Re: [ccp4bb] Live stream of CCP4 Study Weekend?

[Colin Levy]

All working fine for me via Safari on OSX.

I had to enable flash and then it simply worked, I used the link:

https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:4

Colin



On 9 Jan 2019, at 09:42, 
graeme.win...@diamond.ac.uk 
mailto:graeme.win...@diamond.ac.uk>> wrote:

I have enabled Flash but just get a black rectangle and no sound…

Guessing that using Chrome on OS X is not supported?

:-(

On 9 Jan 2019, at 09:33, Marcin Wojdyr 
mailto:woj...@gmail.com>> wrote:

On Wed, 9 Jan 2019 at 10:28, Kay Diederichs
mailto:kay.diederi...@uni-konstanz.de>> wrote:

Sorry, I need some additional help with this.

If I use my browser (Firefox or Chrome on Linux) to go to 
http://sas.stfc.ac.uk/p.jsp?i=2 it gets redirected to 
https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:-1

I also use it on Firefox on Linux and it works for me. I got
redirected to almost the same address, except that the last digit is
4:
https://sas.stfc.ac.uk/vportal/VideoPlayer.jsp?ccsid=C-5d13ead9-b217-4b5b-bceb-bb37e04bbefe:4
(I had to enable Flash)



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[ccp4bb] PDRA position University of Manchester

[Colin Levy]

Please see below for details of a current vacancy here at the University of 
Manchester. Informal enquiries should be made to Prof. Lydia Tabernero 
(lydia.tabern...@manchester.ac.uk).

The closing date for applications is the 22/11/18

Many thanks,

Colin


The University of Manchester

Faculty of Biology, Medicine and Health (FBMH)

Research Associate – Protein Crystallography
(Ref: BMH-12935)

  £32,236 - £35,211 p.a.


Project Title
Inhibiting Dual-Specificity Tyrosine Phosphatases (DUSPs) as a Method for 
Preventing Resistance to Herceptin in Her2-Positive Breast Cancer

Project Description
You will work on an ambitious programme of structure-based drug discovery to 
produce novel drugs to overcome resistance to Herceptin in HER2-positive breast 
cancer.
Molecular and systems-level research during the past two decades have led to 
development of anti-cancer drugs that act by inhibiting specific molecules that 
play key roles in tumorigenesis process or in tumour survival. A prime example 
of this is Herceptin (trastuzumab), an antibody that inhibits HER2 and is used 
to treat HER2-positive breast cancer. Despite its effectiveness, two thirds of 
patients who respond to Herceptin develop resistance and relapse within one 
year. Understanding the molecular basis for such resistance and devising 
methods to prevent or reverse it are therefore of critical importance. Our aim 
is to design new inhibitors of protein phosphatases, which function downstream 
of HER2 and are key regulators of signaling and survival in breast cancer.
We are looking for an enthusiastic individual, highly motivated with efficient 
skills in time managing and project leading. This post offers an excellent 
opportunity to join a dynamic research team focused on drug development in the 
School of Biological Sciences (Faculty of Biology, Medicine and Health) with 
superb multidisciplinary facilities and stimulating working environment.
You must hold a PhD in Structural Biology/ Protein Crystallography/ 
Biochemistry and have a strong background in protein biochemistry and 
crystallisation.

Informal enquiries can be made to Prof. Lydia Tabernero.
Tel: 0161 2757794
Email lydia.tabern...@manchester.ac.uk

Application forms and further particulars can be obtained at 
http://www.manchester.ac.uk/aboutus/jobs/
Closing date: 22/11/2018
Please quote reference BMH-12935



Dr. Colin W. Levy
MIB G016
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk

 Manchester Institute of Biotechnology | University of Manchester | 3.020 
Garside Building | 131 Princess Street | Manchester | M1 7DN












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Re: [ccp4bb] Small molecule not refined in coot.

[Colin Levy]

Hi Michel,

If your ligand is designated as DRG in your pdb then refinement programs will 
anticipate that it is:

Chemical Description
Name5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
Formula C12 H11 N3
Formal charge   0
Molecular weight197.236 g/mol
Component type  NON-POLYMER


If this is not the case then you need to choose a unique identifier, this 
should then allow your cif library to be utilised appropriately during 
refinement.

Colin


[cid:3A59087A-E871-4A15-8C7F-384F6788170E@man.ac.uk]



Dr. Colin W. Levy
MIB G016
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk

 Manchester Institute of Biotechnology | University of Manchester | 3.020 
Garside Building | 131 Princess Street | Manchester | M1 7DN

[cid:image001.png@01D11BB1.F717D2B0][cid:image002.png@01D11BB1.F717D2B0][cid:image003.png@01D11BB1.F717D2B0][cid:image004.png@01D11BB1.F717D2B0][cid:image005.png@01D11BB1.F717D2B0]








On 5 Mar 2018, at 12:30, M T > 
wrote:

Dear all,

I am actually dealing with a structure containing an unnatural ligand.
I generated the pdb file by drawing it on PRODRG server, I did a manual pre-fit 
in the map using coot and I manually merged the pdf file of my protein with the 
one of the ligand.
After that I did few cycles of refinement using Refmac5, with my mtz, my merged 
pdb file and the cif library of the ligand as input files.

First I saw that even if Refmac "completed succesfully" it didn't modify 
coordinates of the ligand, second I saw a warning about the "DRG" molecule in 
the log of Refmac (WARNING: duplicated name of monomer DRG Last entry will be 
used.), third in Coot I cannot use "Real Space Refine Zone" with the ligand and 
when I try to import the CIF dictionary produced by PRODRG (through the server 
or even the one generated through CCP4 ProDrg), it causes Coot crash (** 
(coot-bin:4467): WARNING **: Widget not found: 
cif_dictionary_file_selector_create_molecule_checkbutton 
/programs/i386-mac/ccp4/7.0/ccp4-7.0/bin/coot: line 288:  4467 Segmentation 
fault: 11  $coot_bin "$@").

Clearly I am not a skilled user of all these programs, so I certainly did 
a/some mistake/s, but if someone can give me tips to be able to refine my 
ligand... Should I rename my DRG molecule, should I verify particular things, 
should I use other ways to generate the pdb and the library of my ligand?

Thank you.

P.S.: I am running CCP4 and coot using SBGRID on a Mac.

Michel

Re: [ccp4bb] Residual density feature

[Colin Levy]

Dear all, 

Many thanks for the responses received,

To summarise the options for unidentified blobs appear to be:

1. Build something in and define it as a UNL (unknown ligand)

Some debate arose over the specifics of the term ³unknown ligand² and
wether a broader unknown entity description might be more accurate.

2. Leave the difference density and describe the location of the observed
feature using a SITE record.

As my intention was simply to draw attention to the presence of this
feature whilst not implying any identification I have chosen to go down
the latter route and simply leave the difference density for others to
ponder in the future.

Many thanks,

Colin




Manchester
Protein
Structure
Facility

Dr. Colin W. Levy
MIB G034
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.uk








On 16/06/2015 18:22, Dale Tronrud de...@daletronrud.com wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


On 6/14/2015 2:49 AM, Robbie Joosten wrote:
 Hi Colin,
 
 You can define an UNL (unknown ligand) in the blob. This is the
 standard name for such a compound. It becomes a bit messy in
 refinement in terms of restraints, but it does exactly what you
 want it to do: say you noticed the blob but couldn't figure out
 what it was.
 
   There is danger along this route - but I suppose this is a
philosophical matter.  Your PDB file is your model for what is in the
crystal.  If you don't know what a compound in your crystal is, can
you say that you have modeled it?  What are your intentions when you
place this unknown residue in your model -- Are you just placing a
marker to tell those who follow that you noticed something here or are
you saying this is how electrons are arranged here.

   Recently I was looking at 1I1W for some reason.  It is a very nice
model at 0.89 A resolution.  It contains, however, several single atom
residues of type UNX and the atoms are of type X.  The problem I have
is that these atoms have their occupancy set to 1.0 and have varying B
factors.  What am I supposed to make of a fully occupied atom of
unknown type?

   Apparently I'm not alone in my confusion.  The Electron Density
Server does not supply a map for this entry.  I can see nothing wrong
with the data nor the rest of the model so I presume the service is
failing because it doesn't know how to calculate the scattering of an
atom of unknown type.

   So, my question is - If you place marker atoms to indicate the
binding of any unknown ligand, should the difference density disappear
from your map?  Certainly if you are interested in bootstrapping phase
information you would want this, but is this appropriate for deposition?
Should you be able to say your difference map is flat and your R value
low when all you did was shrug your shoulders and say I don't know?

   There is a, sadly underused, feature of the PDB format called the
SITE record.  With it you can describe the residues of your protein
that form a binding site and give a text description in a REMARK 800
statement.  This option would allow you to acknowledge that something
is binding at this location but leave the difference peak for others
to view and puzzle over on their own.

Dale Tronrud

 Cheers, Robbie
 
 -Original Message- From: CCP4 bulletin board
 [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent:
 Sunday, June 14, 2015 11:36 To: CCP4BB@JISCMAIL.AC.UK Subject:
 Re: [ccp4bb] Residual density feature
 
 Dear Colin,
 
 
 
 I believe people usually refer to it as unidentified blob when
 depositing/writing in
 these
 cases. But I wonder whether others may suggest better options.
 
 
 
 Best,
 
 
 
 D
 
  From: CCP4 bulletin board
 [CCP4BB@JISCMAIL.AC.UK] on behalf of Colin Levy
 [c.l...@manchester.ac.uk] Sent: 14 June 2015 09:53 To: ccp4bb
 Subject: [ccp4bb] Residual density feature
 
 Dear all,
 
 I am currently working on a structure that contains a residual
 density feature located
 within
 the active site. Due to a combination of factors including
 limited occupancy, modest resolution, twinning etc it has not
 been possible to unambiguously identify this feature
 despite
 fairly extensive efforts.
 
 What is the best way of dealing with such a feature when
 depositing the structure?
 Ideally I
 would like to draw attention to the presence of residual density
 whilst not implying
 that I have
 been able to identify it.
 
 Many thanks,
 
 Colin
 
 
 Manchester Protein Structure Facility
 
 Dr. Colin W. Levy MIB G034 Tel.  0161 275 5090 Mob.07786 197 554
 c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk
 
 
 -- This e-mail and any attachments may contain confidential,
 copyright and or privileged material, and are for the use of the
 intended addressee only. If you are not the
 intended
 addressee or an authorised recipient of the addressee please
 notify us of receipt by
 returning
 the e-mail and do not use, copy, retain, distribute or disclose
 the information in or
 attached to
 the e-mail. Any

[ccp4bb] Residual density feature

[Colin Levy]

Dear all,

I am currently working on a structure that contains a residual density feature 
located within the active site. Due to a combination of factors including 
limited occupancy, modest resolution, twinning etc it has not been possible to 
unambiguously identify this feature despite fairly extensive efforts.

What is the best way of dealing with such a feature when depositing the 
structure? Ideally I would like to draw attention to the presence of residual 
density whilst not implying that I have been able to identify it.

Many thanks,

Colin


Manchester
Protein
Structure
Facility

Dr. Colin W. Levy
MIB G034
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk

[ccp4bb] Postdoctoral Opportunity

[Colin Levy]

Please see below for a postdoctoral opportunity here in Manchester.

All enquiries should be made to lydia.tabern...@manchester.ac.uk

Thanks

Colin



Postdoctoral Position in X-ray Crystallography

Structure of the endosomal ESCRT-I complexes

Faculty of Life Sciences, University of Manchester
Manchester, UK

A postdoctoral position is available in the laboratory of Dr Lydia Tabernero to 
study the structural basis for the assembly of a protein complex that is 
essential for mitogenic receptor down regulation. The project will focus on 
understanding the core structure of the endosomal-sorting complex, ESCRT-I 
(Stefani et al., 2011, Curr. Biol. 21, 1245050; Wunderley et al, 2014, J Cell 
Sci. 127, 663-72).
The position is part of an ongoing research collaboration between Dr Lydia 
Tabernero and Professor Philip Woodman directed towards understanding the 
molecular basis for the down-regulation of the epidermal growth factor 
receptor. This is a high-impact fast-moving basic research area with direct 
implications for bettering our understanding of a key cellular process that is 
disrupted in several diseases. The successful applicant will join a 
collaborative team, also involving the laboratories of Professor Philip Woodman 
and Dr Alan Roseman, and will use X-ray crystallography, and other structural 
techniques (EM, SAXS).
The ideal candidate will have a PhD in structural biology, and will have 
experience in recombinant protein expression and X-ray crystallography.
The post is full time for up to 15 months and can be available immediately.

Salary: £29,837

Closing date: 15/08/2014
Reference: LSX-04954
Further particulars and a full description of the project and job 
responsibilities can be found at: www.jobs.manchester.ac.uk
Informal enquiries
Informal enquiries can be made to Dr Lydia Tabernero, Lecturer:
Email: lydia.tabern...@manchester.ac.uk
Telephone: 0161 275 7794
The University of Manchester values a diverse workforce and welcomes 
applications from all sections of the community.



Manchester
Protein
Structure
Facility

Dr. Colin W. Levy
MIB G034
Tel.  0161 275 5090
Mob.07786 197 554
c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk

[ccp4bb] PDRA Position Manchester

[Colin Levy]

Dear All,

please find below details of a PDRA position available at the University of 
Manchester. All enquiries should be made to Dr. Lydia Tabernero, 
lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk.

Thanks,

Colin

Postdoctoral Position in X-ray Crystallography

Structure of the endosomal ESCRT-I core complex

Faculty of Life Sciences, University of Manchester
Manchester, UK

A postdoctoral position is available in the laboratory of Dr Lydia Tabernero to 
study the structural basis for the assembly of a protein complex that is 
essential for mitogenic receptor down regulation. The project will focus on 
understanding the core structure of the endosomal-sorting complex, ESCRT-I 
(Stefani et al., 2011, Curr. Biol. 21, 1245050).
The position is part of an ongoing research collaboration between Dr Lydia 
Tabernero and Professor Philip Woodman directed towards understanding the 
molecular basis for the down-regulation of the epidermal growth factor 
receptor. This is a high-impact fast-moving basic research area with direct 
implications for bettering our understanding of a key cellular process that is 
disrupted in several diseases. The successful applicant will join a 
collaborative team, also involving the laboratories of Professor Philip Woodman 
and Dr Alan Roseman, and will use X-ray crystallography and other structural 
techniques.
The ideal candidate will have (or expect to gain shortly) a PhD in structural 
biology, and will have experience in recombinant protein expression and X-ray 
crystallography.
The post is full time for up to 24 months and can be available immediately.

Salary: £29,541 to £36,298 depending on experience

Closing date :19/03/2013
Reference :LSX-02347
Further particulars and a full description of the project and job 
responsibilities can be found at: 
www.jobs.manchester.ac.ukhttp://www.jobs.manchester.ac.uk
Informal enquiries
Informal enquiries can be made to Dr Lydia Tabernero, Lecturer:
Email: lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk
Telephone: 0161 275 7794
The University of Manchester values a diverse workforce and welcomes 
applications from all sections of the community.

[ccp4bb] Postdoctoral opportunity

[Colin Levy]

Dear BB,
Please see details below of a PDRA position available at the University of 
Manchester in the laboratory of Dr Lydia Tabernero. All enquiries should be 
directed to Dr Tabernero and not myself please.

lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk

Many thanks,

Colin

Postdoctoral Position in X-ray Crystallography

Structure of the endosomal ESCRT-I core complex

Faculty of Life Sciences, University of Manchester
Manchester, UK

A postdoctoral position is available in the laboratory of Dr Lydia Tabernero to 
study the structural basis for the assembly of a protein complex that is 
essential for mitogenic receptor down regulation. The project will focus on 
understanding the core structure of the endosomal-sorting complex, ESCRT-I 
(Stefani et al., 2011, Curr. Biol. 21, 1245050).
The position is part of an ongoing research collaboration between Dr Lydia 
Tabernero and Professor Philip Woodman directed towards understanding the 
molecular basis for the down-regulation of the epidermal growth factor 
receptor. This is a high-impact fast-moving basic research area with direct 
implications for bettering our understanding of a key cellular process that is 
disrupted in several diseases. The successful applicant will join a 
collaborative team, also involving the laboratories of Professor Philip Woodman 
and Dr Alan Roseman, and will use X-ray crystallography and other structural 
techniques.
The ideal candidate will have (or expect to gain shortly) a PhD in structural 
biology, and will have experience in recombinant protein expression and X-ray 
crystallography.
The post is full time for up to 24 months and can be available immediately.

Salary: £29,541 to £36,298 depending on experience

Closing date :19/03/2013
Reference :LSX-02347
Further particulars and a full description of the project and job 
responsibilities can be found at: 
www.jobs.manchester.ac.ukhttp://www.jobs.manchester.ac.uk/
Informal enquiries
Informal enquiries can be made to Dr Lydia Tabernero, Lecturer:
Email: lydia.tabern...@manchester.ac.ukmailto:lydia.tabern...@manchester.ac.uk
Telephone: 0161 275 7794
The University of Manchester values a diverse workforce and welcomes 
applications from all sections of the community.
Manchester
Protein
Structure
Facility

MIB 1.025
Tel 0161 306 5185
c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk

Manchester
Protein
Structure
Facility

MIB 1.025
Tel 0161 306 5185
c.l...@manchester.ac.ukmailto:c.l...@manchester.ac.uk