Re: [ccp4bb] Hydrophobic hotspots

[Debasish Kumar Ghosh]

Hi Hugh,

Waltz is an excellent web-server to give very good results on amyloidogenic 
regions based on sequence stretches (correlate the regions with hydrophobic 
patches by hydropathy plot obtained from Expassy-Protscale). Aggrescan and 
PASTA are two other reliable servers for the same kind of prediction (though I 
have more preference for Waltz).
Based on the 3D structure (pdb structures) you can use the Maestro program 
(from Schrodinger Inc.) to get the aggregation prone surface(s) / aggregation 
prone surface regions.  

Best!!

Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: "Hugh Morgan" <1103e90ebb53-dmarc-requ...@jiscmail.ac.uk>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, July 26, 2017 10:35:07 PM
Subject: [ccp4bb] Hydrophobic hotspots

Hi all, can anyone recommend a program for identifying hydrophobic 
(aggregation) hotspots using either the amino acid sequence and/or structural 
data. 
Thanks in advance for your help
Hugh

Ps. Have tried aggrescan but would like to try a few others and compare, 
ideally a more structural based program.

[ccp4bb] Hydrophobic hotspots

[Hugh Morgan]

Hi all, can anyone recommend a program for identifying hydrophobic 
(aggregation) hotspots using either the amino acid sequence and/or structural 
data. 
Thanks in advance for your help
Hugh

Ps. Have tried aggrescan but would like to try a few others and compare, 
ideally a more structural based program.

Re: [ccp4bb] About weighting factor settings in new ccp4i2

[Christian Roth]

The simple matrix weighting option (x-ray/restraints weight) is under 
main refinement option and set automatically. Change that to manually 
and you can put the value in if you want to avoid too many keywords. 
There is even an option in advanced parameters to run several quick 
refinements to get an idea which weight might be best. Of course this is 
by far not as sophisticated as PDB-REDO.


Christian


Am 24.07.2017 um 23:41 schrieb Jon Agirre:

Dear Xu,

you can input those keywords in the text box under 'Advanced options' 
in the 'refinement' task. Just make sure you click somewhere else 
after you're done putting the keywords in in order to have the text 
validated by the interface.


Best regards,
Jon

On 24 July 2017 at 23:01, Liu, Xu > wrote:


Hi,

In the new cpp4-7.0.042 (ccp4i2), where can I put in the weighting
factor for B factor restrain weight (the ‘WBSKAL' setting) and/or
x-ray terms relative to geometric restrains (the ‘MATRIX’ setting
) in refmac5? Basically I want to plug in those weighting factors
from pdbredo into REFMAC5 for a few more refinement but cannot
find in new ccp4.

Thanks!



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University of York, Heslington, YO10 5DD, York, England
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[ccp4bb] Trainee/student, undergraduate or master student Student internship

[Veli-Pekka Jaakola]

Job ID 213766BR
Position Title Master Student
Division NIBR
Business Unit CBT - NIBR
Country Switzerland
Work Location Basel
Company/Legal Entity Novartis Pharma AG
Functional Area Interns/Students on Novartis Payroll
Job Type Full Time
Employment Type Internship
Job Description Trainee/student, undergraduate or master student Student
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Minimum requirements University or TH master student in biochemistry,
molecular biology, chemistry or life sciences Good knowledge of spoken and
written English is required Experience in biophysics and/or biochemistry
wet bench work and preferably basic knowledge of protein purification.
Further training will be provided in the job. Ability to work in a team and
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https://jobs.brassring.com/tgwebhost/jobdetails.aspx?jobId=2485522=13617=5260=mail=140=1=5260=2485522_5260=0


--
Veli-Pekka Jaakola
Investigator III,
Novartis Institutes for Biomedical Research (NIBR),
Chemical Biology and Therapeutics (CBT),
Lab Jaakola,
Virchov 16-2.249.22,
CH-4056 Basel, SWITZERLAND
Phone: +41 79 609 0014
veli-pekka.jaak...@novartis.com
https://www.linkedin.com/in/vpjaakol
--

Re: [ccp4bb] resolution limits

[Pavel Afonine]

Andrew,

phenix.refine may not use reflection-outliers (Read, R. J. (1999). Acta
Cryst. D55, 1759–1764.). Typically this is just a few reflections. If you
have a good reason to disable this, then use
xray_data.outliers_rejection=false.

P.S.: There is Phenix mailing list for Phenix-related questions.

Pavel

On Wed, Jul 26, 2017 at 12:36 AM, Andrew Marshall <
andrew.c.marsh...@adelaide.edu.au> wrote:

> Dear crystallographers,
>
> I have two datasets that were merged/scaled using ccp4's aimless, with
> resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the
> resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for
> the other. 1) Why does phenix.refine change the low resolution limits of my
> processed data? 2) How can I prevent this?
>
> Thanks,
>
> Andrew
>

[ccp4bb] Software Engineer / Bioinformatician position at PDBe

[john berrisford]

We are looking for a bioinformatician to integrate value-added 
information on enzymes and catalytic binding sites with the PDB 
structure data and make it available programmatically and via PDBe 
website. The work will involve close collaboration with the Thornton 
research group and with UniProt and ChEMBL teams, all co-located at the EBI.


For more details and to apply, please see the listing on the EMBL 
careers site (https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_00941)


Application deadline is 13th August 2017


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

Re: [ccp4bb] resolution limits

[Ian Tickle]

Hi Eleanor, what you say is of course true, particularly in the case of the
1st dataset where probably the indices go down to 52 Ang. but the
measurements only start at 36 Ang.  But still it's hard to see how for the
2nd dataset, if the low res cut-off of the indices and/or measurements is
57 Ang., it manages to 'use' a reflection at 104 Ang.  All depends what you
mean by 'use' of course!

Cheers

-- Ian


On 26 July 2017 at 11:33, Eleanor Dodson  wrote:

> The resolution limits of the measured data are not changed but your output
> file must contain all possible h k l even if there is no observations for
> the lowest resolution ones..
>
> dont worry about it!
>
> Eleanor
>
> On 26 July 2017 at 08:36, Andrew Marshall  edu.au> wrote:
>
>> Dear crystallographers,
>>
>> I have two datasets that were merged/scaled using ccp4's aimless, with
>> resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the
>> resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for
>> the other. 1) Why does phenix.refine change the low resolution limits of my
>> processed data? 2) How can I prevent this?
>>
>> Thanks,
>>
>> Andrew
>>
>
>

Re: [ccp4bb] resolution limits

[Eleanor Dodson]

The resolution limits of the measured data are not changed but your output
file must contain all possible h k l even if there is no observations for
the lowest resolution ones..

dont worry about it!

Eleanor

On 26 July 2017 at 08:36, Andrew Marshall  wrote:

> Dear crystallographers,
>
> I have two datasets that were merged/scaled using ccp4's aimless, with
> resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the
> resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for
> the other. 1) Why does phenix.refine change the low resolution limits of my
> processed data? 2) How can I prevent this?
>
> Thanks,
>
> Andrew
>

[ccp4bb] Postdoc position in ubiquitin signaling

[Sonja Lorenz]

Postdoc Position

Structural Mechanisms of Ubiquitin Ligases in Cancer

A postdoc position is available in the lab of Sonja Lorenz at the  
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http://virchow.uni-wuerzburg.de/lab_pages/slorenz/
http://www.rudolf-virchow-zentrum.de/en/research/research-groups/lorenz-group/research.html


Sonja Lorenz, PhD
Rudolf Virchow Center for Experimental Biomedicine, University of  
Würzburg, Germany

E-mail: sonja.lor...@virchow.uni-wuerzburg.de

[ccp4bb] resolution limits

[Andrew Marshall]

Dear crystallographers,

I have two datasets that were merged/scaled using ccp4's aimless, with
resolution ranges of 52-1.7 and 57-1.9. However, upon refinement, the
resolution range used by phenix.refine is 36-1.7 for one and 104-1.9 for
the other. 1) Why does phenix.refine change the low resolution limits of my
processed data? 2) How can I prevent this?

Thanks,

Andrew