for registration are as follows:
Register between 10 September and 15 October - the fee is £100.00
Register between 16 October and 17 November - the fee is £135.00
Register between 18 November and 7 December - the fee is £170.00
Please note that the closing date is 7 December.
It is also worth pointing out that there are a limited amount of student 
bursaries available - a change from previous years.  In addition to a limited 
number of student bursaries, you will only be able to apply for a bursary 
during the first registration period. Information on this can be found at the 
registration website by clicking on the link for Bursaries from the homepage.
So mark you calendars for 10 September and register early! 
Maeri Howard 
CCP4 Group Administrator 
STFC Daresbury Laboratory, Daresbury UK 

Re: [ccp4bb] Rotation function calculation from 2 patterson maps

[Eleanor Dodson]

ALMN will do this ..

It does not have a GUI - Gr 
#!/bin/csh -f
#
almn \
hklin /y/people/ccp4/projects/insmon/ins_p1_1,55A-I422cell.mtz \
hklin2 /y/people/jean/Youshang/monomeric/datproc/*mtz <
Hi,
I have two patterson maps created from two observed data sets of similar structures. I want to rotate one map against the other and hence to match them to get the corresponding rotation function. Does anyone have experience how I can do that? 

Raja 



  

Re: [ccp4bb] MSE

[P.Artymiuk]

Phil

If MSE were described with ATOM cards then rasmol and other graphics programs
would display it in a sensible manner. This would be contrary to wwPDB policy
which is to make coordinates C++-friendly rather than human-useable.

Pete
Pete Artymiuk

Quoting Phil Evans <[EMAIL PROTECTED]>:

> 
> As an aside, does anyone understand why MSE is not an amino-acid?
> Phil
> 
> 
> On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
> 
> > If your PDB file conforms to standard
> >
> >   http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
> >
> > you could do
> >
> >   % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb
> >
> > You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)
> 

Re: [ccp4bb] solving structure of which 70% is known

[price]

Hi,
- I think someone already pointed out that you should try P6522.
- check that it isn't really a twinned P61 or P65 with 2 per asymmetric unit
- buy DNA with BrdU and some more with IdU, and/or grow your protein 
in SeMet - at your resolution, the more "real" phase info the better!

Phoebe

At 06:30 PM 8/29/2007, you wrote:

Hello,
 I am trying to solve a multi-protein DNA complex structure 
from a 3.6 A native data set. The target structure is a dimer (95 
aa in each monomer) in complex with DNA( 15 base pairs) plus a 
second protein of 131 aa. The data has been scaled to P6(1)22 sp. 
gr. and one target structure is expected to be in the asymmetric 
unit that corresponds to 68% solvent content. 70 % of the target 
structure is known in two parts(two different pdb structures 
previously solved contributing 55% and 15% of the target 
structure). I tried with molrep and phaser considering the first 
part(55%) as the search model but it turned out to no good solution 
which all clashes with symmetry related copies. If I assume the sp. 
gr. is not the case what else I can try. Any suggestion is well appreciated.

Thanks...
Raja


---
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html 

Re: [ccp4bb] MSE

[Joe Krahn]

One more comment on MSE: Does anyone know why MSE was defined without a
'delta' on the selenium? Isn't that obviously wrong? Selenium-delta
should be "SED ", just like S-delta is " SD ", so it can't be left off
just because selenium is not a carbon.

Phil Evans wrote:
> 
> As an aside, does anyone understand why MSE is not an amino-acid?
> Phil
> 
> 
> On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
> 
>> If your PDB file conforms to standard
>>
>>   http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
>>
>> you could do
>>
>>   % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb
>>
>> You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)

Re: [ccp4bb] off-topic-Heat shock protein gets precipitated

[Martin Hallberg]

Dear Shivesh,
Try some buffer screening.
If you have a real-time PCR machine nearby you can easily screen
96 buffer conditions in about an hour.

Check out:
Ericsson et al. Analytical Biochemistry 2006 Aug;357(2):289-98

Best regards,

Martin

On Aug 30, 2007, at 6:06 PM, shivesh kumar wrote:


Dear all
I am trying to purify HSP from C.trachomatis,a 57kDa protein for  
crystallization.The yield is very good.The problem is  
autodegradation and precipitation.I never reached to 1.5mg/ml  
concentration.There is a His-tag at C-ter.I appreciate all the  
suggestins regarding get rid of at least precipitation.Also  
appreciate worth suggestions from groups working with  
chaperonins.Thanx in advance.

Shivesh kumar


.
B. Martin Hallberg, PhD
Assistant professor
Department of Cell and Molecular Biology
Medical Nobel Institute
Karolinska Institutet
Nobels väg 3
SE-171 77 Stockholm
Sweden

Re: [ccp4bb] MSE

[Marko Hyvonen]

> 
> % egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb >
> standard_residues_only.pdb

I think the original request was to extract particular chains, so 
extending the above further to select (say) chain A

egrep '^CRYST|^SCALE|^ATOM.{17}A |^HETATM.{11}(MSE|PTR|SEP|TPO) A' your.pdb > 
standard_residues_in_chainA.pdb 

Marko

> -- Ian
> 
> > -Original Message-
> > From: [EMAIL PROTECTED] 
> > [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans
> > Sent: 30 August 2007 15:45
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: MSE
> > 
> > 
> > As an aside, does anyone understand why MSE is not an amino-acid?
> > Phil
> > 
> > 
> > On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
> > 
> > > If your PDB file conforms to standard
> > >
> > >   http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
> > >
> > > you could do
> > >
> > >   % egrep "^CRYST|^SCALE|^ATOM" your.pdb > 
> > standard_residues_only.pdb
> > >
> > > You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)
> > 
> > 
> 
> 
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 tel:  +44-(0)1223-766 044 / 760 468, fax: 766 002
 ___

[ccp4bb] off-topic-Heat shock protein gets precipitated

[shivesh kumar]

Dear all
I am trying to purify HSP from C.trachomatis,a 57kDa protein for
crystallization.The yield is very good.The problem is autodegradation and
precipitation.I never reached to 1.5mg/ml concentration.There is a His-tag
at C-ter.I appreciate all the suggestins regarding get rid of at least
precipitation.Also appreciate worth suggestions from groups working with
chaperonins.Thanx in advance.
Shivesh kumar

Re: [ccp4bb] MSE

[Joe Krahn]

The problem is that HETATM does NOT mean it is not an amino or nucleic
acid. HETATM is used to describe "non-standard" groups, where the
definition of "standard" means it is from a list of pre-determined,
hard-wired residues with reserved names. It just happens that the list
of selected "standard" residues are only nucleic and amino acids. This
leads people to think that ATOM defines polymers and HETATM defines
non-polymers, but this is wrong.

HETATM exists to allow for new "extended" types to be added to a PDB
file. Because it is possible to chemically modify an amino or nucleic
acid, we will always have to allow for some of these polymer types to be
HET residues, even if we standardize some of the unusual amino acids.

My suggestion is to make common non-polymer residues ATOM types as well,
at the very least for water, which is mopre common than anything else,
and would help avoid the misunderstanding that so many people have about
the purpose of HETATM.

Joe Krahn


Phil Evans wrote:
> 
> As an aside, does anyone understand why MSE is not an amino-acid?
> Phil
> 
> 
> On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
> 
>> If your PDB file conforms to standard
>>
>>   http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
>>
>> you could do
>>
>>   % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb
>>
>> You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

[J . Sanchez-weatherby]

All you need it this pymol script for one molecule, or adapt it for more pdbs
(I might have missed an aa or you may want to include non-standard ones).

open mol.pdb
select 
TRP+HIS+MET+ALA+GLY+PRO+CYS+LYS+TYR+ALA+ILE+VAL+LEU+SER+THR+ASN+ASP+GLN+GLU+PHE+ARG/
save path/mol_out.pdb,(sel01)

Hope this helps

Juan


Antony Oliver wrote:
> Dear Hyunchul,
>
> As far as I am aware - there is no "simple" way to do this - hopefully
> ccp4bb will prove me wrong!
>
> For your "exceptional" cases - I think there is really no other way
> apart from hand-editing or writing your own scripts.
>
> As a suggestion, scripting in PyMol is actually quite powerful, plus you
> can invoke the program without the graphics display - i.e. command line
> only.  If you know the name of the ligand, you can select everything
> else (i.e. the protein) and NOT the ligand - and then save out a new
> coordinates file.
>
> Many regards,
>
> Tony.
>
>
> Hyunchul Kim wrote:
>> I need to do this for many many pdb files so, is there any methods to
>> get protein chain only automatically?
>>
>> Best,
>>
>> Hyunchul
>>
>> 2007-08-30 (木) の 15:16 +0100 に Antony Oliver さんは書きました:
>>
>>> You could simply hand-edit the PDB file to remove the offending ligand.
>>>
>>> Regards,
>>>
>>> Tony.
>>>
>>>
>>>
>>> Hi, all
>>>
>>> I want to write a specific chain structures(protein). I tried PDBSET and
>>> biopython but they couldn't deal with some exceptional case.
>>> For example, some pdb files contain both protein structure and ligand
>>> structure in a given chain ID(e.g. 'A' or ' ')
>>>
>>> How can I obtain full chain structures without ligand structure by other
>>> methods than clicking one by one at any website.
>>>
>>> Thanks in advance.
>>>
>>> Best,
>>> Hyunchul Kim
>>>
>>> --
>>> Dr Antony W Oliver
>>> CR-UK DNA Repair Enzymes Group
>>> Section of Structural Biology
>>> The Institute of Cancer Research
>>> 237 Fulham Road
>>> Chelsea
>>> London SW3 6JB
>>> Phone: 020 7153 5451 / 5571
>>> Fax:   020 7153 5457
>>> E-mail: [EMAIL PROTECTED]
>>> --
>>>
>>>
>>>
>>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable 
>>> Company Limited by
>>> Guarantee, Registered in England under Company No. 534147 with its 
>>> Registered Office at 123 Old
>>> Brompton Road, London SW7 3RP.
>>>
>>> This e-mail message is confidential and for use by the addressee only.  If 
>>> the message is
>>> received by anyone other than the addressee, please return the message to 
>>> the sender by
>>> replying to it and then delete the message from your computer and network.
>>>
>
>
> --
> Dr Antony W Oliver
> CR-UK DNA Repair Enzymes Group
> Section of Structural Biology
> The Institute of Cancer Research
> 237 Fulham Road
> Chelsea
> London SW3 6JB
> Phone: 020 7153 5451 / 5571
> Fax:   020 7153 5457
> E-mail: [EMAIL PROTECTED]
> --
>
>
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by
> Guarantee, Registered in England under Company No. 534147 with its Registered 
> Office at 123 Old
> Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If 
> the message is received
> by anyone other than the addressee, please return the message to the sender 
> by replying to it and
> then delete the message from your computer and network.

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

[Warren DeLano]

Sure -- PyMOL can be used as a command-line tool to do stuff like this.

pymol -qc input.pdb -d 'remove not polymer;save prot_only.pdb'

> -Original Message-
> From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On 
> Behalf Of Hyunchul Kim
> Sent: Thursday, August 30, 2007 7:25 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] How to obtain specific chain protein 
> structures without ligand?
> 
> I need to do this for many many pdb files so, is there any 
> methods to get protein chain only automatically?
> 
> Best,
> 
> Hyunchul
> 
> 2007-08-30 (木) の 15:16 +0100 に Antony Oliver さんは書きました:
> > You could simply hand-edit the PDB file to remove the 
> offending ligand.
> > 
> > Regards,
> > 
> > Tony.
> > 
> > 
> > 
> > Hi, all
> > 
> > I want to write a specific chain structures(protein). I 
> tried PDBSET and
> > biopython but they couldn't deal with some exceptional case.
> > For example, some pdb files contain both protein 
> structure and ligand
> > structure in a given chain ID(e.g. 'A' or ' ')
> > 
> > How can I obtain full chain structures without ligand 
> structure by other
> > methods than clicking one by one at any website.
> > 
> > Thanks in advance.
> > 
> > Best,
> > Hyunchul Kim
> > 
> > --
> > Dr Antony W Oliver
> > CR-UK DNA Repair Enzymes Group
> > Section of Structural Biology
> > The Institute of Cancer Research
> > 237 Fulham Road
> > Chelsea
> > London SW3 6JB
> > Phone: 020 7153 5451 / 5571
> > Fax:   020 7153 5457 
> > E-mail: [EMAIL PROTECTED]
> > --
> > 
> > 
> > 
> > The Institute of Cancer Research: Royal Cancer Hospital, a 
> charitable Company Limited by Guarantee, Registered in 
> England under Company No. 534147 with its Registered Office 
> at 123 Old Brompton Road, London SW7 3RP.
> > 
> > This e-mail message is confidential and for use by the 
> addressee only.  If the message is received by anyone other 
> than the addressee, please return the message to the sender 
> by replying to it and then delete the message from your 
> computer and network.
> 
> 
> 
> 

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

[Paul Emsley]

On Thu, Aug 30, 2007 at 05:43:35PM +0900, Hyunchul Kim wrote:
> Hi, all
> 
> I want to write a specific chain structures(protein). I tried PDBSET and
> biopython but they couldn't deal with some exceptional case.
> For example, some pdb files contain both protein structure and ligand
> structure in a given chain ID(e.g. 'A' or ' ')
> 
> How can I obtain full chain structures without ligand structure by other
> methods than clicking one by one at any website.

Hello Hyunchal Kim, 

It is not clear to me exactly what you want, but you can easily ask
Coot what chains are in a particular molecule and write out a 
selection of those chains.

You can write a script that uses coot without starting up graphics.

The following will write out a pdb file "fragment.pdb" that is 
the first chain of the input "x.pdb". Loop for various values of "x.pdb"
of course.

Paul.



(let ((imol (read-pdb "x.pdb")))
  (let ((ids (chain-ids imol)))
(if (> (length ids) 0)
(let* ((interesting-chain-id (car ids)) ; or some such
   (new-mol (new-molecule-by-atom-selection 
 imol interesting-chain-id)))
  (write-pdb-file new-mol "fragment.pdb") ; or some such

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

[Antony Oliver]

Dear Hyunchul,

As far as I am aware - there is no "simple" way to do this - hopefully 
ccp4bb will prove me wrong!


For your "exceptional" cases - I think there is really no other way 
apart from hand-editing or writing your own scripts.


As a suggestion, scripting in PyMol is actually quite powerful, plus you 
can invoke the program without the graphics display - i.e. command line 
only.  If you know the name of the ligand, you can select everything 
else (i.e. the protein) and NOT the ligand - and then save out a new 
coordinates file. 


Many regards,

Tony.


Hyunchul Kim wrote:

I need to do this for many many pdb files so, is there any methods to
get protein chain only automatically?

Best,

Hyunchul

2007-08-30 (木) の 15:16 +0100 に Antony Oliver さんは書きました:
  

You could simply hand-edit the PDB file to remove the offending ligand.

Regards,

Tony.



Hi, all

I want to write a specific chain structures(protein). I tried PDBSET and
biopython but they couldn't deal with some exceptional case.
For example, some pdb files contain both protein structure and ligand
structure in a given chain ID(e.g. 'A' or ' ')

How can I obtain full chain structures without ligand structure by other
methods than clicking one by one at any website.

Thanks in advance.

Best,
Hyunchul Kim

--
Dr Antony W Oliver
CR-UK DNA Repair Enzymes Group
Section of Structural Biology
The Institute of Cancer Research
237 Fulham Road
Chelsea
London SW3 6JB
Phone: 020 7153 5451 / 5571
Fax:   020 7153 5457 
E-mail: [EMAIL PROTECTED]

--



The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.




--
Dr Antony W Oliver
CR-UK DNA Repair Enzymes Group
Section of Structural Biology
The Institute of Cancer Research
237 Fulham Road
Chelsea
London SW3 6JB
Phone: 020 7153 5451 / 5571
Fax:   020 7153 5457 
E-mail: [EMAIL PROTECTED]

--



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Re: [ccp4bb] MSE

[Ian Tickle]

Phil,

Now you've opened this can of worms I'd like to add phosphoserine,
phosphothreonine & phosphotyrosine to the wish-list of things that look
like amino-acids to me.

So to extend Clemens' suggestion to cover all these:

% egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb >
standard_residues_only.pdb

-- Ian

> -Original Message-
> From: [EMAIL PROTECTED] 
> [mailto:[EMAIL PROTECTED] On Behalf Of Phil Evans
> Sent: 30 August 2007 15:45
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: MSE
> 
> 
> As an aside, does anyone understand why MSE is not an amino-acid?
> Phil
> 
> 
> On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:
> 
> > If your PDB file conforms to standard
> >
> >   http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
> >
> > you could do
> >
> >   % egrep "^CRYST|^SCALE|^ATOM" your.pdb > 
> standard_residues_only.pdb
> >
> > You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)
> 
> 


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Re: [ccp4bb] solving structure of which 70% is known

[Eleanor Dodson]

Raja Dey wrote:

Hello,
 I am trying to solve a multi-protein DNA complex structure from a 3.6 
A native data set. The target structure is a dimer (95 aa in each monomer) in 
complex with DNA( 15 base pairs) plus a second protein of 131 aa. The data has 
been scaled to P6(1)22 sp. gr. and one target structure is expected to be in 
the asymmetric unit that corresponds to 68% solvent content. 70 % of the target 
structure is known in two parts(two different pdb structures previously solved 
contributing 55% and 15% of the target structure). I tried with molrep and 
phaser considering the first part(55%) as the search model but it turned out to 
no good solution which all clashes with symmetry related copies. If I assume 
the sp. gr. is not the case what else I can try. Any suggestion is well 
appreciated.
Thanks...
Raja


  

Have you tried SG P6 5 22?  Same systematic absences..


Eleanor

[ccp4bb] MSE

[Phil Evans]

As an aside, does anyone understand why MSE is not an amino-acid?
Phil


On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote:


If your PDB file conforms to standard

  http://www.wwpdb.org/documentation/format23/sect9.html#ATOM

you could do

  % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb

You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)

Re: [ccp4bb] How to obtain specific chain protein structures without ligand?

[Clemens Vonrhein]

If your PDB file conforms to standard

  http://www.wwpdb.org/documentation/format23/sect9.html#ATOM

you could do

  % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb

You'll miss the 'non-standard' Se-MET residue 'MSE' ;-)

Clemens

On Thu, Aug 30, 2007 at 11:22:29PM +0900, Hyunchul Kim wrote:
> I need to do this for many many pdb files so, is there any methods to
> get protein chain only automatically?
> 
> Best,
> 
> Hyunchul
> 
> 2007-08-30 (???) ??? 15:16 +0100 ??? Antony Oliver :
> > You could simply hand-edit the PDB file to remove the offending ligand.
> > 
> > Regards,
> > 
> > Tony.
> > 
> > 
> > 
> > Hi, all
> > 
> > I want to write a specific chain structures(protein). I tried PDBSET and
> > biopython but they couldn't deal with some exceptional case.
> > For example, some pdb files contain both protein structure and ligand
> > structure in a given chain ID(e.g. 'A' or ' ')
> > 
> > How can I obtain full chain structures without ligand structure by other
> > methods than clicking one by one at any website.
> > 
> > Thanks in advance.
> > 
> > Best,
> > Hyunchul Kim
> > 
> > -- 
> > Dr Antony W Oliver
> > CR-UK DNA Repair Enzymes Group
> > Section of Structural Biology
> > The Institute of Cancer Research
> > 237 Fulham Road
> > Chelsea
> > London SW3 6JB
> > Phone: 020 7153 5451 / 5571
> > Fax:   020 7153 5457 
> > E-mail: [EMAIL PROTECTED]
> > --
> > 
> > 
> > 
> > The Institute of Cancer Research: Royal Cancer Hospital, a charitable 
> > Company Limited by Guarantee, Registered in England under Company No. 
> > 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
> > 
> > This e-mail message is confidential and for use by the addressee only.  If 
> > the message is received by anyone other than the addressee, please return 
> > the message to the sender by replying to it and then delete the message 
> > from your computer and network.
> 

-- 

***
* 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] How to obtain specific chain protein structures without ligand?

[Hyunchul Kim]

I need to do this for many many pdb files so, is there any methods to
get protein chain only automatically?

Best,

Hyunchul

2007-08-30 (木) の 15:16 +0100 に Antony Oliver さんは書きました:
> You could simply hand-edit the PDB file to remove the offending ligand.
> 
> Regards,
> 
> Tony.
> 
> 
> 
> Hi, all
> 
> I want to write a specific chain structures(protein). I tried PDBSET and
> biopython but they couldn't deal with some exceptional case.
> For example, some pdb files contain both protein structure and ligand
> structure in a given chain ID(e.g. 'A' or ' ')
> 
> How can I obtain full chain structures without ligand structure by other
> methods than clicking one by one at any website.
> 
> Thanks in advance.
> 
> Best,
> Hyunchul Kim
> 
> -- 
> Dr Antony W Oliver
> CR-UK DNA Repair Enzymes Group
> Section of Structural Biology
> The Institute of Cancer Research
> 237 Fulham Road
> Chelsea
> London SW3 6JB
> Phone: 020 7153 5451 / 5571
> Fax:   020 7153 5457 
> E-mail: [EMAIL PROTECTED]
> --
> 
> 
> 
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by Guarantee, Registered in England under Company No. 534147 with its 
> Registered Office at 123 Old Brompton Road, London SW7 3RP.
> 
> This e-mail message is confidential and for use by the addressee only.  If 
> the message is received by anyone other than the addressee, please return the 
> message to the sender by replying to it and then delete the message from your 
> computer and network.

[ccp4bb] How to obtain specific chain protein structures without ligand?

[Antony Oliver]

You could simply hand-edit the PDB file to remove the offending ligand.

Regards,

Tony.



   Hi, all

   I want to write a specific chain structures(protein). I tried PDBSET and
   biopython but they couldn't deal with some exceptional case.
   For example, some pdb files contain both protein structure and ligand
   structure in a given chain ID(e.g. 'A' or ' ')

   How can I obtain full chain structures without ligand structure by other
   methods than clicking one by one at any website.

   Thanks in advance.

   Best,
   Hyunchul Kim

--
Dr Antony W Oliver
CR-UK DNA Repair Enzymes Group
Section of Structural Biology
The Institute of Cancer Research
237 Fulham Road
Chelsea
London SW3 6JB
Phone: 020 7153 5451 / 5571
Fax:   020 7153 5457 
E-mail: [EMAIL PROTECTED]

--



The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

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Re: [ccp4bb] The importance of USING our validation tools

[Ambrose Cole]

Just to add to Raji and Dave¹s comments.  It seems to me that over the last
5-10 years learning theory has indeed been discouraged, takes up to much
time etc.  This can be seen in changes that have occurred to the advice
given when writing up a thesis.  People used to write a theory chapter where
they outlined the theory behind the methods they had used.  This showed that
a student had at least some grasp as to what was going on.  In my case at
least this has proved a useful memory tool as it¹s written in my own hand
and is useful when brushing up on theory.  When I was writing up, however,
the usual advice was not to bother as you will only get asked about it in
the viva.  This led many people to avoid theory.
As the techniques used by a crystallographer increase the ability to go into
depth with every skills theory diminishes.  Many of us do some EM, NMR,
fluorescence, kinetics as well as protein purification and molecular biology
and I¹m sure many others.  The temptation to be a Œjack of all trades master
of none¹ is clearly there but it will have a deleterious affect on quality.
When people do PhD¹s they usually concentrate on one or two techniques.  In
my opinion people should be required to at least have gone into depth on
those techniques for their PhD.  This will at least give people a solid
grounding in their initial specialty.
I¹m not saying that everyone should be a grand master of the dark arts, I¹m
certainly not. But a good basis means you can deal with problems in a valid
way.

Amb


On 30/8/07 12:38, "David Briggs" <[EMAIL PROTECTED]> wrote:

> I'm going to agree with Raji's observations, and fan the flames of his point a
> little.
> 
> I count myself as lucky that I have had access to certain people during my
> crystallographic training who had a good understanding of the theory  behind
> crystallography (hopefully I have exploited this luck sufficiently). Despite
> their tutelage, I will hold my hands up and admit that certain technical
> discussions on the bb leave me a little confused occasionally...
> 
> However, I have seen what Raji described going on around me, and it is pretty
> prevalent. Structures are pushed through sometimes, without the PhD student
> really knowing quite what's happened. I cut my teeth on a few structures that
> didn't have the sort of pressure on them that others had, and this allowed me
> to get to grips with what was going on. I also had a few real pigs of projects
> - you tend to learn a lot more when stuff goes wrong - if you bang your data
> through program X and get textbook maps & stats, you haven't really learnt
> anything - if you've struggled with Molecular replacement, your SeMet won't
> crystallise and your heavy atoms won't stick, then you tend to learn how to
> make Phaser run the last half yard etc etc - and that half yard often come
> about from thinking about your problems in the right way - having an
> "old-school" crystallographer to bang ideas off can be invaluable at this
> point. Learning the theory is not always encouraged, and, given that to do it
> properly takes some time and application, it is often towards the bottom of
> the priority list. It would take a ballsy student to say to their boss, "no I
> can't do experiments X,Y & Z until I have read & understood this paper on
> Maximum Likelihood!"
> 
> However, in a system in which there exists a fair amount of pressure and
> competition (exacerbated in the US system, I think), the temptation to hand
> off ALL data to a "structure-solver" can be great. However, if this practice
> continues, as Raji suggests, there will be a lack of properly trained
> crystallographers - and mistakes will be more likely to occur.
> 
> The suggestion of explicitly stating "X crystallised, Y collected data, Z
> phased and refined" in a paper is good one, and some journals (eg Nature) like
> an "author contributions" section. However, if a group is willing to
> 'overlook' problems in their data as recently seen, maybe they cannot be
> trusted to make these statements accurately.
> 
> I think, that the only water-tight way of preventing such mistakes again is to
> have every paper that contains a structure to be reviewed by at least one
> properly-trained crystallographer, and to have the data (pdbs & SFs) made
> available to them.
> 
> just my lunchtime ramble...
> 
> Dave
> 
> On 29/08/2007, Raji Edayathumangalam <[EMAIL PROTECTED]
>  > wrote:
>> I would like to mention some other issues now that Ajees et al. has stirred
>> all sorts of 
>> discussions. I hope I haven't opened Pandora's box.
>> 
>> From what I have learned around here, very often, there seems to be little
>> time allowed or allocated
>> to actually learn--a bit beyond the surface--some of the crystallography or
>> what the 
>> crystallographic software is doing during the structure solution process.
>> 
>> A good deal of the postdocs and students here are under incredible pressure
>> to get the structure
>> DONE

Re: [ccp4bb] The importance of USING our validation tools

[David Briggs]

I'm going to agree with Raji's observations, and fan the flames of his point
a little.

I count myself as lucky that I have had access to certain people during my
crystallographic training who had a good understanding of the theory  behind
crystallography (hopefully I have exploited this luck sufficiently). Despite
their tutelage, I will hold my hands up and admit that certain technical
discussions on the bb leave me a little confused occasionally...

However, I have seen what Raji described going on around me, and it is
pretty prevalent. Structures are pushed through sometimes, without the PhD
student really knowing quite what's happened. I cut my teeth on a few
structures that didn't have the sort of pressure on them that others had,
and this allowed me to get to grips with what was going on. I also had a few
real pigs of projects - you tend to learn a lot more when stuff goes wrong -
if you bang your data through program X and get textbook maps & stats, you
haven't really learnt anything - if you've struggled with Molecular
replacement, your SeMet won't crystallise and your heavy atoms won't stick,
then you tend to learn how to make Phaser run the last half yard etc etc -
and that half yard often come about from thinking about your problems in the
right way - having an "old-school" crystallographer to bang ideas off can be
invaluable at this point. Learning the theory is not always encouraged, and,
given that to do it properly takes some time and application, it is often
towards the bottom of the priority list. It would take a ballsy student to
say to their boss, "no I can't do experiments X,Y & Z until I have read &
understood this paper on Maximum Likelihood!"

However, in a system in which there exists a fair amount of pressure and
competition (exacerbated in the US system, I think), the temptation to hand
off ALL data to a "structure-solver" can be great. However, if this practice
continues, as Raji suggests, there will be a lack of properly trained
crystallographers - and mistakes will be more likely to occur.

The suggestion of explicitly stating "X crystallised, Y collected data, Z
phased and refined" in a paper is good one, and some journals (eg Nature)
like an "author contributions" section. However, if a group is willing to
'overlook' problems in their data as recently seen, maybe they cannot be
trusted to make these statements accurately.

I think, that the only water-tight way of preventing such mistakes again is
to have every paper that contains a structure to be reviewed by at least one
properly-trained crystallographer, and to have the data (pdbs & SFs) made
available to them.

just my lunchtime ramble...

Dave

On 29/08/2007, Raji Edayathumangalam <[EMAIL PROTECTED]> wrote:
>
> I would like to mention some other issues now that Ajees et al. has
> stirred all sorts of
> discussions. I hope I haven't opened Pandora's box.
>
> From what I have learned around here, very often, there seems to be little
> time allowed or allocated
> to actually learn--a bit beyond the surface--some of the crystallography
> or what the
> crystallographic software is doing during the structure solution process.
>
> A good deal of the postdocs and students here are under incredible
> pressure to get the structure
> DONE asap. For some of them, it is their first time solving a crystal
> structure. Yes, the same
> heapful of reasons: because it's "hot", "competitive", grant deadline, PI
> tenure pressure etc. etc.
> Learning takes the backseat and this is total rubbish and very scary, in
> my biased personal opinion.
> Although I think it is the person's responsibility to take the time and
> initiative to learn, I also
> see that the pressure often is insurmountable. Often, the PI and/or
> assigned "structure solver" in
> the lab pretty much takes charge at some early stage of structure
> determination and solves the
> structure with much lesser contribution from the scientist in training
> (student/postdoc). All that
> slog to clone, purify, crystallize, optimize diffraction only to realize
> someone else will come
> along, process the data and "finish up" the structure for you. Such
> 'training' (or lack thereof) is
> a recipe for generating 'bad' structures in future and part of the reason
> for this endless thread.
>
> I think it is NOT as common for someone else to, say, run all the Western
> blots for you, maintain
> your tissue cell lines for you, do your protein preps for you. Is it
> because it is much easier to
> upload someone else's crystallographic data on one's machine and solve the
> structure (since this
> does not demand the same kind of physical labor and effort and is also a
> lot of fun) that this
> happens? I understand when the PI or "structure solver" does the above as
> part of a teamwork and
> allows for the person in question to learn. But often, I see the person is
> somewhat left overwhelmed
> and clueless in the end.
>
> I bring this issue to the forum since I do not know if this phenom

Re: [ccp4bb] Mean phase difference calculation

[Adam Ralph]

There is also a CCP4 prog that compares phase sets,
phistats. Don't know if this does what Phil suggests.

Adam



On Wed, 29 Aug 2007, Phil Evans wrote:

> Kevin
>
> Does this give the correlation between two (weighted) complex Fs,
> which is arguably (ref Bricogne) the best measure, as it corresponds
> to the map correlation but as a function of resolution?
>
> Phil
>
> On 28 Aug 2007, at 17:22, Kevin Cowtan wrote:
>
> > Yup. cphasematch
> >
> > It gives unweighted and weighted mean phase errors and F and E
> > correlations. It'll also try the opposite hand if appropriate.
> >
> > It's in the GUI under Clipper utilities.
> >
> > For an example script, run it in the GUI and then view the command
> > file.
> >
> > Kevin
> >
> > Winter, G (Graeme) wrote:
> >> Hi CCP4BB,
> >> Is there a straightforward way to compute the mean phase
> >> difference between two phase columns in an MTZ file, allowing for
> >> the difference in the origin? I am thinking something like:
> >> Cad together two reflection files - renaming the PHIB column, most
> >> likely
> >> Compute phi offset - apply to get the origins the same
> >> Compute the r.m.s. phase difference in degrees etc.
> >> Also - is there a general feeling as to how useful this is for
> >> comparing the results of phasing between different packages? I was
> >> thinking that PHI_ref could be computed fom the final refined
> >> structure, if this is available, as a benchmark. Alternatively is
> >> there a "correct" way to be doing things like this?
> >> An example script would be really great…
> >> Thanks,
> >> Graeme
>

[ccp4bb] Postdoc protein crystallographer in Greece

[Demetres D. Leonidas]

Dear all,

the following is been sent on behalf of Prof. Tzartos and all inquiries 
should be send to him.


Postdoc protein crystallographer in Greece
A postdoctoral position for a protein crystallographer is immediately 
available at the Laboratory of Molecular Neurobiology and Immunology, 
Department of Biochemistry of the Hellenic Pasteur Institute, Athens, 
Greece (www.pasteur.gr). The major part of the activities of the lab 
involves the expression of extracellular domains (210-220 amino acids 
long) of several subunits of human nicotinic acetylcholine receptors in 
eukaryotic expression systems, construction of mutant forms, 
purification and, recently, crystallization and co-crystallization 
efforts. The lab has some past expertise in protein crystallography (2 
Fab fragments) but the new post-doc will be now the main 
crystallographer of the group.
The new post-doc should have extensive expertise in protein 
crystallization and considerable expertise in crystallographic analysis. 
Expertise in molecular biology approaches is useful but not necessary.
S/he will collaborate closely with members of the lab (mostly with 
expertise in molecular biology & biochemistry) who currently produce 
sufficient amounts of wt and mutant forms of the AChR domains in various 
expression systems, and with collaborating excellent crystallographers 
in neighbouring labs. The main task of the post-doc will be to obtain 
diffraction quality crystals of these domains and their subsequent 
structure determination (of fundamental importance for subsequent drug 
design). S/he may also be involved with new expressions.
The lab is supported by several international grants (3 EC grants, 2 
MDA, 1 AFM etc) and has (or has access to) all needed equipment. The 
post will be supported by an EC grant.
Please send a preliminary request with a CV and a summary of research 
experience and interests to Prof. Socrates Tzartos, emails: 
[EMAIL PROTECTED] and [EMAIL PROTECTED]



--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

[ccp4bb] Postdoc protein crystallographer in Greece

[Demetres D. Leonidas]

Dear all,

the following is been sent on behalf of Prof. Tzartos and all inquiries 
should be send to him.


Postdoc protein crystallographer in Greece
A postdoctoral position for a protein crystallographer is immediately 
available at the Laboratory of Molecular Neurobiology and Immunology, 
Department of Biochemistry of the Hellenic Pasteur Institute, Athens, 
Greece (www.pasteur.gr). The major part of the activities of the lab 
involves the expression of extracellular domains (210-220 amino acids 
long) of several subunits of human nicotinic acetylcholine receptors in 
eukaryotic expression systems, construction of mutant forms, 
purification and, recently, crystallization and co-crystallization 
efforts. The lab has some past expertise in protein crystallography (2 
Fab fragments) but the new post-doc will be now the main 
crystallographer of the group.
The new post-doc should have extensive expertise in protein 
crystallization and considerable expertise in crystallographic analysis. 
Expertise in molecular biology approaches is useful but not necessary.
S/he will collaborate closely with members of the lab (mostly with 
expertise in molecular biology & biochemistry) who currently produce 
sufficient amounts of wt and mutant forms of the AChR domains in various 
expression systems, and with collaborating excellent crystallographers 
in neighbouring labs. The main task of the post-doc will be to obtain 
diffraction quality crystals of these domains and their subsequent 
structure determination (of fundamental importance for subsequent drug 
design). S/he may also be involved with new expressions.
The lab is supported by several international grants (3 EC grants, 2 
MDA, 1 AFM etc) and has (or has access to) all needed equipment. The 
post will be supported by an EC grant.
Please send a preliminary request with a CV and a summary of research 
experience and interests to Prof. Socrates Tzartos, emails: 
[EMAIL PROTECTED] and [EMAIL PROTECTED]


--
Demetres D. Leonidas, Ph.D.
Structural Biology & Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

[ccp4bb] How to obtain specific chain protein structures without ligand?

[Hyunchul Kim]

Hi, all

I want to write a specific chain structures(protein). I tried PDBSET and
biopython but they couldn't deal with some exceptional case.
For example, some pdb files contain both protein structure and ligand
structure in a given chain ID(e.g. 'A' or ' ')

How can I obtain full chain structures without ligand structure by other
methods than clicking one by one at any website.

Thanks in advance.

Best,
Hyunchul Kim
 

Re: [ccp4bb] Question about the percentages of occupancy for dual conformations.

[George M. Sheldrick]

Since you have high-resolution data, you can use SHELXL to refine the 
occupancy, for example so that the sum of the occupancies for the two 
conformations is constrained to be 1.0. As far as I know, this facility is 
not available in other refinement programs.

George

Prof. George M. Sheldrick FRS
Dept. Structural Chemistry, 
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582


On Thu, 30 Aug 2007, Jian Wu wrote:

> Dear all,
> If I have a set of high-resolution data in which there is an important
> residue having apparent dual conformations, my question is:
> how or where could I test and calculate the percentages of occupancy for
> the dual conformations?
> Any suggestion is welcome.
> 
> Yours,
> Jian
> -- 
> Jian Wu
> 
> Ph.D. Student
> Institute of Biochemistry and Cell Biology
> Shanghai Institutes for Biological Sciences
> Chinese Academy of Sciences (CAS)
> Tel: 0086-21-54921117
> Email: [EMAIL PROTECTED]
>