Re: [ccp4bb] BDB rsync

[Bulat Gabidullin]

Hello Eric,

If it's about PDB, it worked for me a few days ago.
(I used *rsync -rlpt -v -z --delete --port=33444
rsync.rcsb.org::ftp_data/structures/divided/pdb/ /yourfolder*)

Bulat Gabidullin
CMCF, Canadian Light Source

On Fri, Jul 5, 2019 at 10:10 AM Eric Williams 
wrote:

> Has anyone successfully accessed the BDB lately? I downloaded the whole
> thing by rsync about a year ago, but I am no longer able to do so. I don't
> seem to be getting any response from the rsync server at all. If others are
> able to access it, I should be looking for a problem on my end. Thanks. :)
>
> Eric
>
> P.S. I've contacted Dr. Vriend, but I haven't heard back yet.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
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>



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[ccp4bb] BDB rsync

[Eric Williams]

Has anyone successfully accessed the BDB lately? I downloaded the whole
thing by rsync about a year ago, but I am no longer able to do so. I don't
seem to be getting any response from the rsync server at all. If others are
able to access it, I should be looking for a problem on my end. Thanks. :)

Eric

P.S. I've contacted Dr. Vriend, but I haven't heard back yet.



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Re: [ccp4bb] resolution

[Gerard Bricogne]

Dear Sam,

 If you have a P1 space group and your dataset was collected in a single
orientation, you will have a great big gaping cusp in it.

 I would suggest that you submit your full dataset to the STARANISO
server at  

  http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi

and take into consideration the distribution of the blue dots. It can be
horrifying: for instance, take a look at 

http://staraniso.globalphasing.org/cgi-bin/RLViewer_PDB_scroll.cgi?ID=6oa7 . 

 The rationale for reducing the resolution at which refinement is done
would be to reduce the proportion (and hence impact) of the systematically
missing data in the cusp, as this gets rapidly worse at high resolution.

 The real remedy is to collect data again, this time in at least two
orientations that are different enough to fill each other's cusps at the
highest resolution. Then you will be able to enjoy the full diffraction
limit (2.0A or better) that your crystal seems willing to give ;-) .


 With best wishes,

  Gerard.

--
On Fri, Jul 05, 2019 at 09:48:35PM +0800, Sam Tang wrote:
> Dear all
> 
> Hello again
> 
> Thanks a lot for the numerous input.
> 
> I received a dataset which was processed to 2.4A but refined to 3A -- this
> was the background I raised this question in the first place. Then I looked
> at the aimless statistics. At 2.4A the high resolution bin CC1/2 0.626,
> I/sigI 2.0, Completeness 84.6, Multiplicity 1.7 (P1 spacegroup).  I suspect
> the reason for the refinement resolution limit to be set at 3 A was simply
> due to better Rw/Rf (0.236/0.294 at 3A; 0.284/0.341 at 2.4A).
> 
> Based on these information am I justified to say that data quality at 2.4 A
> was suboptimal? In this case do you think refining at a (much) lower
> resolution is acceptable?
> 
> Best regards
> 
> Sam
> 
> On Fri, 5 Jul 2019 at 13:43, Sam Tang  wrote:
> 
> > Hello everyone
> >
> > Sorry for a naive question. Is there any circumstances where one may wish
> > to refine to a lower resolution? For example if one has a dataset processed
> > to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
> >
> > Thanks!
> >
> > Sam Tang
> >
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] resolution

[Robbie Joosten]

You cannot directly compare R-factors because they are calculated over 
different sets of data. It's apples and oranges. 

Your R-factor gap is a bit large too, perhaps your model can be improved a bit 
for instance by using tighter geometric restraints.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Sam Tang
> Sent: Friday, July 05, 2019 15:49
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] resolution
> 
> Dear all
> 
> Hello again
> 
> Thanks a lot for the numerous input.
> 
> I received a dataset which was processed to 2.4A but refined to 3A -- this was
> the background I raised this question in the first place. Then I looked at the
> aimless statistics. At 2.4A the high resolution bin CC1/2 0.626, I/sigI 2.0,
> Completeness 84.6, Multiplicity 1.7 (P1 spacegroup).  I suspect the reason for
> the refinement resolution limit to be set at 3 A was simply due to better
> Rw/Rf (0.236/0.294 at 3A; 0.284/0.341 at 2.4A).
> 
> Based on these information am I justified to say that data quality at 2.4 A 
> was
> suboptimal? In this case do you think refining at a (much) lower resolution is
> acceptable?
> 
> 
> Best regards
> 
> Sam
> 
> On Fri, 5 Jul 2019 at 13:43, Sam Tang  wrote:
> 
> 
>   Hello everyone
> 
>   Sorry for a naive question. Is there any circumstances where one
> may wish to refine to a lower resolution? For example if one has a dataset
> processed to 2 A, is there any good reasons for he/she to refine to only, say
> 2.5 A?
> 
>   Thanks!
> 
>   Sam Tang
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1




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Re: [ccp4bb] resolution

[Mark J van Raaij]

looks like a case of the "if Rfree is lower than 0.300 the structure is 
perfect, if Rfree is higher than 0.300 your structure is completely rubbish" 
police striking again (some reviewers are like this). A bit like if p is 
smaller than 0.05 the effect is definitely real and if p is just about 0.05 
there is definitely no effect...
I would include data to 2.4Å. Or perhaps, try steps and look at maps at 2.4, 
2.5, 2.6Å etc. and then decide (PDBredo can do this automagically). And then 
take 2.4Å or some limit much closer to 2.4Å than 3.0Å.
At 2.4Å (or 2.5Å or 2.6Å) there would be much more info and maps should look 
better than at 3.0Å, even if the Rs are a bit higher.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


> On 5 Jul 2019, at 15:48, Sam Tang  wrote:
> 
> Dear all
> 
> Hello again
> 
> Thanks a lot for the numerous input. 
> 
> I received a dataset which was processed to 2.4A but refined to 3A -- this 
> was the background I raised this question in the first place. Then I looked 
> at the aimless statistics. At 2.4A the high resolution bin CC1/2 0.626, 
> I/sigI 2.0, Completeness 84.6, Multiplicity 1.7 (P1 spacegroup).  I suspect 
> the reason for the refinement resolution limit to be set at 3 A was simply 
> due to better Rw/Rf (0.236/0.294 at 3A; 0.284/0.341 at 2.4A).
> 
> Based on these information am I justified to say that data quality at 2.4 A 
> was suboptimal? In this case do you think refining at a (much) lower 
> resolution is acceptable?
> 
> Best regards
> 
> Sam
> 
> On Fri, 5 Jul 2019 at 13:43, Sam Tang  > wrote:
> Hello everyone
> 
> Sorry for a naive question. Is there any circumstances where one may wish to 
> refine to a lower resolution? For example if one has a dataset processed to 2 
> A, is there any good reasons for he/she to refine to only, say 2.5 A?
> 
> Thanks!
> 
> Sam Tang
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] resolution

[Eleanor Dodson]

Well - i would always do the final refinement to the highest resolution
with CC1/2 > 0.5

There may be other problems with the data  - completeness low for current
standards ..
Does multiplicity fall off with resolution etc?
Is there considerable anisotropy?

both sets of R factors look surprisingly high.. but see above for possible
reasons..

Eleanor


On Fri, 5 Jul 2019 at 14:49, Sam Tang  wrote:

> Dear all
>
> Hello again
>
> Thanks a lot for the numerous input.
>
> I received a dataset which was processed to 2.4A but refined to 3A -- this
> was the background I raised this question in the first place. Then I looked
> at the aimless statistics. At 2.4A the high resolution bin CC1/2 0.626,
> I/sigI 2.0, Completeness 84.6, Multiplicity 1.7 (P1 spacegroup).  I suspect
> the reason for the refinement resolution limit to be set at 3 A was simply
> due to better Rw/Rf (0.236/0.294 at 3A; 0.284/0.341 at 2.4A).
>
> Based on these information am I justified to say that data quality at 2.4
> A was suboptimal? In this case do you think refining at a (much) lower
> resolution is acceptable?
>
> Best regards
>
> Sam
>
> On Fri, 5 Jul 2019 at 13:43, Sam Tang  wrote:
>
>> Hello everyone
>>
>> Sorry for a naive question. Is there any circumstances where one may wish
>> to refine to a lower resolution? For example if one has a dataset processed
>> to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
>>
>> Thanks!
>>
>> Sam Tang
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] resolution

[Sam Tang]

Dear all

Hello again

Thanks a lot for the numerous input.

I received a dataset which was processed to 2.4A but refined to 3A -- this
was the background I raised this question in the first place. Then I looked
at the aimless statistics. At 2.4A the high resolution bin CC1/2 0.626,
I/sigI 2.0, Completeness 84.6, Multiplicity 1.7 (P1 spacegroup).  I suspect
the reason for the refinement resolution limit to be set at 3 A was simply
due to better Rw/Rf (0.236/0.294 at 3A; 0.284/0.341 at 2.4A).

Based on these information am I justified to say that data quality at 2.4 A
was suboptimal? In this case do you think refining at a (much) lower
resolution is acceptable?

Best regards

Sam

On Fri, 5 Jul 2019 at 13:43, Sam Tang  wrote:

> Hello everyone
>
> Sorry for a naive question. Is there any circumstances where one may wish
> to refine to a lower resolution? For example if one has a dataset processed
> to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
>
> Thanks!
>
> Sam Tang
>



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[ccp4bb] PhD student position available in CBB Poznan, Poland

[Mirek Gilski]

Dear all,

I'd like to draw your attention to the opening for PhD student position 
at Center for Biocrystallographic Research (Poznan, Poland),
to work on a combination of protein crystallography and supramolecular 
chemistry (project PI prof. Mariusz Jaskolski)


More information about the offer at:
Euraxess https://www.euraxess.pl/jobs/421381

The project overview can be found at:
http://www.man.poznan.pl/CBB/JOBS/POF.pdf

The deadline for applications is 18th August 2019.

For further information, please do not hesitate contact me directly at 
mi...@amu.edu.pl


I would be grateful if you could forward this opportunity to potential 
applicants.



Kind regards,
Mirek Gilski



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[ccp4bb] Electron Cryo-microscopy support technician at CSSB (Hamburg, DE)

[Thomas White]

The Department of Chemistry, Biochemistry and Molecular Biology of the
Faculty MIN (University of Hamburg) invites applications for employment
as:

Electron cryo-microscopy Support (m/f/D)
Salary Level 13 TV-L

The position commences as soon as possible and is permanent.  This
position is also suitable for part time employment.

The Central Facility "Electron cryo-microscopy" (CryoEM) at the Centre
for Structural Systems Biology (CSSB) Hamburg, a multi-user-facility,
provides essential structural information for research groups of the
UHH and other research groups participating in the CSSB co-operation.
These insights are of fundamental importance for Bachelor, Master and
doctoral theses as well as for publications. The facility currently
comprises five electron cryo-microscopes: two Titan Krios instruments
with phase plate, energy filter, K2/3 and Falcon 3 direct detectors, a
Talos Arctica with phase plate and Falcon 3 direct detector, a Talos
L120C and an Aquilos FIB cryo-SEM for preparing lamellae of vitrified
cells plus auxiliary equipment to complete the workflows. Independent
scientific research in the area of structural and cell biology,
especially in the field of infection biology, as part of scientific
collaborations and involvement in electron microscopy method
development for structural biology applications are highly encouraged.

Responsibilities:

The post holder will have responsibility for ensuring the day-to-day
running of the electron microscopes and of the related auxiliary and
preparatory equipment to the level of optimal system performance at the
Facility in accordance with the Senior Staff Scientist CryoEM. This
includes initial fault diagnosis, participation in repair and
maintenance work, coordination with home technology, installation and
update of the data collection software (both manufacturer provided and
academic alternative developments) in collaboration with the Facility's
data processing scientist.

As part of the team, the post holder will assist with the
establishment, optimisation and expansion of dedicated workflows for
the different cryoEM modalities (in particular single particle analysis
and tomography) including the regular implementation of significant new
developments. A particular local emphasis is put on correlative
microscopy, and close interaction with the Advanced Light and
Fluorescence Microscopy Facility at CSSB is desired. Another
responsibility of the job holder is to support the other staff members
with the development and implementation of the training and induction
concept for academic users.

Requirements:

A university degree in chemistry, biology, physics or another relevant
subject

Required skills and personal qualities:

* Sound research experience and knowledge in electron cryo-microscopy,
and the corresponding underlying theoretical and technical principles
(e.g. electron optics, vacuum systems etc.) and procedures

* Extensive knowledge of the relevant control software of electron
microscopes

* Solid experience in fault finding of complex electron microscopes and
in user training for electron microscopic and auxiliary equipment

* Excellent English language skills (both written and oral)

* Good basic understanding of cell biology and experience in infection
biology and correl- ative microscopy methods are desirable

* Willingness to share knowledge

* Good team player

* The ability to communicate effectively with a wide range of people

* Very good organisational and interpersonal as well as negotiating
skills (when dealing with industrial partners)

The Free and Hanseatic City of Hamburg promotes equal opportunity. As
women are currently under-represented at this salary level at
Universität Hamburg according to the evaluation conducted under the
Hamburg act on gender equality (Hamburgisches Gleichstellungsgesetz,
HambGleiG), we encourage women to apply for this position. Equally
qualified and suitable female applicants will receive preference.

We explicitly encourage persons with an immigrant background to apply.

Equally qualified severely disabled applicants or applicants with
equivalent status will receive preference.

For further information please contact Prof Dr Kay Grünewald by email on
debora.l...@cssb-hamburg.de

Please send your complete application including the reference number by
29 August 2019 to:

Universität Hamburg
Stellenausschreibungen
Reference no. 602/8
Mittelweg 177
20148 Hamburg

or via email: bewerbun...@verw.uni-hamburg.de

Please do not submit original documents as we are not able to return
them. Any documents submitted will be destroyed after the application
process has concluded.

This posting as PDF:
https://www.uni-hamburg.de/en/uhh/stellenangebote/technisches-und-verwaltungspersonal/29-08-19-tvp-602-8-engl.pdf



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[ccp4bb] Vacancy - Teaching Fellow in Structural Biology & Biochemistry, Portsmouth, UK

[John McGeehan]

Dear Colleagues,

We have a new 3 year Teaching Fellow / Senior Teaching Fellow position in
the School of Biological Sciences at the University of Portsmouth, UK.

In light of recent research success securing £5.8 million to create the Centre
for Enzyme Innovation
,
the School of Biological Sciences
 is seeking to
appoint a committed individual to a full time Teaching Fellow / Senior
Teaching Fellow in the area of structural biology and biochemistry on a
three year fixed term contract. The Department is based within the Faculty
of Science and holds strong teaching and research links. The Department
performed very well in the Research Excellence Framework (REF2014), is
ranked 3rd among the Alliance group in this subject area (UoA3) and
reported 90% of its research as being world leading or internationally
excellent. The department is well regarded as shown in league tables (3rd
in the Guardian league table) and has good student satisfaction in this
subject area. At an institutional level, we have recently been awarded Gold
standard in the Teaching Excellence Framework.

The successful candidate will contribute to the teaching in the area of
structural biology and biochemistry and also to the general teaching
activities and pastoral care at foundation, undergraduate and postgraduate
level. In addition to holding a PhD and having published in relevant
peer-review journals, it is essential that the appointee is able to
demonstrate experience of teaching in the broad area of biochemistry and
structural biology.


Teaching Fellow: *£35,211 - £38,460 per annum *
Senior Teaching Fellow: *£39,609 - £48,677 per annum  *
Closing date: * 17 July 2019 *
Interview date:  *25 July 2019*

For detailed information about the vacancy, please select this link: ZZ005416
- Teaching Fellow or Senior Teaching Fellow in Structural Biology and
Biochemistry.docx

or contact Dr Darren Mernagh (Head of Department) via
email:darren.mern...@port.ac.uk

Applications can be made on our recruitment website

.

Best Regards,
John
-- 
*Professor John McGeehan*
--
Director, Centre for Enzyme Innovation (web
),
Institute of Biological and Biomedical Sciences (web
),
School of Biological Sciences,
University of Portsmouth,
King Henry Building,
PO1 2DY, UK
--
Email: john.mcgee...@port.ac.uk
Tel:+44 (0) 2392 842042
*PA: Jacky Dillon *
Email: jacky.dil...@port.ac.uk
Tel: +44 (0) 23 92842023

- *An interview with the BBSRC, 2019*  -



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Re: [ccp4bb] resolution

[Robbie Joosten]

Another reason to cut the data (temporarily!) is to avoid discussion later when 
you try to publish your model. You need to be able to defend your high 
resolution cut-off against the R-merge zealots. The paired refinement test to 
find a good resolution cut-off works well for that. It is based on model 
refinement and works best when your model is already quite good. Also, the test 
can only be unbiased if you haven't yet used your high-resolution data. 

Whatever the outcome of your resolution cut-off choice, please deposit all 
recorded reflections!

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Alexandre Ourjoumtsev
> Sent: Friday, July 05, 2019 09:40
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] resolution
> 
> Dear Graeme,
> 
> 
> Right, but you are talking about weights that reflect the data quality and say
> nothing about that of the starting model ; however refinement is a
> comparison of a model with data.
> 
> 
> The higher resolution of the data, the more sensitive they to model
> imperfections.
> 
> Refinement targets are sums over reflections, and each refinement term is a
> function with multiple minima; the higher the resoluion, the more frequent
> these minima.
> 
> 
> If the starting model is too far from the answer, a presence of high-
> resolution data prevents the refinement from moving the model as far as
> necessary; it is trapped by multiple local minima of the crystallographic
> functions that include such high-resolution terms. Removing such terms
> removes or at least attenuate the intermediate local minima and improves
> the convergence. One does not care about the statistices but about
> convergence ("the model stops improving" further than with these data).
> Increaing the resolution step-by-step was the standard refinement strategy
> till the end of 90ths.
> 
> Right, using ML-based targets introduced weights based on comparison of
> Fmodel with Fobs and allowed to do such attenuation in a "soft way". This
> was great and indeed replaced the "before-ML refinement strategy".
> However, such an artificial cut-off of highest-resolution data (temporary, at
> early refinement stages) can be useful in some situations even now and can
> improve convergence even with the modern tools. First cycles of a rigid-body
> refinement can be an example.
> 
> 
> Another reason for a (temporary) removing of higher-resolution data is a
> heavy (systematic) incompleteness of data in the higher-resolution shells.
> 
> 
> 
> With best regards,
> 
> 
> Sacha
> 
> 
> - Le 5 Juil 19, à 8:05, graeme.win...@diamond.ac.uk
>  a écrit :
> 
> 
>   Pavel,
> 
>   Please correct if wrong, but I thought most refinement programs
> used the weights e.g. sig(I/F) with I/F so would not really have a hard cut 
> off
> anyway? You’re just making the stats worse but the model should stay ~ the
> same (unless you have outliers in there)
> 
>   Clearly there will be a point where the model stops improving, which
> is the “true” limit…
> 
>   Cheers Graeme
> 
> 
> 
>   On 5 Jul 2019, at 06:49, Pavel Afonine
> mailto:pafon...@gmail.com>> wrote:
> 
>   Hi Sam Tang,
> 
>   Sorry for a naive question. Is there any circumstances where one
> may wish to refine to a lower resolution? For example if one has a dataset
> processed to 2 A, is there any good reasons for he/she to refine to only, say
> 2.5 A?
> 
>   yes, certainly. For example, when information content in the data
> can justify it.. Randy Read can comment on this more! Also instead of a hard
> cutoff using a smooth weight based attenuation may be even better. AFAIK,
> no refinement program can do this smartly currently.
>   Pavel
> 
>   
> 
>   To unsubscribe from the CCP4BB list, click the following link:
>   https://www.jiscmail.ac.uk/cgi-
> bin/webadmin?SUBED1=CCP4BB=1
> 
> 
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>   

Re: [ccp4bb] resolution

[Alexandre Ourjoumtsev]

Dear Graeme, 

Right, but you are talking about weights that reflect the data quality and say 
nothing about that of the starting model ; however refinement is a comparison 
of a model with data. 

The higher resolution of the data, the more sensitive they to model 
imperfections. 
Refinement targets are sums over reflections, and each refinement term is a 
function with multiple minima; the higher the resoluion, the more frequent 
these minima. 

If the starting model is too far from the answer, a presence of high-resolution 
data prevents the refinement from moving the model as far as necessary; it is 
trapped by multiple local minima of the crystallographic functions that include 
such high-resolution terms. Removing such terms removes or at least attenuate 
the intermediate local minima and improves the convergence. One does not care 
about the statistices but about convergence (" the model stops improving" 
further than with these data). Increaing the resolution step-by-step was the 
standard refinement strategy till the end of 90ths. 

Right, using ML-based targets introduced weights based on comparison of Fmodel 
with Fobs and allowed to do such attenuation in a "soft way". This was great 
and indeed replaced the "before-ML refinement strategy". However, such an 
artificial cut-off of highest-resolution data (temporary, at early refinement 
stages) can be useful in some situations even now and can improve convergence 
even with the modern tools. First cycles of a rigid-body refinement can be an 
example. 

Another reason for a (temporary) removing of higher-resolution data is a heavy 
(systematic) incompleteness of data in the higher-resolution shells. 

With best regards, 

Sacha 

- Le 5 Juil 19, à 8:05, graeme.win...@diamond.ac.uk 
 a écrit : 

> Pavel,

> Please correct if wrong, but I thought most refinement programs used the 
> weights
> e.g. sig(I/F) with I/F so would not really have a hard cut off anyway? You’re
> just making the stats worse but the model should stay ~ the same (unless you
> have outliers in there)

> Clearly there will be a point where the model stops improving, which is the
> “true” limit…

> Cheers Graeme

> On 5 Jul 2019, at 06:49, Pavel Afonine
> mailto:pafon...@gmail.com>> wrote:

> Hi Sam Tang,

> Sorry for a naive question. Is there any circumstances where one may wish to
> refine to a lower resolution? For example if one has a dataset processed to 2
> A, is there any good reasons for he/she to refine to only, say 2.5 A?

> yes, certainly. For example, when information content in the data can justify
> it.. Randy Read can comment on this more! Also instead of a hard cutoff using 
> a
> smooth weight based attenuation may be even better. AFAIK, no refinement
> program can do this smartly currently.
> Pavel

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Re: [ccp4bb] resolution

[graeme.win...@diamond.ac.uk]

Pavel,

Please correct if wrong, but I thought most refinement programs used the 
weights e.g. sig(I/F) with I/F so would not really have a hard cut off anyway? 
You’re just making the stats worse but the model should stay ~ the same (unless 
you have outliers in there)

Clearly there will be a point where the model stops improving, which is the 
“true” limit…

Cheers Graeme



On 5 Jul 2019, at 06:49, Pavel Afonine 
mailto:pafon...@gmail.com>> wrote:

Hi Sam Tang,

Sorry for a naive question. Is there any circumstances where one may wish to 
refine to a lower resolution? For example if one has a dataset processed to 2 
A, is there any good reasons for he/she to refine to only, say 2.5 A?

yes, certainly. For example, when information content in the data can justify 
it.. Randy Read can comment on this more! Also instead of a hard cutoff using a 
smooth weight based attenuation may be even better. AFAIK, no refinement 
program can do this smartly currently.
Pavel



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