[ccp4bb] Phd and postdoc positions in Structural biology

[Magnus Wolf-Watz]

Hi

The Magnus Wolf-Watz lab in Umeå, Sweden has two openings in structural biology:

One PhD position directed at human protein kinases and their linkage to human 
cancer application deadline May 20

One Postdoc in structural biology of silk and cellulose modifying enzymes, 
application deadline April 15!

See below and www.biostruct.umu.se for more information

PhD position in biochemistry; structural biology of cancer linked protein 
kinases

A PhD position in biochemistry is available in the laboratory of Professor 
Magnus Wolf-Watz at the Department of Chemistry, Umeå University, Sweden. The 
PhD project is aimed at uncovering novel molecular mechanisms underlying the 
function of human protein kinases. Focus will be on two specific protein 
kinases that are intimately linked to a number of disorders in humans including 
various forms of cancer. The doctoral student will enter a multidisciplinary 
project that is built on collaborations with both Professor Kwangho Nam at 
University of Texas Arlington and with Marené Landström (Professor in pathology 
at Umeå University). The doctoral student will be trained in structural 
biology, protein production, biochemistry and biophysics and will collaborate 
with both cell biologists and computational chemists. Structural biology may go 
in any of the directions; single particle cryo EM, x-ray crystallography or 
protein NMR spectroscopy depending on the development of the research project 
and also depending on the interests of the doctoral student. The position is in 
part funded by the National Institute of Health (NIH).
2-year postdoc fellowship: Green Structural Biology in cellulose and silk 
biotechnology
An important aspect of green chemistry and a sustainable and circular economy 
is to develop environmentally friendly methodology to retrieve valuable 
chemicals from complex biomaterials. This interdisciplinary project tackles 
this challenging task by exploring the molecular mechanisms underlying 
enzymatic processing of recalcitrant natural polymers: cellulose and silk 
fibers. In the project we focus on two enzymes that bring novel functionality 
in cellulose and silk bio-processing by softening their structure and paving 
the way for further biocatalytic transformation of the fibers.
We are seeking a structural biologist with a strong background in biochemistry 
and/or protein production with different expression organisms. The structural 
biology background may be in any of the areas of NMR spectroscopy, single 
particle cryo EM or x-ray crystallography.   The successful candidate will have 
the possibility to define and shape the project dependent on background and 
ambitions and may focus on both enzymes and/or the structures of cellulose and 
silk-based biomaterials.


Please contact Magnus W-W for further information and guide to the application,


---
Dr. Magnus Wolf-Watz
Professor
Umeå University
Chemistry Department
Integrated Structural Biology (ISB), Twitter @ISB_UmU
Phone:+46 90 786 76 90
Lab Home Page: 
www.biostruct.umu.se/principal-investigators/magnus-wolf-watz/
Twitter: @watz_wolf





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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Average B factors with TLS

[Schreuder, Herman /DE]

This is a very good point. I never was very happy with calculating the average 
of all B-factors. E.g. if one adds a lot of high-B water molecules, the average 
B goes up, but with the structure itself nothing changes. Instead of 
calculating the average B, it would probably better to calculate the “Wilson 
B-factor” of the calculated intensities and compare this to the observed Wilson 
B-factor.

My 2 cts, Herman

Von: CCP4 bulletin board  Im Auftrag von Edward Berry
Gesendet: Mittwoch, 8. April 2020 03:52
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Average B factors with TLS

EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Apologies for my previous email appearing to put words in Dale's mouth- I'm 
using my school's
webmail and it apparently doesn't indicate the quoted text.
The following is what I added:

I think it is not just that the distribution is asymmetric and limited to 
positive numbers-
it is due to the fact that "log" and "average" do not commute (the average of 
the logs
is not the log of the averages), and the logarithmic/exponential relation 
between intensity and B.

The wilson B is obtained from the slope of ln vs S^2.
from the relation  ~ exp(-2BS^2).
We can take that slope as the rise over run in the range from S=0 to s=1/(3A), 
even though
the real Wilson plot will follow it only around 3A and beyond.

 in a shell at resolution S will be down by a factor of
 exp(-2BS^2)  compared to  at S=0
for S=(1/3A) this is a factor of exp(-0.222*B)
   for B=10, this is a factor of 0.108
   for B=100, this will be a factor of 2.3E-10

Now if for half the atoms B is 10 and for the other half B is 100
 at 3 A will be something like (.108 + 2.3E-10)/2 = 0.054
(This is a little over my head because we are combining contribution of the
two sets of atoms to each reflection in the shell, and they add vectorially.
Maybe a factor of sqrt(2) is appropriate for random phases.
But for order of magnitude:)

The slope from S^2=0 to S^2=(1/3A)^2 =
-2B ={ ln(0.054) - ln(1) }/{. - 0}
-2B =  -26.3
B(wilson) = 13.2
Bave = (10+100)/2 = 55
The log of the average is larger than the average of the logs.

Another way of looking at it, the contribution of those atoms with B=100 at 3A 
is completely negligible compared to the contribution of the atoms
with B=10, so the slope around 3A reflects only the B-factor of the 
well-ordered atoms, and the slope measured there should give B=10, not 13.

If atoms were randomly distributed and we could apply Wilson over the  entire 
resol range, we still wouldn't get a straight line if there is a range of 
atomic B-factors.
It would be like "curve peeling" in analyzing two simultaneous first-order 
reactions with different half-time: semilog plot of dissociation of a mixture 
of fast and slow hemoglobin. Near zero time the curve is steep as the fast 
molecules dissociate, then it flattens out and becomes linear with a smaller 
slope as only slow molecules are still dissociating. So (in the absence of a 
curve-fitting program) you calculate the rate constant for the slow molecules 
from the linear region at long time, and extrapolate the line back to zero time 
to get the initial percent slow. Then you can calculate the amount of slow at 
any time point and subtract that from the total to get the amount of fast, and 
re-plot that on semilog to get the fast rate constant.

By analyzing our Wilson plots at 3A (or more generally at the highest 
resolution available) we are getting the B-factor for the slowest-decaying 
(lowest B-factor) atoms, getting B=10 not 13 in this case.





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[ccp4bb] Increase in R-factor following REFMAC

[Kyle Gregory]

Hello,

I haven't seen this before but doing a round of refinment with REFMAC, after 
molecular replacement with phaser, my R factor and R free have increased?

Also is it weird that my Rfree is smaller than my R factor?


Result:

Initial Final
R factor0.3621  0.3761
R free  0.3108  0.4733
Rms BondLength  0.0076  0.0057
Rms BondAngle   1.6504  1.5193
Rms ChirVolume  0.0600  0.0526
My map was ok(ish) but there was indication of anistropy so I attempted to 
improve it by using STARANISO and re-ran phaser with the output, and this is 
the results I see following REFMAC.

Thanks,

Kyle



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Re: [ccp4bb] Increase in R-factor following REFMAC

[Eleanor Dodson]

Well - there is something funny about your first Rfree - it shouldnt be
significantly lower than R?
I suspect there is some muddle over the assignment of Rfree - one used for
Phaser and a different value for REFMAC?

And of course at low resolution especiall Rfactors are very sensitive to
scaling procedures..
Eleanor

On Wed, 8 Apr 2020 at 14:08, Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote:

> Hello,
>
> I haven't seen this before but doing a round of refinment with REFMAC,
> after molecular replacement with phaser, my R factor and R free have
> increased?
>
> Also is it weird that my Rfree is smaller than my R factor?
>
> *Result:*
> Initial Final
> R factor 0.3621 0.3761
> R free 0.3108 0.4733
> Rms BondLength 0.0076 0.0057
> Rms BondAngle 1.6504 1.5193
> Rms ChirVolume 0.0600 0.0526
> My map was ok(ish) but there was indication of anistropy so I attempted to
> improve it by using STARANISO and re-ran phaser with the output, and this
> is the results I see following REFMAC.
>
> Thanks,
>
> Kyle
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC

[Schreuder, Herman /DE]

I guess the molecular replacement model has never been refined against this 
data set, so there is no reason why the Rfree should be better or worse than 
the Rfactor. The difference is larger than I would expect, but it may just be a 
statistical fluke. That the Rfree goes up significantly during refinement is 
what I would expect and suggests that the model needs significant rebuilding 
and refinement. Similar, the Rfactor going slightly up may indicate that the 
model is moving out of a false local minimum.

I would just continue rebuilding and refinement and see what happens.

Best,
Herman

Von: CCP4 bulletin board  Im Auftrag von Eleanor Dodson
Gesendet: Mittwoch, 8. April 2020 15:36
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Well - there is something funny about your first Rfree - it shouldnt be 
significantly lower than R?
I suspect there is some muddle over the assignment of Rfree - one used for 
Phaser and a different value for REFMAC?

And of course at low resolution especiall Rfactors are very sensitive to 
scaling procedures..
Eleanor

On Wed, 8 Apr 2020 at 14:08, Kyle Gregory 
<3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>
 wrote:
Hello,

I haven't seen this before but doing a round of refinment with REFMAC, after 
molecular replacement with phaser, my R factor and R free have increased?

Also is it weird that my Rfree is smaller than my R factor?

Result:
Initial
Final
R factor
0.3621
0.3761
R free
0.3108
0.4733
Rms BondLength
0.0076
0.0057
Rms BondAngle
1.6504
1.5193
Rms ChirVolume
0.0600
0.0526
My map was ok(ish) but there was indication of anistropy so I attempted to 
improve it by using STARANISO and re-ran phaser with the output, and this is 
the results I see following REFMAC.

Thanks,

Kyle



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Re: [ccp4bb] Coot 0.9 Released

[Clement Degut]

At the moment I am struggling a bit to have it to compile under
WSL2-ubuntu18.04
But the pre release version included in the ccpem nightly 20200327 is
working well, it is a bit laggy when showing maps and you end up having to
decrease the map radius a bit.
but overall it is perfectly usable.
The compatibility is great, but WSL2 is not meant for graphics and is not
happy when openGL is involved.

Clément

On Sat, 4 Apr 2020 at 20:52, Kay Diederichs 
wrote:

> has anybody tried to run coot-0.9 on Windows under WSL2 (
> https://pureinfotech.com/install-windows-subsystem-linux-2-windows-10/ )
> ? WSL2 is supposed to provide good compatibility between Windows and Linux.
> To try this, one needs to become participant of the Windows Insider Program
> ( https://insider.windows.com ).
>
> HTH,
> Kay
>
> On Thu, 2 Apr 2020 16:59:22 +0100, Aleksandr Sverzhinsky <
> aleksandr.sverzhin...@umontreal.ca> wrote:
>
> >This is great! Do you have an idea when this version will be available
> for WinCoot?
> >
> >
> >
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[ccp4bb] Support and Resources for COVID-19 Related Crystallography Research - MiTeGen

[Benjamin Apker]

Dear CCP4,

We have always been proud to be a part of this incredible community, but
are now even more so. Thank you to everyone contributing to the massive
efforts to combat this epidemic.

Given our unique position of having connections at nearly every MX beamline
and with a large number of researchers around the world, we would like to
do our part to contribute in this unprecedented time.

To this end, we have put together the following COVID-19 efforts, which I
was encouraged to share with this message forum:

• *COVID-19 Reseacher Resource Page*

- which we are focusing on updating and sharing calls for beamtime,
initiatives, data, funding opportunities, etc.

If you have information that you would like to see added, we are happy to
do so. In addition, we are able to echo them to our mailing list and social
media following.

• *COVID-19 Related Order Priority Program*
  -
we are prioritizing and rushing orders for materials for this urgent work
and also helping cover some of the costs.

Again, from all of us on the MiTeGen team, thank you to everyone in this
community for all of your contributions to COVID-19 related and all of the
other critical research.

Best wishes for safety and health,
Ben

-- 
Benjamin Apker
Chief Operating Officer
MiTeGen

95 Brown Road
MS 1034, Suite 183
Ithaca, NY 14850
office: +1-607-266-8877
fax:+1-607-697-0400
___
This message contains confidential information and is intended only for the
individual named. If you are not the named addressee you should not
disseminate, distribute or copy this e-mail. Please notify the sender
immediately by e-mail if you have received this e-mail by mistake and
delete this e-mail from your system. E-mail transmission cannot be
guaranteed to be secure or error-free as information could be intercepted,
corrupted, lost, destroyed, arrive late or incomplete, or contain viruses.
The sender therefore does not accept liability for any errors or omissions
in the contents of this message, which arise as a result of e-mail
transmission. MiTeGen, 95 Brown Road, Suite 183, Ithaca,NY 14850.



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Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC

[Dale Tronrud]

   In addition, REFMAC has tightened your model's geometry which can
cause a slight increase in the working R.  A one percent increase in
while in the upper thirties is slight.

Dale Tronrud

On 4/8/2020 7:30 AM, Schreuder, Herman /DE wrote:
> I guess the molecular replacement model has never been refined against
> this data set, so there is no reason why the Rfree should be better or
> worse than the Rfactor. The difference is larger than I would expect,
> but it may just be a statistical fluke. That the Rfree goes up
> significantly during refinement is what I would expect and suggests that
> the model needs significant rebuilding and refinement. Similar, the
> Rfactor going slightly up may indicate that the model is moving out of a
> false local minimum.
> 
>  
> 
> I would just continue rebuilding and refinement and see what happens.
> 
>  
> 
> Best,
> 
> Herman
> 
>  
> 
> *Von:* CCP4 bulletin board  *Im Auftrag von
> *Eleanor Dodson
> *Gesendet:* Mittwoch, 8. April 2020 15:36
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] Re: [ccp4bb] Increase in R-factor following REFMAC
> 
>  
> 
> *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk
> 
> 
>  
> 
> Well - there is something funny about your first Rfree - it shouldnt be
> significantly lower than R?
> 
> I suspect there is some muddle over the assignment of Rfree - one used
> for Phaser and a different value for REFMAC?
> 
>  
> 
> And of course at low resolution especiall Rfactors are very sensitive to
> scaling procedures.. 
> 
> Eleanor
> 
>  
> 
> On Wed, 8 Apr 2020 at 14:08, Kyle Gregory
> <3632e92fcc15-dmarc-requ...@jiscmail.ac.uk
> > wrote:
> 
> Hello,
> 
> I haven't seen this before but doing a round of refinment with
> REFMAC, after molecular replacement with phaser, my R factor and R
> free have increased?
> 
> Also is it weird that my Rfree is smaller than my R factor?
> 
> *Result:*
> 
>   
> 
> *Initial*
> 
>   
> 
> *Final*
> 
> *R factor *
> 
>   
> 
> 0.3621
> 
>   
> 
> 0.3761
> 
> *R free *
> 
>   
> 
> 0.3108
> 
>   
> 
> 0.4733
> 
> *Rms BondLength *
> 
>   
> 
> 0.0076
> 
>   
> 
> 0.0057
> 
> *Rms BondAngle *
> 
>   
> 
> 1.6504
> 
>   
> 
> 1.5193
> 
> *Rms ChirVolume *
> 
>   
> 
> 0.0600
> 
>   
> 
> 0.0526
> 
> My map was ok(ish) but there was indication of anistropy so I
> attempted to improve it by using STARANISO and re-ran phaser with
> the output, and this is the results I see following REFMAC.
> 
> Thanks,
> 
> Kyle
> 
>  
> 
> 
> 
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> 
> 
> 
> 
>  
> 
> 
> 
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> 
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[ccp4bb] Structural Alignment

[Armando Albert]

Dear all, 
I want to align two structures and then, I want to align several sequences to 
that structural alignment. 
How can I do this?
Armando



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Re: [ccp4bb] Structural Alignment

[Guillaume Gaullier]

Hi Armando,

This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ 


More specifically, its matchmaker command will align two structures and print 
the corresponding sequence alignment: 
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html 

You can then save the sequence alignment to a file, and use it in your favorite 
sequence alignment program along with the sequences for which you don’t have a 
structure.

This is one option among many, as pretty much every structure visualization 
program can superimpose two similar structures (but I don’t know how many of 
them make it as easy to save the sequence alignment).

Hope this helps,

Guillaume


> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
> 
> Dear all, 
> I want to align two structures and then, I want to align several sequences to 
> that structural alignment. 
> How can I do this?
> Armando
> 
> 
> 
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Re: [ccp4bb] Structural Alignment

[Nicholas Gao]

Hi Armando,

The PyMol version of this would involve the 'align' command:
https://pymolwiki.org/index.php/Align

Import your two structures into a PyMol session. In the command line of
PyMol, run "align NameOfStructure1, NameOfStructure2,
object=SomeNameYouMadeUp". Next, run "save SomeNameYouMadeUp.aln,
SomeNameYouMadeUp".  This will product a 2D sequence alignment that you can
then take off to other sequence aligners to use as a reference in
subsequent sequence alignments.

-Nick

On Wed, Apr 8, 2020 at 1:22 PM Guillaume Gaullier 
wrote:

> Hi Armando,
>
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/
>
> More specifically, its matchmaker command will align two structures and
> print the corresponding sequence alignment:
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> Dear all,
> I want to align two structures and then, I want to align several sequences
> to that structural alignment.
> How can I do this?
> Armando
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
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>
>
>
> --
>
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Re: [ccp4bb] Structural Alignment

[Jim Fairman]

I used STRAP back in the late 2000s to do structure-based sequence
alignments of some TonB Dependent transporters:
http://www.bioinformatics.org/strap/

Looks like it is still being updated.

Cheers, Jim
--
Jim Fairman
C: 1-240-479-6575


On Wed, Apr 8, 2020 at 10:22 AM Guillaume Gaullier 
wrote:

> Hi Armando,
>
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/
>
> More specifically, its matchmaker command will align two structures and
> print the corresponding sequence alignment:
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> Dear all,
> I want to align two structures and then, I want to align several sequences
> to that structural alignment.
> How can I do this?
> Armando
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
> --
>
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Re: [ccp4bb] Structural Alignment

[Armando Albert]

Thank you all, 
I have done it with chimera. It does structural alignment and use it as a 
template. Then, you can add sequences one after the other and align to this 
template. 
You can save this alignment in clustalw format and load it to ESPrit3 and do a 
nice picture. 
Armando



> El 8 abr 2020, a las 19:22, Guillaume Gaullier  
> escribió:
> 
> Hi Armando,
> 
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/ 
> 
> 
> More specifically, its matchmaker command will align two structures and print 
> the corresponding sequence alignment: 
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html 
> 
> You can then save the sequence alignment to a file, and use it in your 
> favorite sequence alignment program along with the sequences for which you 
> don’t have a structure.
> 
> This is one option among many, as pretty much every structure visualization 
> program can superimpose two similar structures (but I don’t know how many of 
> them make it as easy to save the sequence alignment).
> 
> Hope this helps,
> 
> Guillaume
> 
> 
>> On 8 Apr 2020, at 19:04, Armando Albert > > wrote:
>> 
>> Dear all, 
>> I want to align two structures and then, I want to align several sequences 
>> to that structural alignment. 
>> How can I do this?
>> Armando
>> 
>> 
>> 
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Re: [ccp4bb] Structural Alignment

[Rajiv gandhi.s]

UCSF chimera or chimeraX versions both could do the alignment of multiple
structures that also pop up the sequence alignment with secondary
structures highlighted in different colors through Match Maker. Up-to six
structures I have aligned.


Best regards
Rajivgandhi Sundaram.


On Wed, Apr 8, 2020, 11:09 PM Armando Albert  wrote:

> Thank you all,
> I have done it with chimera. It does structural alignment and use it as a
> template. Then, you can add sequences one after the other and align to this
> template.
> You can save this alignment in clustalw format and load it to ESPrit3 and
> do a nice picture.
> Armando
>
>
>
> El 8 abr 2020, a las 19:22, Guillaume Gaullier 
> escribió:
>
> Hi Armando,
>
> This seems doable with ChimeraX: https://www.cgl.ucsf.edu/chimerax/
>
> More specifically, its matchmaker command will align two structures and
> print the corresponding sequence alignment:
> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/matchmaker.html
> You can then save the sequence alignment to a file, and use it in your
> favorite sequence alignment program along with the sequences for which you
> don’t have a structure.
>
> This is one option among many, as pretty much every structure
> visualization program can superimpose two similar structures (but I don’t
> know how many of them make it as easy to save the sequence alignment).
>
> Hope this helps,
>
> Guillaume
>
>
> On 8 Apr 2020, at 19:04, Armando Albert  wrote:
>
> Dear all,
> I want to align two structures and then, I want to align several sequences
> to that structural alignment.
> How can I do this?
> Armando
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
>
>
>
> --
>
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