Re: [ccp4bb] Van der waals force

2017-12-07 Thread HERMAN VAN TILBEURGH 
jiri, VDW forces are always acting and between any pair of atoms 
the optimal distance (most favourable interaction energy) depends on the pair 
of atoms involved in the interaction, but is a big bitter than the sum of 
atomic radii
all the best
herman
Herman van Tilbeurgh
Professor structural biology
Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à 
l'appliqué

Institut de Biologie Intégrative de la Cellule - I2BC
UMR 9198 CNRS- Université Paris Sud
Team: Fonction et Architecture des Assemblages MacroMoléculaires
http://www.i2bc.paris-saclay.fr/spip.php?article256

Batiment 430
91405 Orsay
France

Tel: 33 1 69 15 31 55
fax: 33 1 69 85 37 15
herman.van-tilbeu...@u-psud.fr






> Le 8 déc. 2017 à 08:52, KLAHOLZ bruno  a écrit :
> 
>  
> Hello,
>  
> van der Waals interactions are very weak, this is why we usually speak about 
> van der Waals contacts rather than interactions.
> These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate 
> a close contact or steric clash of an atomic model under refinement), 
> corresponding to the packing of the van der Waals spheres of the individual 
> atoms.
> In hydrogen bond interactions, the term “interaction” normally implies 
> sharing a hydrogen atom between two polar residues, for example between the 
> hydroxyl group of a threonine side chain with a carbonyl group of the main 
> chain peptide backbone; in there one should take into account the geometry as 
> well (e.g. ~120°-180° is favorable, 90° is not). Note that some positions 
> such as Calpha-H can be slightly polarized (these contribute to bifurcated 
> H-bonds in beta sheets for example, see e.g. 
> https://www.ncbi.nlm.nih.gov/pubmed/12220491 
>  ).
> In the context of series of van der Waals contacts between hydrophobic 
> residues there can be additive effects of the weak interactions with then sum 
> up, but in this context one should also consider entropic effects such as 
> de-solvatation which becomes favorable energetically.
>  
> Hope this helps.
>  
> Best regards,
>  
> Bruno
>  
>  
> ###
> Bruno P. Klaholz
> Centre for Integrative Biology
> Institute of Genetics and of Molecular and Cellular Biology
> 67404 ILLKIRCH
> FRANCE
> http://igbmc.fr/Klaholz 
>  
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] On Behalf Of chemocev marker
> Sent: 08 December 2017 07:55
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Van der waals force
>  
> Hi
> I just have a basic question if the Van der waals interaction will exist 
> between the hydrophobic residues or it can also be contributed by the polar 
> residues as well. What distance is required for the Van der waals 
> interaction. 
> 
> best
> 
> Jiri

Re: [ccp4bb] Van der waals force

2017-12-07 Thread Bruno KLAHOLZ 

Hello,

van der Waals interactions are very weak, this is why we usually speak about 
van der Waals contacts rather than interactions.
These are usually in the range of 3.5-3.8/4 Å (smaller than that may indicate a 
close contact or steric clash of an atomic model under refinement), 
corresponding to the packing of the van der Waals spheres of the individual 
atoms.
In hydrogen bond interactions, the term “interaction” normally implies sharing 
a hydrogen atom between two polar residues, for example between the hydroxyl 
group of a threonine side chain with a carbonyl group of the main chain peptide 
backbone; in there one should take into account the geometry as well (e.g. 
~120°-180° is favorable, 90° is not). Note that some positions such as Calpha-H 
can be slightly polarized (these contribute to bifurcated H-bonds in beta 
sheets for example, see e.g. https://www.ncbi.nlm.nih.gov/pubmed/12220491 ).
In the context of series of van der Waals contacts between hydrophobic residues 
there can be additive effects of the weak interactions with then sum up, but in 
this context one should also consider entropic effects such as de-solvatation 
which becomes favorable energetically.

Hope this helps.

Best regards,

Bruno


###
Bruno P. Klaholz
Centre for Integrative Biology
Institute of Genetics and of Molecular and Cellular Biology
67404 ILLKIRCH
FRANCE
http://igbmc.fr/Klaholz




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of chemocev 
marker
Sent: 08 December 2017 07:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Van der waals force

Hi
I just have a basic question if the Van der waals interaction will exist 
between the hydrophobic residues or it can also be contributed by the polar 
residues as well. What distance is required for the Van der waals interaction.
best
Jiri

Re: [ccp4bb] ITC data clarification.

2017-12-07 Thread HERMAN VAN TILBEURGH 
hi dharma

your ITC data suggest at least that your complex also exists  in solution
ITC never will answer to the question whether this is a “biological” interface
one way getting around this, would be to check the  response of your mutant 
versus WT  in biological assay
ALA substitutions soemtimes are not drastic enough to interrupt protein protein 
interactions
introduction of a charged residue facing a hydrophobic pocket often is more 
efficient

good luck
Herman van Tilbeurgh
Professor structural biology
Directeur Adjoint Ecole Doctorale Innovation Thérapeutique: du fondamental à 
l'appliqué

Institut de Biologie Intégrative de la Cellule - I2BC
UMR 9198 CNRS- Université Paris Sud
Team: Fonction et Architecture des Assemblages MacroMoléculaires
http://www.i2bc.paris-saclay.fr/spip.php?article256

Batiment 430
91405 Orsay
France

Tel: 33 1 69 15 31 55
fax: 33 1 69 85 37 15
herman.van-tilbeu...@u-psud.fr






> Le 8 déc. 2017 à 02:15, Dharma  a écrit :
> 
> Hello CCP4 users,
> Based on the crystal structure of a two molecule protein complex, I have 
> mutated (alanine substitutions) one of the putative binding interface. The 
> mutant binds with much higher affinity than the wild type. 
> However, the signature plot of ITC data reveals a decrease in the enthalpy 
> but increase on the entropy (deltaS). Thus overall increase in deltaG.
> I want to know if it’s relevant biological interface or a crystal artifact. 
> Suggestions please.
> 
> Thanks 
> Regards 
> Dharma 
> Sent from my iPhone

[ccp4bb] Van der waals force

2017-12-07 Thread chemocev marker 
Hi
I just have a basic question if the Van der waals interaction will exist
between the hydrophobic residues or it can also be contributed by the polar
residues as well. What distance is required for the Van der waals
interaction.

best

Jiri

[ccp4bb] ITC data clarification.

2017-12-07 Thread Dharma 
Hello CCP4 users,
Based on the crystal structure of a two molecule protein complex, I have 
mutated (alanine substitutions) one of the putative binding interface. The 
mutant binds with much higher affinity than the wild type. 
However, the signature plot of ITC data reveals a decrease in the enthalpy but 
increase on the entropy (deltaS). Thus overall increase in deltaG.
I want to know if it’s relevant biological interface or a crystal artifact. 
Suggestions please.

Thanks 
Regards 
Dharma 
Sent from my iPhone

[ccp4bb] Postdoctoral Fellow Position

2017-12-07 Thread Vijay Parashar 
Postdoctoral Fellow Position
Parashar laboratory at University of Delaware College of Health Sciences, is 
currently seeking a Postdoctoral Fellow to perform structure-function studies 
of proteins regulating bacterial signaling.
 Qualifications:·  Ph.D. in Biochemistry, Molecular Biology, Structural 
Biology, or a related field·  Experience with cloning, protein expression, 
and protein purification methods·  A sound understanding of methods and 
approaches relating to macromolecular crystallography preferred·  Ability 
to plan and carry out research projects independently·  Ability to work on 
own initiative and take personal responsibility for delivery of work·  
Excellent problem solving, interpersonal, communication and presentation 
skills·  A working knowledge of bacterial genetics and computational 
modeling of protein-ligand interactions preferred Responsibilities include:·
  Performing experiments for cloning, protein expression, and purification of 
proteins for biochemical and structural studies; robotic screens for 
crystallization; optimizing crystallization conditions; and collecting and 
analyzing diffraction data.·  Performing model building and structure 
refinement.·  Maintaining laboratory equipment to meet unique needs of the 
research activity·  Assisting with preparation of grant proposals, 
presentations and publications·  Actively seeking new collaborative 
projects within the department and externally University of Delaware is well 
equipped with state-of-the-art equipment for molecular biology, protein 
purification, and crystallography, including crystallization robot, crystal 
imaging system, and X-ray generator. Please visit Parashar Laboratory website 
for more information. For consideration, please send your CV, list of three 
references and other relevant information to paras...@udel.edu with subject 
line "postdoctoral application".

Re: [ccp4bb] covalent bond

2017-12-07 Thread Nigel Moriarty 
Gerado

John is correct that you can modify the restraints model to include a
covalent bond. Also in more recent version of Phenix, if the input geometry
is approximately correct, the bond can be automatically linked.

If you send me the input file, I'll take a closer look.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

On Thu, Dec 7, 2017 at 9:51 AM, Tanner, John J. 
wrote:

> You can add a covalent bond by modifying this part of the PHENIX .def file
> via the gui:
>
>   geometry_restraints.edits {
> excessive_bond_distance_limit = 10
> bond {
>   action = *add delete change
>   atom_selection_1 = None
>   atom_selection_2 = None
>   symmetry_operation = None
>   distance_ideal = None
>   sigma = None
>   slack = None
> }
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Chair, Biochemistry Department Graduate Admissions Committee
> Department of Biochemistry
> University of Missouri-Columbia
> 117 Schweitzer Hall
> 503 S College Avenue
> 
> Columbia, MO 65211
> Phone: 573-884-1280 <(573)%20884-1280>
> Fax: 573-882-5635 <(573)%20882-5635>
> Email: tanne...@missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
> On Dec 7, 2017, at 11:40 AM, Eleanor Dodson <176a9d5ebad7-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
> Is that format correct?
> Eleanor
>
> On 7 December 2017 at 17:32, gerardo andres <130afa955101-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
>> Hi everyone. I´m trying to make a covalent bond between a cystein residue
>> of a protein and its ligand, but always that I do the refinement by Phenix,
>> the ligand is placed outside of its electronic density. I edited the PDB
>> file like this:
>> LINK SG  CYS A 215 C02 LIG C   1 , but this is
>> not working.  Someone has some idea to address this problem?
>>
>> Thanks,
>>
>> Gerardo
>>
>
>
>

Re: [ccp4bb] covalent bond

2017-12-07 Thread Tanner, John J. 
You can add a covalent bond by modifying this part of the PHENIX .def file via 
the gui:

  geometry_restraints.edits {
excessive_bond_distance_limit = 10
bond {
  action = *add delete change
  atom_selection_1 = None
  atom_selection_2 = None
  symmetry_operation = None
  distance_ideal = None
  sigma = None
  slack = None
}

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A

On Dec 7, 2017, at 11:40 AM, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Is that format correct?
Eleanor

On 7 December 2017 at 17:32, gerardo andres 
<130afa955101-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hi everyone. I´m trying to make a covalent bond between a cystein residue of a 
protein and its ligand, but always that I do the refinement by Phenix, the 
ligand is placed outside of its electronic density. I edited the PDB file like 
this:
LINK SG  CYS A 215 C02 LIG C   1 , but this is not 
working.  Someone has some idea to address this problem?

Thanks,

Gerardo

Re: [ccp4bb] covalent bond

2017-12-07 Thread Eleanor Dodson 
Is that format correct?
Eleanor

On 7 December 2017 at 17:32, gerardo andres <
130afa955101-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hi everyone. I´m trying to make a covalent bond between a cystein residue
> of a protein and its ligand, but always that I do the refinement by Phenix,
> the ligand is placed outside of its electronic density. I edited the PDB
> file like this:
> LINK SG  CYS A 215 C02 LIG C   1 , but this is not
> working.  Someone has some idea to address this problem?
>
> Thanks,
>
> Gerardo
>

[ccp4bb] covalent bond

2017-12-07 Thread gerardo andres 
Hi everyone. I´m trying to make a covalent bond between a cystein residue of a 
protein and its ligand, but always that I do the refinement by Phenix, the 
ligand is placed outside of its electronic density. I edited the PDB file like 
this: LINK         SG  CYS A 215                 C02 LIG C   1 , but this is 
not working.  Someone has some idea to address this problem?
Thanks,
Gerardo

[ccp4bb] Open Research Positions: Structural Biophysics of Protein Allostery, in New York City

2017-12-07 Thread Daniel Keedy 
The Daniel Keedy Lab at the ADVANCED SCIENCE RESEARCH CENTER (ASRC) AT CUNY in 
New York City has available positions for a POSTDOCTORAL SCHOLAR and a RESEARCH 
ASSOCIATE starting in 2018.  The lab’s goal is to elucidate the role of protein 
flexibility in allosteric regulation — and to use that knowledge to control the 
function of dynamic, biomedically important enzymes such as tyrosine 
phosphatases.  To do so, we combine cutting-edge experimental and computational 
techniques in structural biology, including multitemperature X-ray 
crystallography, high-throughput protein:ligand structure determination, and 
new algorithms for modeling alternative protein conformations based on electron 
density maps.

REQUIREMENTS FOR THE POSTDOCTORAL SCHOLAR POSITION:
a PhD in structural biology, biophysics, computational biology, or a related 
field; multiple years of experience studying proteins or other macromolecules; 
and excitement to try new techniques at both the bench and the keyboard.  
Familiarity with X-ray crystallography, a programming language, and the command 
line are preferred.

REQUIREMENTS FOR THE RESEARCH ASSOCIATE POSITION:
an MS, BS, or similar degree in biochemistry, molecular biology, or a related 
field; experience conducting research in a laboratory setting; and excellent 
organizational and communication skills.  Experience with cloning, protein 
purification, and/or X-ray crystallography are preferred.

ABOUT THE ASRC:
The ADVANCED SCIENCE RESEARCH CENTER (ASRC) at the Graduate Center of the City 
University of New York (CUNY) elevates scientific research and education at 
CUNY through initiatives in five distinctive, but increasingly interconnected 
disciplines: STRUCTURAL BIOLOGY, NANOSCIENCE, PHOTONICS, NEUROSCIENCE, and 
ENVIRONMENTAL SCIENCES.  The ASRC promotes a collaborative, interdisciplinary 
research culture with researchers from each of the initiatives working 
side-by-side in the ASRC’s core facilities, sharing equipment that is among the 
most advanced available.  The ASRC is next-door to the cutting-edge 
inter-institutional NEW YORK STRUCTURAL BIOLOGY CENTER (NYSBC), and is also 
just 70 miles from the newly-constructed NATIONAL SYNCHROTRON LIGHT SOURCE II 
(NSLS-II), now the brightest synchrotron light source in the US.

Contact Dr. Keedy at 
daniel.ke...@asrc.cuny.edu with a brief 
description of your research experience, why you are interested in the lab, and 
your future research goals.  Come join us!

PDF flyer available here -- please download and circulate!
http://tinyurl.com/keedy-lab-ad-2017

—
Daniel A. Keedy, Ph.D.
Assistant Professor
Structural Biology Initiative, CUNY Advanced Science Research Center
Department of Chemistry and Biochemistry, City College of New York
http://structbio.asrc.cuny.edu/people/dr-daniel-keedy/
daniel.ke...@asrc.cuny.edu
(919) 724-6064

Re: [ccp4bb] secondary structure prediction

2017-12-07 Thread Phoebe A. Rice 
I'm fond of RaptorX


++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

pr...@uchicago.edu
https://voices.uchicago.edu/phoebericelab/


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Missoury Sophia 
[sophia.misso...@u-psud.fr]
Sent: Wednesday, December 06, 2017 9:20 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] secondary structure prediction

Modeller


Sophia Missoury





De: "Smith Liu" 
À: CCP4BB@JISCMAIL.AC.UK
Envoyé: Mercredi 6 Décembre 2017 16:04:12
Objet: Re: [ccp4bb] secondary structure prediction

Rosetta




[https://nos.netease.com/mail-online/qiyelogo/defaultAvatar.png]
Smith Liu

邮箱：smith_liu...@163.com


签名由 网易邮箱大师 定制


在2017年12月06日 22:14，zheng zhou 写道：
Dear CCP4 community,

Sorry for the off-topic question. I am trying to design constructs for
structure studies. It only has a homolog structure in PDB with
sequence identity ~20%. When I blast against PDB sequence, there are
quite a few motif hits (30~40aa, identity 40~50%). Any prediction
tools utilize this information?

Thanks for your advice in advance.

Best,

Zheng

Re: [ccp4bb] secondary structure prediction

2017-12-07 Thread Smith Liu 
yes




| |
Smith Liu
|
|
邮箱：smith_liu...@163.com
|

签名由 网易邮箱大师 定制




在2017年12月07日 09:11，zheng zhou 写道：
Thanks for many advices. I was not clear in the previous email. I know
the close homologous protein (20% identity, total 500aa), but the
fragment hits (30~40aa, identity 40~50%) are from other proteins in
PDB. I am trying to see whether the fragments from non-homologous
proteins may help the secondary structure prediction.

Best,
Z

On Wed, Dec 6, 2017 at 10:14 PM, zheng zhou  wrote:
> Dear CCP4 community,
>
> Sorry for the off-topic question. I am trying to design constructs for
> structure studies. It only has a homolog structure in PDB with
> sequence identity ~20%. When I blast against PDB sequence, there are
> quite a few motif hits (30~40aa, identity 40~50%). Any prediction
> tools utilize this information?
>
> Thanks for your advice in advance.
>
> Best,
>
> Zheng

[ccp4bb] Data analysis for Electron Microscopy, Machine Vision, and Team Leader positions at Diamond Light Source

2017-12-07 Thread Alun Ashton 
Dear All,

Please find enclosed details of positions with the Data Analysis Group at 
Diamond Light Source:

Job Title: Data Analysis Scientist / Senior Software Scientist - Electron 
Microscopy
Post Type: Full time / 3 year Fixed Term Contract
Salary information: £32,805 to £38,593 (Discretionary range to £44,382) / 
Senior role: £42,297 to £49,761 (Discretionary range to £57,225)
Application deadline: 07/01/2018 
http://www.diamond.ac.uk/Careers/Vacancies/All/129_17_CH.html 

Job Title: Data Analysis Scientist - Machine Vision
Post Type: Full time / 3 year Fixed Term Contract
Salary information: £32,805 to £38,593 (Discretionary range to £44,382) 
Application deadline: 07/01/2018
http://www.diamond.ac.uk/Careers/Vacancies/All/128_17_CH.html   

Job Title: Senior Software Engineer - Team Leader
Post Type: Full time / Permanent
Salary information: £42,297 to £49,761 (Discretionary range to £57,225)
Application deadline: 07/01/2018
http://www.diamond.ac.uk/Careers/Vacancies/All/130_17_CH.html  

Further details and other opportunities available at: 
http://www.diamond.ac.uk/Careers/Vacancies.html  

Alun
___
Alun Ashton, alun.ashton @ diamond.ac.uk Tel: +44 1235 778404
Group Leader - Data Analysis Software,www.diamond.ac.uk 
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.



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[ccp4bb] PostDoctoral Position in Structural Biology - Structural Studies of Ribosome Functional Complexes

2017-12-07 Thread Yury Polikanov 
Dear Colleagues,

We
​ ​
have an open position for a P
ost
D
oc
​ ​
in my laboratory
​
at the University of Illinois at Chicago, USA
​ ​
(https://bios.uic.edu/bios/people/faculty/yury-polikanov).
​ ​
The research in o
ur laboratory is focused on understanding basic principles of protein
synthesis in bacteria, the modes of action of ribosome-targeting
antibiotics, and mechanisms of drug resistance at a structural level. We
use macromolecular X-ray crystallography approach to determine
high-resolution structures of ribosome functional complexes.

​​
The successful candidate should hold a PhD in chemistry, biochemistry
,
biophysics
or related areas and experience in structural biology.
​ ​
​
​
The successful candidate
​ ​
should
 also
have an excellent track record and experience in X-ray crystallography as
well as
​ ​
in
protein expression
,
purification
​
,
crystallization, data collection, structure determination
,
and model refinement.
​
 Advanced computer s
kills together with
experience
​ ​
i
n complementary biochemical and biophysical techniques related to the
studies of the 70S ribosome
would be a benefit.
​ ​
Preference will be given to those who have a strong drive
,
motivation
, and passion for discovery
.

​
Applicants should submit
​ ​
cover letter,
curriculum vitae
​ ​
(CV)
,
​ ​
and contact information for
t
hree
references
​ ​
directly
to Dr.
​ ​
Y
ury Polikanov
(
yu...@uic.edu
).

W
ith best regards,
Yury

​
​
-- 
--
Yury Polikanov, Ph.D.
Assistant Professor
Department of Biological Sciences
College of Liberal Arts and Sciences
University of Illinois at Chicago
900 South Ashland Avenue, MBRB 4170
Chicago, IL 60607
Tel: 1-312-413-2408 (Office)
Tel: 1-312-355-0463 (Laboratory)
Fax: 1-312-413-2691
E-mail: yu...@uic.edu
Web-Page: *http://bios.uic.edu/bios/people/faculty/yury-polikanov
*​​

--
​

[ccp4bb] Problems with QT graphs in Aimless log files

2017-12-07 Thread Derek Logan 
Hi,

I'm running CCP4 version 7.0.047 on a number of Linux PCs with OpenSUSE Linux 
as part of a course. I'm having problems with visualising Aimless log files, at 
least the graphical part. The graphs simply don't show up in the QT visualiser. 
Scala doesn't suffer from the same problem. Has anyone else run into this? I 
had a similar problem with Phaser output 4 years ago on the Windows systems 
that we used then, and that was due to the lack of a User: line in the Phaser 
output that meant that the log file couldn't be parsed properly. Could this be 
a related problem? I don't have this issue on my Mac.

Thanks
Derek Logan

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

2017-12-07 Thread Xiao Lei 
I see. Thanks Eleanor!

On Thu, Dec 7, 2017 at 4:33 AM, Eleanor Dodson 
wrote:

> Rf_used is the R factor for the non-free reflections.
>
> If you do the plot the 4SSQ/L**2 is converted to As..
>
> E
>
> On 7 December 2017 at 11:50, Xiao Lei  wrote:
>
>> Thanks Eleanor, yes, I looked at that table and tried to find out the
>> Rfree and R, I know the 4SSQ/LL means column means resolution bins but I
>> did not know what column means Rfac (The Rf_free means Rfree I guess).
>>
>>
>> On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
>> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>>
>>> Dont you look at the graphs from the log file?
>>>
>>> This table gives you all sorts of information including R and Rfree in
>>> resolution shells..
>>>
>>> Eleanor
>>> Things for loggraph, R factor and
>>> others
>>>
>>>
>>> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
>>> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
>>> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
>>> :Cycle   11. % observed v. resln :N:1,3:
>>> $$
>>> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
>>> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
>>> $$
>>>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2
>>> 539.4  0.59  0.62
>>>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5
>>> 412.9  0.57  0.58
>>>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6
>>> 431.4  0.57  0.57
>>>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3
>>> 455.8  0.59  0.59
>>>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2
>>> 354.8  0.55  0.54
>>>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1
>>> 304.8  0.57  0.54
>>>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5
>>> 229.6  0.60  0.58
>>>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8
>>> 195.7  0.52  0.50
>>>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4
>>> 170.1  0.59  0.56
>>>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1
>>> 144.9  0.61  0.57
>>>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1
>>> 115.1  0.57  0.53
>>>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5
>>> 110.5  0.60  0.58
>>>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.4
>>> 96.3  0.54  0.53
>>>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.4
>>> 84.0  0.55  0.53
>>>  0.2147427  99.1887.670.9  0.53  0.52 40088.9
>>> 71.3  0.53  0.52
>>>  0.2297702  98.6877.361.2  0.52  0.52 39580.2
>>> 61.7  0.54  0.53
>>>  0.2447963  98.9265.652.3  0.48  0.48 42865.5
>>> 53.7  0.54  0.54
>>>  0.2588198  98.4856.844.6  0.46  0.46 43753.5
>>> 43.6  0.49  0.49
>>>  0.2738375  98.6647.737.5  0.43  0.43 42848.0
>>> 37.6  0.47  0.48
>>>  0.2888611  98.2440.932.1  0.42  0.42 45041.8
>>> 32.1  0.50  0.50
>>> $$
>>>
>>>
>>>
>>> On 7 December 2017 at 01:07, Bernhard Rupp 
>>> wrote:
>>>
 You can find these numbers in the header of the output model coordinate
 file.



 BR



 *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
 Of *Xiao Lei
 *Sent:* Wednesday, December 6, 2017 2:40 PM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* [ccp4bb] How to find the Rfree and R in the highest
 resolution bin in Refmac 5?



 Dear All,

 I am asking how to find the Rfree and R in the highest resolution bin
 in Refmac 5 output?

 I used Refmac5 in refinement of protein structure at 3A resolution.
 Output of Refmac5 gives Rfee and R as:

   InitialFinal

R factor0.2900   0.2052

  R free0.3015   0.2639


 I'd also like to see the Rfree and R in the highest resolution bin. I
 checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
 with columns of Rf_free and WR_free, I searched in internet and still could
 not understand the Rf_free and WR_free label meaning.  I'd like to find
 something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
 value in the parenthesis).



 thanks ahead.





>>>
>>>
>>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

2017-12-07 Thread Eleanor Dodson 
Rf_used is the R factor for the non-free reflections.

If you do the plot the 4SSQ/L**2 is converted to As..

E

On 7 December 2017 at 11:50, Xiao Lei  wrote:

> Thanks Eleanor, yes, I looked at that table and tried to find out the
> Rfree and R, I know the 4SSQ/LL means column means resolution bins but I
> did not know what column means Rfac (The Rf_free means Rfree I guess).
>
>
> On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <176a9d5ebad7-dmarc-
> requ...@jiscmail.ac.uk> wrote:
>
>> Dont you look at the graphs from the log file?
>>
>> This table gives you all sorts of information including R and Rfree in
>> resolution shells..
>>
>> Eleanor
>> Things for loggraph, R factor and
>> others
>>
>>
>> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
>> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
>> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
>> :Cycle   11. % observed v. resln :N:1,3:
>> $$
>> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
>> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
>> $$
>>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2
>> 539.4  0.59  0.62
>>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5
>> 412.9  0.57  0.58
>>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6
>> 431.4  0.57  0.57
>>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3
>> 455.8  0.59  0.59
>>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2
>> 354.8  0.55  0.54
>>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1
>> 304.8  0.57  0.54
>>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5
>> 229.6  0.60  0.58
>>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8
>> 195.7  0.52  0.50
>>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4
>> 170.1  0.59  0.56
>>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1
>> 144.9  0.61  0.57
>>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1
>> 115.1  0.57  0.53
>>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5
>> 110.5  0.60  0.58
>>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.4
>> 96.3  0.54  0.53
>>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.4
>> 84.0  0.55  0.53
>>  0.2147427  99.1887.670.9  0.53  0.52 40088.9
>> 71.3  0.53  0.52
>>  0.2297702  98.6877.361.2  0.52  0.52 39580.2
>> 61.7  0.54  0.53
>>  0.2447963  98.9265.652.3  0.48  0.48 42865.5
>> 53.7  0.54  0.54
>>  0.2588198  98.4856.844.6  0.46  0.46 43753.5
>> 43.6  0.49  0.49
>>  0.2738375  98.6647.737.5  0.43  0.43 42848.0
>> 37.6  0.47  0.48
>>  0.2888611  98.2440.932.1  0.42  0.42 45041.8
>> 32.1  0.50  0.50
>> $$
>>
>>
>>
>> On 7 December 2017 at 01:07, Bernhard Rupp 
>> wrote:
>>
>>> You can find these numbers in the header of the output model coordinate
>>> file.
>>>
>>>
>>>
>>> BR
>>>
>>>
>>>
>>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>> Of *Xiao Lei
>>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>>> resolution bin in Refmac 5?
>>>
>>>
>>>
>>> Dear All,
>>>
>>> I am asking how to find the Rfree and R in the highest resolution bin in
>>> Refmac 5 output?
>>>
>>> I used Refmac5 in refinement of protein structure at 3A resolution.
>>> Output of Refmac5 gives Rfee and R as:
>>>
>>>   InitialFinal
>>>
>>>R factor0.2900   0.2052
>>>
>>>  R free0.3015   0.2639
>>>
>>>
>>> I'd also like to see the Rfree and R in the highest resolution bin. I
>>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>>> with columns of Rf_free and WR_free, I searched in internet and still could
>>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>>> value in the parenthesis).
>>>
>>>
>>>
>>> thanks ahead.
>>>
>>>
>>>
>>>
>>>
>>
>>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

2017-12-07 Thread Xiao Lei 
Thanks Eleanor, yes, I looked at that table and tried to find out the Rfree
and R, I know the 4SSQ/LL means column means resolution bins but I did not
know what column means Rfac (The Rf_free means Rfree I guess).

On Thu, Dec 7, 2017 at 2:58 AM, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Dont you look at the graphs from the log file?
>
> This table gives you all sorts of information including R and Rfree in
> resolution shells..
>
> Eleanor
> Things for loggraph, R factor and
> others
>
>
> $TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
> $GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
> :Cycle   11.  and  v. resln :N:1,4,5,9,10:
> :Cycle   11. % observed v. resln :N:1,3:
> $$
> M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
> NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
> $$
>  0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2   539.4
> 0.59  0.62
>  0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5   412.9
> 0.57  0.58
>  0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6   431.4
> 0.57  0.57
>  0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3   455.8
> 0.59  0.59
>  0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2   354.8
> 0.55  0.54
>  0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1   304.8
> 0.57  0.54
>  0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5   229.6
> 0.60  0.58
>  0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8   195.7
> 0.52  0.50
>  0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4   170.1
> 0.59  0.56
>  0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1   144.9
> 0.61  0.57
>  0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1   115.1
> 0.57  0.53
>  0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5   110.5
> 0.60  0.58
>  0.1856963  99.12   116.693.8  0.55  0.53 390   113.496.3
> 0.54  0.53
>  0.1997194  99.09   100.779.4  0.55  0.54 405   106.484.0
> 0.55  0.53
>  0.2147427  99.1887.670.9  0.53  0.52 40088.971.3
> 0.53  0.52
>  0.2297702  98.6877.361.2  0.52  0.52 39580.261.7
> 0.54  0.53
>  0.2447963  98.9265.652.3  0.48  0.48 42865.553.7
> 0.54  0.54
>  0.2588198  98.4856.844.6  0.46  0.46 43753.543.6
> 0.49  0.49
>  0.2738375  98.6647.737.5  0.43  0.43 42848.037.6
> 0.47  0.48
>  0.2888611  98.2440.932.1  0.42  0.42 45041.832.1
> 0.50  0.50
> $$
>
>
>
> On 7 December 2017 at 01:07, Bernhard Rupp 
> wrote:
>
>> You can find these numbers in the header of the output model coordinate
>> file.
>>
>>
>>
>> BR
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Xiao Lei
>> *Sent:* Wednesday, December 6, 2017 2:40 PM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] How to find the Rfree and R in the highest
>> resolution bin in Refmac 5?
>>
>>
>>
>> Dear All,
>>
>> I am asking how to find the Rfree and R in the highest resolution bin in
>> Refmac 5 output?
>>
>> I used Refmac5 in refinement of protein structure at 3A resolution.
>> Output of Refmac5 gives Rfee and R as:
>>
>>   InitialFinal
>>
>>R factor0.2900   0.2052
>>
>>  R free0.3015   0.2639
>>
>>
>> I'd also like to see the Rfree and R in the highest resolution bin. I
>> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
>> with columns of Rf_free and WR_free, I searched in internet and still could
>> not understand the Rf_free and WR_free label meaning.  I'd like to find
>> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
>> value in the parenthesis).
>>
>>
>>
>> thanks ahead.
>>
>>
>>
>>
>>
>
>

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

2017-12-07 Thread Xiao Lei 
This works. Thanks a lot Bernhard.

On Wed, Dec 6, 2017 at 5:07 PM, Bernhard Rupp 
wrote:

> You can find these numbers in the header of the output model coordinate
> file.
>
>
>
> BR
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Wednesday, December 6, 2017 2:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] How to find the Rfree and R in the highest resolution
> bin in Refmac 5?
>
>
>
> Dear All,
>
> I am asking how to find the Rfree and R in the highest resolution bin in
> Refmac 5 output?
>
> I used Refmac5 in refinement of protein structure at 3A resolution.
> Output of Refmac5 gives Rfee and R as:
>
>   InitialFinal
>
>R factor0.2900   0.2052
>
>  R free0.3015   0.2639
>
>
> I'd also like to see the Rfree and R in the highest resolution bin. I
> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
> with columns of Rf_free and WR_free, I searched in internet and still could
> not understand the Rf_free and WR_free label meaning.  I'd like to find
> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
> value in the parenthesis).
>
>
>
> thanks ahead.
>
>
>
>
>

[ccp4bb] Postdoctoral Fellowship in Structural Biology at TIFR Hyderabad, India

2017-12-07 Thread Kalyaneswar Mandal 
‘Postdoctoral Fellow’ position in structural biology at TIFR, Hyderabad, India
 A ‘Postdoctoral Fellow’ position in structural biology is available in the 
laboratory of Dr. Kalyaneswar Mandal at the Tata Institute of Fundamental 
Research Hyderabad, India. The position is funded by the Wellcome Trust /DBT 
India Alliance award. The research entails systematic development of 
non-natural protein inhibitors to prevent invasion of malaria parasite into 
human erythrocyte. The successful candidate will join a team of researchers 
that would employ a combination of synthetic organic chemistry, structural 
biology and chemical biology tools to understand and control the molecular 
basis of specific protein-protein interactions.
The candidate should have a Ph.D. degree with significant expertise in protein 
Xray crystallography. The salary will be commensurate with experience. 
Interested and highly motivated individuals are encouraged to send a letter of 
intent and a CV with a list of publications, research experiences and contact 
information of two referees via email to kman...@tifrh.res.in 
 with the subject line ‘Application for 
Postdoctoral Position’.

 
--
> 
> Kalyaneswar Mandal, Ph.D.
> Tata Institute of Fundamental Research Hyderabad
> Center for Interdisciplinary Sciences
> Gopanpally, Hyderabad-500107
> Phone (office): +91-40-20203092
> Web: https://www.tifrh.res.in/~kmandal/

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

2017-12-07 Thread Eleanor Dodson 
Dont you look at the graphs from the log file?

This table gives you all sorts of information including R and Rfree in
resolution shells..

Eleanor
Things for loggraph, R factor and
others


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.0081365  96.51   726.5   585.6  0.51  0.55  72   686.2   539.4
0.59  0.62
 0.0232411  98.00   498.1   446.2  0.54  0.56 131   489.5   412.9
0.57  0.58
 0.0373086  97.10   536.9   429.7  0.55  0.56 164   563.6   431.4
0.57  0.57
 0.0523605  96.71   600.3   450.7  0.55  0.55 211   595.3   455.8
0.59  0.59
 0.0674075  96.11   516.0   355.9  0.56  0.56 199   552.2   354.8
0.55  0.54
 0.0824558  97.20   425.2   288.7  0.56  0.55 228   425.1   304.8
0.57  0.54
 0.0965010  97.84   322.6   230.4  0.55  0.53 256   320.5   229.6
0.60  0.58
 0.1115376  98.91   252.1   193.5  0.55  0.53 273   256.8   195.7
0.52  0.50
 0.1265727  99.11   213.0   170.2  0.53  0.51 289   209.4   170.1
0.59  0.56
 0.1416121  99.21   174.5   142.0  0.54  0.52 307   171.1   144.9
0.61  0.57
 0.1556381  99.31   144.9   122.6  0.47  0.45 341   136.1   115.1
0.57  0.53
 0.1706677  99.12   129.9   107.6  0.55  0.52 339   129.5   110.5
0.60  0.58
 0.1856963  99.12   116.693.8  0.55  0.53 390   113.496.3
0.54  0.53
 0.1997194  99.09   100.779.4  0.55  0.54 405   106.484.0
0.55  0.53
 0.2147427  99.1887.670.9  0.53  0.52 40088.971.3
0.53  0.52
 0.2297702  98.6877.361.2  0.52  0.52 39580.261.7
0.54  0.53
 0.2447963  98.9265.652.3  0.48  0.48 42865.553.7
0.54  0.54
 0.2588198  98.4856.844.6  0.46  0.46 43753.543.6
0.49  0.49
 0.2738375  98.6647.737.5  0.43  0.43 42848.037.6
0.47  0.48
 0.2888611  98.2440.932.1  0.42  0.42 45041.832.1
0.50  0.50
$$



On 7 December 2017 at 01:07, Bernhard Rupp  wrote:

> You can find these numbers in the header of the output model coordinate
> file.
>
>
>
> BR
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao
> Lei
> *Sent:* Wednesday, December 6, 2017 2:40 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] How to find the Rfree and R in the highest resolution
> bin in Refmac 5?
>
>
>
> Dear All,
>
> I am asking how to find the Rfree and R in the highest resolution bin in
> Refmac 5 output?
>
> I used Refmac5 in refinement of protein structure at 3A resolution.
> Output of Refmac5 gives Rfee and R as:
>
>   InitialFinal
>
>R factor0.2900   0.2052
>
>  R free0.3015   0.2639
>
>
> I'd also like to see the Rfree and R in the highest resolution bin. I
> checked log file in Refmac5 and found M(4SSQ/LL) resolution range table
> with columns of Rf_free and WR_free, I searched in internet and still could
> not understand the Rf_free and WR_free label meaning.  I'd like to find
> something like Rfree XXX (XXX);  R XXX (XXX)  (the highest resolution bin
> value in the parenthesis).
>
>
>
> thanks ahead.
>
>
>
>
>

[ccp4bb] Postdoc in structural biology of protein evolution and adaptation

2017-12-07 Thread Maria Selmer 
Dear all,

We are looking for a postdoc to work within a multidisciplinary project 
“Evolution of new genes and proteins” at Uppsala University, Sweden 
(http://uu.se/en/). The project is financed by the Wallenberg foundation and 
aims to understand how structure and function are intertwined in the evolution 
and adaptation of proteins. The successful candidate should have an excellent 
track record and experience in X-ray crystallography as well as protein 
expression and purification. Experience of complementary techniques in 
biochemistry and biophysics would be a benefit. The postdoc will within this 
project work on structure-function studies of proteins from bacteria and fish, 
in extensive collaboration with geneticists, bioinformaticians and 
computational biochemists. The position is for 2 years.

On-line advert with more information and instructions for on-line application: 
http://www.uu.se/en/about-uu/join-us/details/?positionId=181076
For more information, you are welcome to contact maria.sel...@icm.uu.se
To be eligable for a postdoctoral position, the applicant’s Ph.D. degree must 
have been obtained no more than three years prior to the application date; 
however, periods of sick leave or parental leave are deducted from the 
three-year period. 

Maria

Prof. Maria Selmer  
Deputy Head of Department
Cell and Molecular Biology, Uppsala University
BMC, Box 596
SE-75124 Uppsala
Sweden

Telephone: +46-(0)18-4714177
Fax: +46-(0)18-536971

[ccp4bb] structural biologist to work on cancer drug discovery

2017-12-07 Thread Thomas Edwards 
Please respond direct to Alex.


Dear Colleagues,

I have a 16 month postdoctoral position available immediately in my lab at the 
Astbury Centre, University of Leeds, for a versatile structural biologist to 
work on cancer drug discovery in a collaboration with the Northern Institute 
for Cancer Research at Newcastle University. For more details and to apply 
please follow this link:

http://jobs.leeds.ac.uk/FBSMB1123

…or for informal enquiries please contact me directly.

Best,
Alex

--
Prof Alexander L Breeze
Professor of Biomolecular NMR
Director of NMR, Astbury BioStructure Laboratory
Astbury Centre for Structural Molecular Biology
School of Molecular and Cellular Biology
University of Leeds
Leeds
LS2 9JT, UK
E: a.l.bre...@leeds.ac.uk
T: +44 113 343 0087



NB click on the link below to register for the Astbury Conversation. Abstract 
submissions now open.


T.A.Edwards Ph.D.
Deputy Director Astbury Centre for Structural Molecular Biology
Ass. Professor, Director of Research, School of Molecular and Cellular Biology
Garstang 8.53d
University of Leeds, Leeds, LS2 9JT 
Telephone: 0113 343 3031
http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=TE
PoPPI (Perturbations of Protein-Protein Interactions) project: 
http://www.poppi.website/
Invention, my dear friends, is 93% perspiration, 6% electricity, 4% 
evaporation, and 2% butterscotch ripple. ~Willy Wonka
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