[ccp4bb] workshop on cryo-EM and single-particle analysis in Melbourne, Australia

[Hans Elmlund]

Dear All:


The ARC Centre of Excellence for Advanced Molecular Imaging and EMBL
Australia announce a workshop on cryo-EM and single-particle analysis to be
held at Monash University, Melbourne, Australia, 1-3 February 2017,
preceding the LorneProteins meeting . The
workshop will include hands-on practicals in addition to
problem-solving-oriented talks from leading software developers in the
field, including



*Steven Ludtke*, lead developer of the popular, all-purpose *EMAN2
 *suite of programs

*Hans Elmlund, *lead developer of the *SIMPLE/PRIME
* suite of programs for *ab intio *3D
reconstruction

*Jose Miguel de la Rosa Trevin *and* Roberto Marabini*, developers of the
integrative software tool *Scipion *



The workshop will cover all computational aspects of single-particle
analysis, including 2D analysis, 3D starting model generation,
heterogeneity analysis, and high-resolution refinement. You will be
introduced to and get the opportunity to try out the latest developments in
the field.



We will accept 40 students. To apply go to



 http://simplecryoem.com/workshop.html



The registration fee is 300 AUD and once your registration is confirmed you
will be sent an invoice. Confirmation letters and invoices will be sent by
Dec 1 2016.



Looking forward to see you in Melbourne,



The organisers:
*Dominika Elmlund & Hans Elmlund*

Re: [ccp4bb] High B factor

[Dale Tronrud]

   It seems to be common for people to make the incorrect assumption
that the average of the atomic B factors in the PDB file should equal
the Wilson B.  The Wilson B is actually a weighted average of the
individual B factors where the weighting is rather mysterious, but the
small B factors have much higher weight than the larger ones. While the
Wilson B is simply a property of your data set the average of the atomic
B factors will also depend on choices you have made in building your
model.

   In your case the core of your protein does have B factors that match
your Wilson B.  The fact that you have loops that have larger B's
doesn't really mean there is a problem, because those atoms don't
contribute much to the higher resolution reflections and don't come into
the calculation of the Wilson B.

   The average of your B factors will increase if you choose to build
model for more disordered regions, while the Wilson B will, of course,
remain the same.  The average B factor will be larger, for example, if
you are more aggressive in building water molecules.  This does not
indicate a problem but is an unavoidable consequence of your choice to
take more risks.

Dale



On 10/13/2016 12:16 AM, sunanda williams wrote:
> Sorry for not making the problem clear!
> The overall B factor for the 3.0 A structure is around 98.00 A*2. Most
> of the deposited structures in the PDB site around this resolution
> has an av B around 70 A*2
> All other statistics looks fine. I got a warning message while trying to
> upload the structure in PDB that 98 was higher than the norm!
> The reason why the structure has such a high B factor could be due to
> disordered loops... All the same I was wondering how acceptable this
> structure would be to picky reviewers..
> And 'better the B factors' means bring them down...sorry couldn't phrase
> it 'better'! I am going to try doing refinement with group B factors!
> Would that help?
> Thanks Robbie, I think this I need to make the best of the model I have.
> Prof. Sekar will try PDB_redo..Thanks!
> 
> 
> 
> On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine  > wrote:
> 
> I fully agree with Dale in not understanding what the problem is.
> Perhaps I have a better chance if you clearly explain what exactly
> you mean by "is there any way to better the B factors".
> Pavel
> 
> 
> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud
> > wrote:
> 
>I'm sorry but I don't understand what your problem is.  Do
> you think
> the B factors are too small for a 3A data set?  A range of 70 to
> 75 is a
> little smaller than usual but probably not out of bounds.
> 
> Dale Tronrud
> 
> On 10/12/2016 7:59 PM, sunanda williams wrote:
> > Hi all,
> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B
> value is
> > around 98. The B value is especially high at the N terminus
> and two loop
> > regions (around 120-150 AA).
> > The rest of the structure averaged around 70-75. Has anyone
> faced such a
> > scenario? How reliable is the structure and is there any way
> to better
> > the B factors.
> > Any help is appreciated.
> > Thank you!!
> 
> 
> 



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[ccp4bb] crunch2 failed

[Raja Dey]

Dear Members,
crunch2 job failed with an error message.

#CCP4I TERMINATION STATUS 0 "crank::crank binary and crank XML version do
not match while executing "error $message"
 Can someone give any solution?

Thanks,
Raj

[ccp4bb] Job posting: Postdoctoral position in X-ray crystallography and protein biochemistry

[James Bardwell]

A postdoctoral position Bardwell Lab at the University of Michigan and the
Howard Hughes Medical Institute is available for an expert in X-ray
crystallography and protein biochemistry. The Bardwell laboratory focuses
on discovering and characterizing new chaperone proteins, including
structural dissection of chaperone mechanism. The lab is well funded by
both HHMI and NIH sources, and features state-of-the-art crystallography
and biophysics equipment. The incoming postdoc will have the benefit of
interfacing with the strong structural biology community at University of
Michigan, including the Center for Structural Biology, as well as priority
access to LS-CAT at the Advanced Photon Source. Examples of recent
crystallography publications from the Bardwell lab are below. Interested
applicants should send CV and statement of interest to James Bardwell at
jbard...@umich.edu.

Recent Bardwell lab crystallography projects:
http://www.nature.com/articles/ncomms12549
http://www.nature.com/nsmb/journal/v23/n7/full/nsmb.3237.html

Re: [ccp4bb] autoSHARP: Am I on the right track?

[Thanh Nguyen]

Hi Mohamed,

Did you check the model after autoSHARP? If yes, then how does it look like? ‎I 
guess your solution given by autoSHARP was not correct one and it couldn't 
build the proper model. That is the reason why you see a lot of dummy atoms. I 
would say the dummy atoms are not useful at all. Because if they are, bucaneer 
could have been able to build the proper model. So, it's better to try again 
another phasing determination rather than spend time with a dummy model.

Best,
Thanh N



  Original Message  
From: Mohamed Noor
Sent: jueves, 13 de octubre de 2016 16:35
To: CCP4BB@JISCMAIL.AC.UK
Reply To: Mohamed Noor
Subject: [ccp4bb] autoSHARP: Am I on the right track?

Dear all

Following on the previous thread on Fe-SAD, there is a solution(?) from 
autoSHARP with an OK-ish map and model. A quick refinement with phenix.refine 
gave me an R/Rfree of 28/31 % (2 A, although for the phasing run I told 
autoSHARP to use only up to 2.5 A). However, the model was filled in with about 
6000 dummy atoms (DUM) plus some regions with just Gly. I did provide a 
sequence file, so not sure why it didn't build them in. When I deleted all the 
DUM atoms, the R/Rfree increased to about 48 %.

I am wondering, are the positions of DUM atoms correct and I just need to build 
it manually somehow?

Thanks.
Mohamed

[ccp4bb] autoSHARP: Am I on the right track?

[Mohamed Noor]

Dear all

Following on the previous thread on Fe-SAD, there is a solution(?) from 
autoSHARP with an OK-ish map and model. A quick refinement with phenix.refine 
gave me an R/Rfree of 28/31 % (2 A, although for the phasing run I told 
autoSHARP to use only up to 2.5 A). However, the model was filled in with about 
6000 dummy atoms (DUM) plus some regions with just Gly. I did provide a 
sequence file, so not sure why it didn't build them in. When I deleted all the 
DUM atoms, the R/Rfree increased to about 48 %.

I am wondering, are the positions of DUM atoms correct and I just need to build 
it manually somehow?

Thanks.
Mohamed

[ccp4bb] Job posting: Postdoctoral positions in structural biology of herpesviruses

[Heldwein, Katya]

Postdoctoral positions are available in the laboratory of Katya Heldwein 
at Tufts University School of Medicine (Boston, MA). Her lab 
investigates the mechanisms by which herpesviruses manipulate host 
membranes and intracellular traffic to enter and escape from the host 
cells using a combination of biophysical, biochemical and cell 
biological approaches.


Applicants should hold a PhD in a biological science and have at least 
one first-author publication in a major peer-reviewed journal. 
Applicants with research experience in membrane protein biochemistry, 
macromolecular structure determination (x-ray crystallography or 
electron microscopy), single-molecule spectroscopy, or virology are 
especially encouraged to apply. Fluency in oral and written English is 
essential.


To apply, please, submit a CV, a cover letter with a summary of previous 
research and a description of future research interests, and names of 3 
references to Dr. Katya Heldwein by e-mail: katya.heldw...@tufts.edu 
. Information for the Heldwein lab can 
be found at: http://sites.tufts.edu/heldweinlab/.



--
Ekaterina Heldwein, Ph.D.
Associate Professor
Department of Molecular Biology and Microbiology
Tufts University School of Medicine
136 Harrison Ave
Boston, MA 02111
 
phone: 617-636-0858

fax: 617-636-0337
e-mail: katya.heldw...@tufts.edu

Re: [ccp4bb] Metrics for hkl2map (Fe SAD)

[Fabio Dall'Antonia]

Dear Mohamed,

more important than the absolute values of CCall/CCweak is the 
distribution of these statistics among the solution-trials of one SHELXD 
computation job (i.e. based on a particular data set).


In the HKL2MAP scatter-plot, there should be at least one, or a set of, 
solutions that are clearly separate in both CCall and CCweak from the 
bulk of trials - representing a bimodal distribution. Importantly, the 
best solution is promising if it is maximal in *both* CCall and CCweak.
On the contrary, to my experience, two "best" solutions that are apart 
from the rest, but one maximal in CCall and the other in CCweak, point 
at the presence of not-completely-wrong, but incomplete substructures 
(in terms of correct sites).


Absolute "threshold values" for CC are hard to define, since these 
statistics depend on various factors, among these importantly the data 
resolution. But with all caution and no guarantee, I would start to call 
SAD solution trials "promising", if their CFOM = CCall + CCweak exceeds 30%.



Best wishes
Fabio



Dear all

I am trying to solve a structure using Fe SAD collected with mini-kappa from several 
non-isomorphic crystals (following on from the previous 
threadhttps://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1608=CCP4BB=0=35088).
 Xtriage suggests weak anomalous signal to 4 A.

For the SHELX pipeline using hkl2map, are there any metrics/numbers that I can 
use to judge the quality of each dataset? For example, what should be the value 
of CCall/CCweak to decide between strong/promising and useless cases?

Is there any difference between using CRANK2 and hkl2map, considering that the 
underlying software are the same?

Will the wavy Rmerge affect the 'solvability'?

Thanks.
Mohamed



--
Dr. rer. nat. Fabio Dall'Antonia
European Molecular Biology Laboratory c/o DESY
Notkestraße 85, Bldg. 25a
D-22607 Hamburg

phone:  +49 (0)40 89902-178
fax:+49 (0)40 89902-149
e-mail: fabio.dallanto...@embl-hamburg.de

Re: [ccp4bb] Software to know the common folds in a protein

[Bernhard Rupp]

“Do not be embarrassed by your failures, learn from them and start again.”

Nice quote, except when it refers to the brain surgeon working on you

Cheers, BR



On Thu, Oct 13, 2016 at 3:38 PM, Vikram Dalal 
wrote:

> Thank you all for suggestions.
>
>
>
>
> “Do not be embarrassed by your failures, learn from them and start again.”
>
> Thanks & Regards,
> VIKRAM DALAL
> Research Scholar
> Macromolecular Crystallographic Unit
> Department of Biotechnology
> Indian Institute of Technology
> Roorkee (INDIA)
>
>
>
>
>
>
>
> On Thu, Oct 13, 2016 at 6:36 PM, Christian Roth <
> christianroth...@gmail.com> wrote:
>
>> Hi,
>>
>> You could try the DALI server or pdbefold. Both give you pretty much the
>> same information.
>>
>> Christian
>>
>> Am 13.10.2016 um 13:03 schrieb Vikram Dalal:
>>
>> Hi everyone,
>>
>> We are solving a protein structure and we want to know the folds which
>> are present in it. Suggest me the best software or server which can be used
>> to find the common folds in my protein.
>>
>>
>>
>>
>> Thanks & Regards,
>>
>>
>>
>>
>>
>>
>


-- 
-
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
The hard part about playing chicken
is to know when to flinch
-

Re: [ccp4bb] Software to know the common folds in a protein

[Vikram Dalal]

Thank you all for suggestions.




“Do not be embarrassed by your failures, learn from them and start again.”

Thanks & Regards,
VIKRAM DALAL
Research Scholar
Macromolecular Crystallographic Unit
Department of Biotechnology
Indian Institute of Technology
Roorkee (INDIA)







On Thu, Oct 13, 2016 at 6:36 PM, Christian Roth 
wrote:

> Hi,
>
> You could try the DALI server or pdbefold. Both give you pretty much the
> same information.
>
> Christian
>
> Am 13.10.2016 um 13:03 schrieb Vikram Dalal:
>
> Hi everyone,
>
> We are solving a protein structure and we want to know the folds which are
> present in it. Suggest me the best software or server which can be used to
> find the common folds in my protein.
>
>
>
>
> Thanks & Regards,
>
>
>
>
>
>

Re: [ccp4bb] Software to know the common folds in a protein

[Christian Roth]

Hi,

You could try the DALI server or pdbefold. Both give you pretty much the 
same information.


Christian


Am 13.10.2016 um 13:03 schrieb Vikram Dalal:

Hi everyone,

We are solving a protein structure and we want to know the folds which 
are present in it. Suggest me the best software or server which can be 
used to find the common folds in my protein.





Thanks & Regards,

[ccp4bb] Software to know the common folds in a protein

[Vikram Dalal]

Hi everyone,

We are solving a protein structure and we want to know the folds which are
present in it. Suggest me the best software or server which can be used to
find the common folds in my protein.




Thanks & Regards,

Re: [ccp4bb] Coot on MacOsX undo button

[Paul Emsley]

On 12/10/2016 19:03, Jan van Agthoven wrote:


Looks like the undo button on Coot doesn't work. I installed Coot-0.8.6 on 
MacOsx El
Capitan. Anyone knows what could be the problem?


Perhaps you have started coot from a directory to which you do not have write access? What 
does it say in the terminal? That should be pretty clear about the problem.



Or where to report the bug?


If this is not a CCP4 problem, then the Coot mailing list (on Jiscmail).

Paul.

Re: [ccp4bb] High B factor

[sunanda williams]

Sorry for not making the problem clear!
The overall B factor for the 3.0 A structure is around 98.00 A*2. Most of
the deposited structures in the PDB site around this resolution
has an av B around 70 A*2
All other statistics looks fine. I got a warning message while trying to
upload the structure in PDB that 98 was higher than the norm!
The reason why the structure has such a high B factor could be due to
disordered loops... All the same I was wondering how acceptable this
structure would be to picky reviewers..
And 'better the B factors' means bring them down...sorry couldn't phrase it
'better'! I am going to try doing refinement with group B factors! Would
that help?
Thanks Robbie, I think this I need to make the best of the model I have.
Prof. Sekar will try PDB_redo..Thanks!



On Thu, Oct 13, 2016 at 11:41 AM, Pavel Afonine  wrote:

> I fully agree with Dale in not understanding what the problem is. Perhaps
> I have a better chance if you clearly explain what exactly you mean by "is
> there any way to better the B factors".
> Pavel
>
>
> On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud 
> wrote:
>
>>I'm sorry but I don't understand what your problem is.  Do you think
>> the B factors are too small for a 3A data set?  A range of 70 to 75 is a
>> little smaller than usual but probably not out of bounds.
>>
>> Dale Tronrud
>>
>> On 10/12/2016 7:59 PM, sunanda williams wrote:
>> > Hi all,
>> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
>> > around 98. The B value is especially high at the N terminus and two loop
>> > regions (around 120-150 AA).
>> > The rest of the structure averaged around 70-75. Has anyone faced such a
>> > scenario? How reliable is the structure and is there any way to better
>> > the B factors.
>> > Any help is appreciated.
>> > Thank you!!
>>
>
>

Re: [ccp4bb] High B factor

[Carlos CONTRERAS-MARTEL]

Hi Sunanda

They don't need to be "better" ... they need to be in agreement with you 
experimental B factor ... Wilson plot?


Best

Carlos

On 10/13/16 04:59, sunanda williams wrote:

Hi all,
I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is 
around 98. The B value is especially high at the N terminus and two 
loop regions (around 120-150 AA).
The rest of the structure averaged around 70-75. Has anyone faced such 
a scenario? How reliable is the structure and is there any way to 
better the B factors.

Any help is appreciated.
Thank you!!



--
 Carlos CONTRERAS MARTEL, Ph.D.
 (CR1 CNRS)

 carlos.contreras-mar...@ibs.fr

 "Bacterial Pathogenesis Group"
Institut de Biologie Structurale
 UMR5075 CEA-CNRS-UGA

  IBS
  Campus EPN
  71, avenue des Martyrs
  CS 10090
  38044 Grenoble CEDEX 9
  FRANCE


 tel : (+33) (0)4 57 42 86 41

http://www.ibs.fr/groupes/groupe-pathogenie-bacterienne/?lang=fr
http://www.ibs.fr/groups/bacterial-pathogenesis-group/?lang=en

Re: [ccp4bb] High B factor

[Pavel Afonine]

I fully agree with Dale in not understanding what the problem is. Perhaps I
have a better chance if you clearly explain what exactly you mean by "is
there any way to better the B factors".
Pavel

On Thu, Oct 13, 2016 at 12:57 PM, Dale Tronrud 
wrote:

>I'm sorry but I don't understand what your problem is.  Do you think
> the B factors are too small for a 3A data set?  A range of 70 to 75 is a
> little smaller than usual but probably not out of bounds.
>
> Dale Tronrud
>
> On 10/12/2016 7:59 PM, sunanda williams wrote:
> > Hi all,
> > I have a structure at 3.0 A and R/Rfree of 24/28. The mean B value is
> > around 98. The B value is especially high at the N terminus and two loop
> > regions (around 120-150 AA).
> > The rest of the structure averaged around 70-75. Has anyone faced such a
> > scenario? How reliable is the structure and is there any way to better
> > the B factors.
> > Any help is appreciated.
> > Thank you!!
>