[ccp4bb] Studentships in Newcastle

[Martin Noble]

Dear all,

Please find attached an advert for a Ph.D. studentship to apply structural 
biology and inhibitor design
to tackle protein arginine methyl transferases in a collaboration between the 
departments of chemistry and
the Northern Institute for Cancer Research.

Best wishes,

Martin Noble



Professor Martin Noble
Northern Institute for Cancer Research
Paul O'Gorman Building
Medical School
Newcastle University
Framlington Place
Newcastle Upon Tyne
NE2 4HH

E-mail: martin.no...@ncl.ac.uk
Direct line: +44 (0) 191 208 4466









PhDadvertNCL.pdf
Description: PhDadvertNCL.pdf

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Boaz Shaanan]

Hi Christian,

I usually send the pdb back to the tlsmd server after any manipulation of the 
model just to be on the safe side. I'm not sure whether that'll make any 
difference in your case but it's perhaps worth trying.

   Cheers,

Boaz 


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian Roth 
[christian.r...@bbz.uni-leipzig.de]
Sent: Thursday, June 18, 2015 11:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue?

Hi all,

I refine a structure with TLS and restrained refinement in Refmac. After
the run finished, I fixed a few outliers manually in Coot, saved that
file and used that with the original TLS file from TLSMD for the next
round of refinement. As soon as the restrained refinement starts the
R-factors are going up and stabilise than at a higher values compared to
the previous run.
If I switch of the TLS refinement and just do restrained refinement with
the same input files the R-values start initially at a higher values and
than decrease till they stabilise. Unfortunately the final values are
about 1.5 % higher, compared to the run with TLS before manual
rebuilding. So TLS seems to me beneficial and I would like to use it,
but somehow a strange combination of wrong files?, wrong
parametrization? or whatever prevent me of doing that.
Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Shane Caldwell]

Hi Christian, I've seen this behaviour as well. I'm not an expert but I
rationalized the situation as the TLS parameters for an incomplete model
getting overfit as the missing/wrong parts of the model pull on the TLS
parameters. REFMAC doesn't alternate between TLS and coordinate refinement,
so you can get stuck in a local minimum that moving atoms and refining
individual B-factors won't get you out of. As more of the model is built
correctly, the drift of this refinement gets less and less.

I've found that refining comparatively few TLS cycles (I usually do 3)
before the restrained refinement tends to avoid this problem most of the
time - don't let the TLS refinement converge. Sometimes I'll let the
coordinate step converge, then run another TLS refinement to bootstrap
things along, but usually the stats only marginally improve at that point.
In cases where I've made substantial rebuilds, it's sometimes been
necessary to turn off TLS and refine without it like you do, then
re-introduce the same TLS groups, setting the B-factors to fixed values.
Not really ideal, but it gets there. Hopefully others have some more
theoretically-sound advice.

A good thing to look at doing, especially if TLS is behaving weirdly, is to
check with the PARVATI server (http://skuld.bmsc.washington.edu/parvati/).
If your TLS group boundaries set off flags, you have some more work to do
on the refinement.


Shane Caldwell
McGill University

On Thu, Jun 18, 2015 at 4:30 PM, Christian Roth <
christian.r...@bbz.uni-leipzig.de> wrote:

> Hi all,
>
> I refine a structure with TLS and restrained refinement in Refmac. After
> the run finished, I fixed a few outliers manually in Coot, saved that file
> and used that with the original TLS file from TLSMD for the next round of
> refinement. As soon as the restrained refinement starts the R-factors are
> going up and stabilise than at a higher values compared to the previous run.
> If I switch of the TLS refinement and just do restrained refinement with
> the same input files the R-values start initially at a higher values and
> than decrease till they stabilise. Unfortunately the final values are about
> 1.5 % higher, compared to the run with TLS before manual rebuilding. So TLS
> seems to me beneficial and I would like to use it, but somehow a strange
> combination of wrong files?, wrong parametrization? or whatever prevent me
> of doing that.
> Has anyone an idea what might be the cause of that strange behaviour.
>
> Thank you very much in advance.
>
> Cheers
>
> Christian
>

[ccp4bb] Refmac refinement R factors going up..... TLS issue?

[Christian Roth]

Hi all,

I refine a structure with TLS and restrained refinement in Refmac. After 
the run finished, I fixed a few outliers manually in Coot, saved that 
file and used that with the original TLS file from TLSMD for the next 
round of refinement. As soon as the restrained refinement starts the 
R-factors are going up and stabilise than at a higher values compared to 
the previous run.
If I switch of the TLS refinement and just do restrained refinement with 
the same input files the R-values start initially at a higher values and 
than decrease till they stabilise. Unfortunately the final values are 
about 1.5 % higher, compared to the run with TLS before manual 
rebuilding. So TLS seems to me beneficial and I would like to use it, 
but somehow a strange combination of wrong files?, wrong 
parametrization? or whatever prevent me of doing that.

Has anyone an idea what might be the cause of that strange behaviour.

Thank you very much in advance.

Cheers

Christian

Re: [ccp4bb] Refmac_5.8.0103: No reflections in resolution bin ???????

[Eleanor Dodson]

Just what it says - if you look at the log file (search for $TABLE) you
will see a resolution bin has no reflections. Maybe your data is very
incomplete at high resolution? Maybe the cell is very smal and you can
reduce the numbers of bins..

So suggestions would be - change the resolution range, reduce the number of
bins from the default of 20  (keyword BINS )

But starrt by looking in the log file.
Eleanor

On 18 June 2015 at 10:32, Manal A Swairjo  wrote:

>  In running refmac (restrained refinement, P21 space group, 68-1.94
> Angstrom data), the program stops with the error:
>
> Refmac_5.8.0103:  No reflections in resolution bin ???
>
>
>
> Any idea what is causing this?
>
>
>
> Manal A. Swairjo, Ph.D.
>
> Assistant Professor
>
> Graduate College of Biomedical Sciences
>
> Western University of Health Sciences
>
> 309 E. Second Street
>
> Pomona CA 91766-1854
>
> Cell: 619 206 3864
>
> Office: 909 469 8201
>
> Lab: 909 469 8222
>
> Fax: 909-469-5577
>
> email: mswai...@westernu.edu
>
> website:
> http://www.westernu.edu/biomedical-sciences/biomedical-sciences-research/biomedical-sciences-swairjo-lab/
>
>
>

[ccp4bb] Refmac_5.8.0103: No reflections in resolution bin ???????

[Manal A Swairjo]

In running refmac (restrained refinement, P21 space group, 68-1.94 Angstrom 
data), the program stops with the error:
Refmac_5.8.0103:  No reflections in resolution bin ???

Any idea what is causing this?

Manal A. Swairjo, Ph.D.
Assistant Professor
Graduate College of Biomedical Sciences
Western University of Health Sciences
309 E. Second Street
Pomona CA 91766-1854
Cell: 619 206 3864
Office: 909 469 8201
Lab: 909 469 8222
Fax: 909-469-5577
email: mswai...@westernu.edu
website: 
http://www.westernu.edu/biomedical-sciences/biomedical-sciences-research/biomedical-sciences-swairjo-lab/