Re: [ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

[Harshavardhan Khare]

Hi Jacob,

Principal component analysis (pca) might work but it will modify the
original dimensions as a linear combination, which might make it difficult
to derive physical meaning out of it. May be, you could use decision trees
which give results that are easier to interpret. Looking at decision trees
can also help in the analysis of pca results.
Easy to use implementation of decision trees can be found in weka software-
http://www.cs.waikato.ac.nz/ml/weka/

Regards,
Harsh

On Wednesday, July 8, 2015, Tim Gruene  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jacob,
>
> information about Thomas Schneider's program 'escet' that you remember
> can be found at
> http://www.embl-hamburg.de/~tschneider/escet/index.html
>
> Best,
> Tim
>
> On 07/08/2015 03:03 AM, Keller, Jacob wrote:
> > Is anyone aware of a way to classify large numbers (100s) of
> > conformationally-diverse crystal structures of a single protein
> > (here calmodulin)? Pairwise RMSD matrixes seem possible, but may be
> > complicated since there are two somewhat stable lobes, and the
> > flexible linker in the middle. What I am imagining is a sort of
> > multidimensional tree depicting the relationships in conformation
> > space of the various structures.
> >
> > I remember something for this called esct or similar, but can't
> > seem to google it.
> >
> > Any thoughts?
> >
> > Jacob
> >
> > *** Jacob Pearson Keller,
> > PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr,
> > Ashburn, VA 20147 email: kell...@janelia.hhmi.org 
> > ***
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
> phone: +49 (0)551 39 22149
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1
>
> iD8DBQFVnMgsUxlJ7aRr7hoRAjWwAKDrqxpq1ixeKNB+mc3h6gDxbJ8RlACePX0P
> Ai4HP3/ZY7tcdrPWJCVjhMc=
> =rhyn
> -END PGP SIGNATURE-
>

[ccp4bb] Postdoctoral position in protein crystallography available at The Institute of Cancer Research, London, UK

[Rob Van Montfort]

The Institute of Cancer Research, London, is one of the world’s most 
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A postdoctoral position is available in Dr Rob van Montfort’s Hit Discovery and 
Structural Design Team within the CTU. The Post-doc will be involved in 
high-throughput X-ray crystallography, fragment-based screening and 
structure-based drug design and will be responsible for crystallisation, 
structure determination and structural analysis of protein-ligand complexes 
from one or more of the CTU’s drug discovery programmes. The successful 
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closely with the biology, computational chemistry and medicinal chemistry teams 
at the CTU, and will therefore be expected to work across the two sites in 
Chelsea, London and Sutton, Surrey.
Applicants must have a PhD in a biological or physical science, and experience 
in macromolecular crystallography (to include protein biochemistry, protein 
crystallisation, and protein crystallography). Experience in molecular biology, 
structure-based drug design, and/or biophysics will be an advantage.
Appointment will be to a Postdoctoral Training Fellowship with starting salary 
in the range of £33,110 to £36,858 p.a. inclusive (based on previous 
experience). Appointment will be for 1 year in the first instance, and benefits 
from a contributory defined benefit pension scheme and generous leave 
entitlement. Further information can be found in the full job description at 
www.icr.ac.uk, reference 1477714.
Informal enquiries to 
rob.vanmontf...@icr.ac.uk or 
isaac.westw...@icr.ac.uk. Please DO NOT send 
your application to Dr van Montfort or Dr Westwood; CVs must be submitted via 
the ICR website. The closing date of the vacancy is 6th August 2015. We expect 
to carry out on-site interviews with shortlisted candidates in September.


Dr. Rob van Montfort
Team Leader Hit Discovery and Structural Design
Sections of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 (Sutton)
+44-(0)20-7153-5142 (Chelsea)
Email: rob.vanmontf...@icr.ac.uk






The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
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Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

[Jose Manuel Duarte]

This looks like the mapping you are after:

http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html

It maps only the structured PDB data items to their equivalent mmCIF 
items. For instance REMARK 2 is not there, but REMARK 200 is. The 
resolution value should then be in "REMARK 200 RESOLUTION RANGE HIGH" 
(corresponding to mmCIF data item _refine.ls_d_res_high).


Jose


On 07.07.2015 19:05, Phil Jeffrey wrote:
I'm updating some code to have limited mmCIF/PDB format 
interoperability and have hit a snag.  While I can infer the 
connection between some data items in the PDB header REMARK and the 
items in mmCIF I can't definitively deduce some others.  In particular 
the mapping of

REMARK  2  RESOLUTION
seems a little ambiguous and the dictionary documentation doesn't help 
in this regard.


Does anyone know where to find an explicit mapping of one data field 
to another between the two formats ?  (I don't expect there to be a 
data field in the PDB header for everything in mmCIF but I do for the 
reverse case).



Thanks
Phil Jeffrey
Princeton

[ccp4bb] Powerful new search from pdbe.org

[John Berrisford]

Have you ever searched the PDB and needed to answer questions like these?

 * Which structure is the best for the molecule you are interested in?
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 * How many different macromolecules have you worked on?
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The new search system at PDBe.org, using cleaned data and standardised 
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We also list papers which mention a PDB code, whether or not the paper 
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At 10am UK time on the 21st July we will be presenting a webinar 
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Regards
John

--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

[ccp4bb] Apply now for an EMBL-EBI course in "Structural Bioinformatics"

[Gerard DVD Kleywegt]

Hi all,

Applications are invited for a course on Structural Bioinformatics that is 
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This course will explore bioinformatics data resources and tools that are 
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- Day 1 - Monday 12 October - Bringing structure to biology
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- Day 3 - Wednesday 14 October - Genetic variation and protein structure
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- Day 5 - Friday 16 October - Small molecules with big effects

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For more information about the course and details of how to apply, please 
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Feel free to pass on this information to anyone who might be interested!

Best wishes,

--Gerard

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

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

[John Berrisford]

REMARK 2 is generated from
_refine.ls_d_res_high

http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_refine.ls_d_res_high.html

Regards

John

On Wednesday 08 July 2015 15:04:45 Jose Manuel Duarte wrote:
> This looks like the mapping you are after:
> 
> http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html
> 
> It maps only the structured PDB data items to their equivalent mmCIF
> items. For instance REMARK 2 is not there, but REMARK 200 is. The
> resolution value should then be in "REMARK 200 RESOLUTION RANGE HIGH"
> (corresponding to mmCIF data item _refine.ls_d_res_high).
> 
> Jose
> 
> On 07.07.2015 19:05, Phil Jeffrey wrote:
> > I'm updating some code to have limited mmCIF/PDB format
> > interoperability and have hit a snag.  While I can infer the
> > connection between some data items in the PDB header REMARK and the
> > items in mmCIF I can't definitively deduce some others.  In particular
> > the mapping of
> > REMARK  2  RESOLUTION
> > seems a little ambiguous and the dictionary documentation doesn't help
> > in this regard.
> >
> > Does anyone know where to find an explicit mapping of one data field
> > to another between the two formats ?  (I don't expect there to be a
> > data field in the PDB header for everything in mmCIF but I do for the
> > reverse case).
> >
> >
> > Thanks
> > Phil Jeffrey
> > Princeton
> 

-- 
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

[Phil Jeffrey]

Thanks Jose - I missed that one.

REMARK 2 is somewhat ambiguous with:
_refine.ls_d_res_high
and
_reflns.d_resolution_high

although the former makes more sense and seems to be what corresponds to 
REMARK 2.  Haven't yet seen an entry with only _reflns.d_resolution_high 
and not _refine.ls_d_res_high but there are several where the resolution 
of refinement is apparently significantly higher than the resolution of 
the source data: 1AU7, 1AW7 etc.


Cheers
Phil Jeffrey
Princeton


On 7/8/15 10:04 AM, Jose Manuel Duarte wrote:

This looks like the mapping you are after:

http://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html

It maps only the structured PDB data items to their equivalent mmCIF
items. For instance REMARK 2 is not there, but REMARK 200 is. The
resolution value should then be in "REMARK 200 RESOLUTION RANGE HIGH"
(corresponding to mmCIF data item _refine.ls_d_res_high).

Jose

Re: [ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

[Shane Caldwell]

It's not ccp4, but I've successfully used MultiSeq in VMD to make a
1-dimensional tree from a large group of conformations. Though like you
mention, the big conformational changes might not be handled well in the
STAMP alignment of that package.

ProSMART might be more appropriate if you have rigid domains and a flexible
connecting region, as it uses local structural alignments so keeps hinged
movements from having a disproportionate impact on the alignment.

Shane Caldwell
McGill University



On Tue, Jul 7, 2015 at 9:03 PM, Keller, Jacob 
wrote:

> Is anyone aware of a way to classify large numbers (100s) of
> conformationally-diverse crystal structures of a single protein (here
> calmodulin)? Pairwise RMSD matrixes seem possible, but may be complicated
> since there are two somewhat stable lobes, and the flexible linker in the
> middle. What I am imagining is a sort of multidimensional tree depicting
> the relationships in conformation space of the various structures.
>
> I remember something for this called esct or similar, but can't seem to
> google it.
>
> Any thoughts?
>
> Jacob
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>

[ccp4bb] Dials

[David Schuller]

Does this look like a suitable solution for those who like dials while 
model building?


http://petapixel.com/2015/07/07/review-palettes-modular-photo-editing-controls-are-pricey-but-powerful/

http://www.cnet.com/news/buttons-and-sliders-and-knobs-oh-my-palette-offers-a-more-physical-interface-for-pcs/

http://palettegear.com/

Palette tactile controllers - a core unit hooks up to the computer via 
USB cord. Dials, buttons and sliders can be arranged in flexible 
configurations and snap together magnetically.


They advertise compatibility for Mac and Windows. No mention of Linux. 
It looks like a lot of effort and expense went into aesthetics and this 
makes the price somewhat high.


Still, there has not been a really good solution for a control interface 
with more than one dial for a while now.


Cheers,

--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Model parts rearrangement

[Bernhard Rupp (Hofkristallrat a.D.)]

Hi Fellows, 

I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a  reference model, where
the parts form a correct ASU. 

Is the a program/script that can accomplish this assembly of parts onto the
correct model given the 
reference model?

This is probably a common nuisance with a tool already available.

Best regards,  BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-

Re: [ccp4bb] Model parts rearrangement

[Keller, Jacob]

Two possibilities:

"Cealign" all scraps onto reference in pymol

Achesym server: a generally wonderfully useful way automatically to collect 
fragments into one unit cell

JPK


-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard 
Rupp (Hofkristallrat a.D.)
Sent: Wednesday, July 08, 2015 3:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Model parts rearrangement

Hi Fellows, 

I seek advice for a trivial but tedious problem: I have rebuilt, automatically 
and manually, several parts of a structure, which of course, are all over the 
place in different ASUs. I also have a  reference model, where the parts form a 
correct ASU. 

Is the a program/script that can accomplish this assembly of parts onto the 
correct model given the reference model?

This is probably a common nuisance with a tool already available.

Best regards,  BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself in places where no one has been 
before.
-

Re: [ccp4bb] Model parts rearrangement

[Boaz Shaanan]

Hi Bernhard,  symmatch in the ccp4 suite comes to mind but also any superposition program will superimpose your scattered pieces onto the relevant part of your reference structure, won't it? 
Cheers, Boaz 



 Original message 
From: "Bernhard Rupp (Hofkristallrat a.D.)"  
Date: 
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Model parts rearrangement 




Hi Fellows, 

I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a  reference model, where
the parts form a correct ASU. 

Is the a program/script that can accomplish this assembly of parts onto the
correct model given the 
reference model?

This is probably a common nuisance with a tool already available.

Best regards,  BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-

Re: [ccp4bb] Model parts rearrangement

[Jacqueline Vitali]

coot, lsq command

i have not checked chimera but it may have too. (I think so)

For coot. I used it recently for a small molecule. 

And pymol

Finally the superpose server may do it.

On Jul 8, 2015, at 3:41 PM, Bernhard Rupp (Hofkristallrat a.D.) 
 wrote:

> Hi Fellows, 
> 
> I seek advice for a trivial but tedious problem: I have rebuilt,
> automatically and manually, several parts of a
> structure, which of course, are all over the place in different ASUs. I also
> have a  reference model, where
> the parts form a correct ASU. 
> 
> Is the a program/script that can accomplish this assembly of parts onto the
> correct model given the 
> reference model?
> 
> This is probably a common nuisance with a tool already available.
> 
> Best regards,  BR
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> hofkristall...@gmail.com
> http://www.ruppweb.org/
> -
> The man who follows the crowd will get
> no further than the crowd.
> The man who walks alone will find himself
> in places where no one has been before.
> -

Re: [ccp4bb] Model parts rearrangement

[Andrew Purkiss-Trew]

Having just faced this problem, I used the coot 'symm shift reference  
chain here' command (in Extensions / Modelling menu) to assemble the  
model from the scattered fragments.


This should be scriptable, but I didn't think it was worth the effort  
for the 20 odd fragments I had.


Hope this helps,

Andy Purkiss.

Quoting "Bernhard Rupp (Hofkristallrat a.D.)" :


Hi Fellows,

I seek advice for a trivial but tedious problem: I have rebuilt,
automatically and manually, several parts of a
structure, which of course, are all over the place in different ASUs. I also
have a  reference model, where
the parts form a correct ASU.

Is the a program/script that can accomplish this assembly of parts onto the
correct model given the
reference model?

This is probably a common nuisance with a tool already available.

Best regards,  BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The man who follows the crowd will get
no further than the crowd.
The man who walks alone will find himself
in places where no one has been before.
-






This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] DNA RNA annealing problem

[Craig Bingman]

The concentration of oligonucleotide seems much lower than you will ultimately 
need for biophysical work.  Annealing two strands is a bimolecular reaction and 
it will be driven by mass action more to completion at higher total 
oligonucleotide concentrations.  I also agree with the posts that have 
suggested higher salt concentrations.  The charge density of double-stranded 
nucleic acids is much higher than for extended or even helical single-stranded 
nucleic acids.  Higher salt will more effectively screen those charges and 
promote double helix formation.  Tris would not be my first choice for pH 
control in a sample that is going to experience a 75C shift in temperature.  
The pKa temperature coefficient for Tris is about -0.03 pH units per degree C, 
so the pH will change by over two pH units during your annealing protocol.  If 
you are starting at pH 7.5, and 95C the pH will shift to just above 5.  The pKa 
of cytosine is about 4.5 in solution, and in a highly negatively charged 
oligomer, it should shift to higher values.  Protonated bases will not form 
Watson-Crick base-pairs as expected.  I think you might do better with a buffer 
with a lower temperature coefficient.  Back in the day, we used to anneal our 
oligonucleotides in cacodylate buffer.  Sure it is toxic but it has a nearly 
flat temperature dependence and very few bacteria will live on cacodylate.  

On Jul 3, 2015, at 10:14 AM, ChenWeiFei  wrote:

> Dear all,
> I want to get a complex of DNA-RNA-protein. But I have a big problem of 
> annealing DNA-RNA.
> The length of DNA is 19nt and RNA is 17nt.
> Annealing protocol:
> 2uM DNA
> 2uM RNA
> 10mM Tris-Hcl
> 100mMNaCl
> 1mMEDTA
> 
> Heated to 95 for 5min, cooling down slowly for nearly 2h to room temperature.
> 
> I can just get a result of two single strand DNA/RNA. PAGE analysis.
> 
> No double helix was founded.
> 
> Does anyone have the same problem or know how to fix it.
> 
> Thank you for your answering.
> 
> Best regards,
> Weifei