Re: [ccp4bb] Iphone app to display protein models

[Francois Berenger]

On 01/27/2012 04:00 PM, Shiva Bhowmik wrote:

Dear All,

I was wondering if there is any IOS5 based app to display protein
models, which are not in public database, on Iphone.


Better than this: Jolecule from Dr. Bosco Ho.

"Jolecule works in HTML5 browsers such as Chrome and Safari, mostly in 
Firefox, and even on the iPad"


http://jolecule.appspot.com/

However, if you intend to keep your PDB secret, I'm not sure
it is wise to use any webservice.

Regards,
Francois.


There is an app
called Molecules for displaying models but that utilizes coordinates
from RCSB and pubchem.

Thanks,

Shiva

[ccp4bb] Iphone app to display protein models

[Shiva Bhowmik]

Dear All,

I was wondering if there is any IOS5 based app to display protein models,
which are not in public database, on Iphone. There is an app called
Molecules for displaying models but that utilizes coordinates from RCSB and
pubchem.

Thanks,

Shiva

Re: [ccp4bb] Coot on an SGI

[William G. Scott]

Dear Gina:

I think Coot 0.0.33 originated sometime early in the Nixon administration, and 
I finally parted with my SGIs a few years ago, so am not in a good position to 
advise.  I seem vaguely to remember some non-canonical naming of the files.  
What happens if you make a symbolic link from the one you have to the one that 
is required?

As I recall, coot on an SGI (at least on my R1, which I think has a 
processor almost as fast as that in my generation A iPod touch) was impossibly 
slow.  By contrast, I can run the very latest svn revision of coot in stereo on 
a $270 Zalman monitor attached to a $600 mac mini.

I'm sorry this doesn't answer your question, but I think an ancient version of 
coot on an ancient computer will just be a world of hurt.

-- Bill

William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
 

On Jan 26, 2012, at 8:59 AM, Clayton, Gina wrote:

> Hi there
> 
> we are trying to install Coot onto one of our old SGIs and so we installed 
> Coot 0.0.33 (IRIX). However when starting Coot,  such as in the Coot 
> (install) directory,  we get an error message stating thatlib "libgcc_s.so is 
> required but can not be found. We have the sgi freeware gcc_lib installed 
> (the link on the Coot page to sgi.freeware, is dead ) but can only find 
> libgcc_a in our gcc_lib. 
> 
> Can someone tell us how we can get hold of the right library?
> 
> Thanks so much for any help
> Gina 
> 
> 
> NOTICE: This email message is for the sole use of the intended recipient(s) 
> and may contain confidential and privileged information. Any unauthorized 
> review, use, disclosure or distribution is prohibited. If you are not the 
> intended recipient, please contact the sender by reply email and destroy all 
> copies of the original message.

[ccp4bb] CCP4 win dev

[Bernhard Rupp (Hofkristallrat a.D.)]

Dear ccp4 win developers: I would like to compile Ian's EDSTAT program using
my windows7/64 ifort compiler. I have a few questions re library linking and
win-compliable source distribution -  wonder who I may kindly harass
off-board.

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
b...@hofkristallamt.org
http://www.ruppweb.org/
-
No animals were hurt or killed during the 
production of this email.
-

[ccp4bb] Job Posting on Behalf of Albert Einstein College of Medicine

[Meghan jobtarget]

*POST-DOCTORAL POSITION*



Three post-doctoral positions are available to join a multi-disciplinary
research group investigating the regulation of biological motors activity
from the cellular to the molecular level. The group is formed by the
laboratories of Gary Gerfen, Ao Ma, David Sharp and Hernando Sosa in the
Department of Physiology and Biophysics of the Albert Einstein College of
Medicine.  For these positions the ideal candidates would have experience
in the general areas of cell biology, structural biology, molecular
simulation and statistical mechanics. Expertise with one or more of the
following techniques will be required: protein expression and purification,
cell imaging, electron paramagnetic resonance (EPR), electron microscopy
and molecular dynamics simulations.



For this project we have state of the art facilities present in each of the
participating laboratories and at the core facilities of the Albert College
of Medicine. These capabilities include EPR (PELDOR, high frequency,
HYSCORE), several modalities of fluorescence microscopy (con-focal, epi,
tirf, single-molecule polarization etc), cryo-electron microscopy and
state-of-the-art Linux clusters for molecular simulations. All four
laboratories in the group are located in the Albert Einstein College of
Medicine in New York City, which offers excellent opportunities for
stimulating and highly inter-disciplinary scientific interactions within
the group, between theory/simulation and experiments, with the rest of the
college and with many other scientific institutions in the New York
area.  Interested
candidates please send an email letter, CV and reference names to either:
Gary Gerfen (gary.ger...@einstein.yu.edu), Ao Ma (ao...@einstein.yu.edu),
David Sharp (david.sh...@einstein.yu.edu), Hernando Sosa (
hernando.s...@einstein.yu.edu
).



Yeshiva University is an equal opportunity employer committed to workforce
diversity.

Re: [ccp4bb] Problem with getting Rfree and Rf down

[James Holton]

Merging in radiation damaged data can indeed raise R/Rfree because the 
structure factors no longer correspond to the native structure.  Rather, 
they are an intensity-average of the native and damaged structures, and 
that can be hard to fit to a coordinate model!   How much damage is too 
much?  I'd say its when the change in the data or "error due to damage" 
becomes comparable with the lowest error you could hope to get when 
fitting a model to the native data: ~20-30% (R/Rfree).  This generally 
happens after about 20-30 MGy (Banumathi et al. 2006; Owen et al, 2006; 
Kmetko et al. 2006).


However, "redundancy" and "radiation damage" are not the same thing.  
Contrary to popular belief, it IS possible to take many many exposures 
from the same crystal without doing any more damage than the usual ~100 
exposures.  How?  What manner of trickery is this?  Simple!  You use a 
shorter exposure time.


Personally, I always think about "redundancy" or "multiplicity" in the 
context of a fixed crystal "lifedose" 
(http://dx.doi.org/10.1107/S0909049509004361).  That is, you only get so 
many seconds of shutter-open time before the crystal is dead.  So, to 
me, "strategy" is nothing more than deciding how to divide up those 
shutter-open seconds, and the only way to increase 
redundancy/multiplicity is to shorten the exposure time.  Which, by the 
way, is almost always a good idea.


-James Holton
MAD Scientist

On 1/24/2012 11:52 AM, Miguel Ortiz Lombardia wrote:

El 24/01/12 18:56, Greg Costakes escribió:

Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.


But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded. This is not at all unusual. In
the absence of a deep understanding of refinement, intuition suggests
that degraded data should produce degraded models. If Rwork and Rfree
are measuring anything useful they should go up redundancy in those
not-so-unusual cases. Or intuition is misguiding me again.


-- Miguel


---
Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907


** Hard work often pays of in time, but Procrastination always pays off
now **


*From: *"Dale Tronrud"
*To: *"Greg Costakes"
*Cc: *CCP4BB@JISCMAIL.AC.UK
*Sent: *Tuesday, January 24, 2012 12:43:43 PM
*Subject: *Re: [ccp4bb] Problem with getting Rfree and Rf down


Is this observation about redundancies a general rule that I missed?
It seems rather surprising to me.  What have results have others seen?

Dale Tronrud

On 01/24/12 07:23, Greg Costakes wrote:

snip...
Higher redundancies (>7 or so) do tend to increase overall R/Rfree.
snip...


---

Greg Costakes
PhD Candidate
Department of Structural Biology
Purdue University
Hockmeyer Hall, Room 320
240 S. Martin Jischke Drive, West Lafayette, IN 47907





** Hard work often pays of in time, but Procrastination always pays off
now **


*From: *"Sam Arnosti"
*To: *CCP4BB@JISCMAIL.AC.UK
*Sent: *Monday, January 23, 2012 4:48:50 PM
*Subject: *[ccp4bb] Problem with getting Rfree and Rf down

Hi every one

I have some crystals in the space group P3121. I collect 180 frames of

data.

My crystals do not diffract better than at most 2.0 angstrom, but the Rf
barely goes below 23%,

and Rfree also remains somewhere between 28-33%. I have tried to refine
my data as much as I can.

I do not know whether the problem is because of the bad diffraction or
collecting extra frames.

The structure factors are also high but they get better as the crystals
diffract better.

Thanks

Sam

Re: [ccp4bb] Introducing an ELN

[Jacob Keller]

Can't you get a plug-in for that?

JPK

On Thu, Jan 26, 2012 at 11:35 AM, Dale Tronrud
 wrote:
>   Unless you have written on the paper using cursive script.  Many schools
> in the US have stopped teaching longhand reading/writing so in a generation
> or two many paper records will be undecipherable to all but historians.  My
> wife has some handwritten letters from ancestors written in German around
> 1920 that even Germans have great trouble reading today.
>
>   The paper is holding up quite well though.  ;-)
>
> Dale Tronrud
>
> On 01/26/12 08:30, Phoebe Rice wrote:
>> As the proud owner of a carefully organized, highly annotated VMS backup 
>> tape (reel-to-reel, of course), my main concern is that paper is the only 
>> format that we'll be able to count on reading a decade (or more) from now.
>>
>> =
>> Phoebe A. Rice
>> Dept. of Biochemistry & Molecular Biology
>> The University of Chicago
>> phone 773 834 1723
>> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
>> http://www.rsc.org/shop/books/2008/9780854042722.asp
>>
>>
>>  Original message 
>>> Date: Thu, 26 Jan 2012 16:50:04 +0100
>>> From: CCP4 bulletin board  (on behalf of Anastassis 
>>> Perrakis )
>>> Subject: Re: [ccp4bb] Introducing an ELN
>>> To: CCP4BB@JISCMAIL.AC.UK
>>>
>>>   I think that all these points are interesting and
>>>   valid.
>>>   On Jan 25, 2012, at 10:37, Chris Morris wrote:
>>>
>>>     Tassos reports:
>>>
>>>       1. None of the twenty test-users was satisfied
>>>       with any of the two
>>>
>>>       solutions - and each was annoyed for a different
>>>       reason.
>>>
>>>     This suggests that the choice of ELN is not the
>>>     most difficult part of the adoption process. Maybe
>>>     the test users at the NKI were annoyed by the idea
>>>     of using an ELN at all.
>>>
>>>   That would surely apply to some users. Some were
>>>   actually very keen, and thats why they signed up for
>>>   it.
>>>
>>>     In my experience, the hardest part is ensuring
>>>     that it provides benefits to the people who have
>>>     to enter the data, and provides them early. The
>>>     fact that it will make information retrieval
>>>     easier in three years is not enough.
>>>
>>>     I suggest focussing on electronic support for
>>>     housekeeping: booking time on an instrument,
>>>     finding the files the instrument created, ordering
>>>     oligos, recording when you use the last of a
>>>     reagent. Scientists work very independently in
>>>     most respects, but they do have certain
>>>     obligations that flow from sharing the lab space.
>>>     You can make use of these to encourage compliance
>>>     with the ELN. If you do, then most of the science
>>>     will get recorded in passing.
>>>
>>>   I think that this was exactly one of the problems.
>>>   The ELNs we tested had no option for booking
>>>   instruments, no way to find files from instruments
>>>   let alone read them (it would support only TIF,
>>>   JPEG, Doc, XLS, PDF), and would not do stock
>>>   keeping: all these are thought to be out of the ELN
>>>   scope. And that makes an ELN inherently less useful.
>>>   Lack of instrument support is another issue: a
>>>   machine that would allow us to import real
>>>   chromatograms to ELN would be cool - alas, the
>>>   solution that was suggested to us is to save as PDF
>>>   or XLS and reload ...! (it took 3 weeks to come back
>>>   with this great plan!)
>>>   For the rest I have nothing much to say, I basically
>>>   agree.
>>>   A.
>>>
>>>     I suggest also ensuring that it includes
>>>     electronic tools that actually help. Two examples
>>>     from PiMS are primer design, and automatically
>>>     uploading and interpreting results from the
>>>     Caliper GX instrument.
>>>
>>>     It must allow round trips with spreadsheets, i.e.
>>>     dump ELN data as a spreadsheet, edit it, upload it
>>>     again. Despite their substantial disadvantages,
>>>     some scientists will not give them up. It should
>>>     also allow crossreferencing with paper note books.
>>>     Some will continue to use a lab notebook. When
>>>     they discover that the ELN serves as a searchable
>>>     index to it, they will warm to the ELN.
>>>
>>>     I suggest aiming for "no paper" at your lab
>>>     progress meetings within say 12 months. When you
>>>     reach that point, everything important is in the
>>>     ELN. Before then, the ELN is not giving real
>>>     value.
>>>
>>>     You will need someone who is keen on the
>>>     introduction of the ELN, to customise it, provide
>>>     first line user support, and act as a single point
>>>     of contact with the supplier. This might be a
>>>     scientist or an IT person. I have also seen this
>>>     done well by a technician, Delphine Chesnel when
>>>     she was at the EMBL Hamburg. If you can't find
>>>     such a "champion", then introduction will not be
>>>    

Re: [ccp4bb] Introducing an ELN

[Dale Tronrud]

   Unless you have written on the paper using cursive script.  Many schools
in the US have stopped teaching longhand reading/writing so in a generation
or two many paper records will be undecipherable to all but historians.  My
wife has some handwritten letters from ancestors written in German around
1920 that even Germans have great trouble reading today.

   The paper is holding up quite well though.  ;-)

Dale Tronrud

On 01/26/12 08:30, Phoebe Rice wrote:
> As the proud owner of a carefully organized, highly annotated VMS backup tape 
> (reel-to-reel, of course), my main concern is that paper is the only format 
> that we'll be able to count on reading a decade (or more) from now.
> 
> =
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> phone 773 834 1723
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
> http://www.rsc.org/shop/books/2008/9780854042722.asp
> 
> 
>  Original message 
>> Date: Thu, 26 Jan 2012 16:50:04 +0100
>> From: CCP4 bulletin board  (on behalf of Anastassis 
>> Perrakis )
>> Subject: Re: [ccp4bb] Introducing an ELN  
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>>   I think that all these points are interesting and
>>   valid. 
>>   On Jan 25, 2012, at 10:37, Chris Morris wrote:
>>
>> Tassos reports:
>>
>>   1. None of the twenty test-users was satisfied
>>   with any of the two
>>
>>   solutions - and each was annoyed for a different
>>   reason.
>>
>> This suggests that the choice of ELN is not the
>> most difficult part of the adoption process. Maybe
>> the test users at the NKI were annoyed by the idea
>> of using an ELN at all.
>>
>>   That would surely apply to some users. Some were
>>   actually very keen, and thats why they signed up for
>>   it. 
>>
>> In my experience, the hardest part is ensuring
>> that it provides benefits to the people who have
>> to enter the data, and provides them early. The
>> fact that it will make information retrieval
>> easier in three years is not enough.
>>
>> I suggest focussing on electronic support for
>> housekeeping: booking time on an instrument,
>> finding the files the instrument created, ordering
>> oligos, recording when you use the last of a
>> reagent. Scientists work very independently in
>> most respects, but they do have certain
>> obligations that flow from sharing the lab space.
>> You can make use of these to encourage compliance
>> with the ELN. If you do, then most of the science
>> will get recorded in passing.
>>
>>   I think that this was exactly one of the problems.
>>   The ELNs we tested had no option for booking
>>   instruments, no way to find files from instruments
>>   let alone read them (it would support only TIF,
>>   JPEG, Doc, XLS, PDF), and would not do stock
>>   keeping: all these are thought to be out of the ELN
>>   scope. And that makes an ELN inherently less useful.
>>   Lack of instrument support is another issue: a
>>   machine that would allow us to import real
>>   chromatograms to ELN would be cool - alas, the
>>   solution that was suggested to us is to save as PDF
>>   or XLS and reload ...! (it took 3 weeks to come back
>>   with this great plan!)
>>   For the rest I have nothing much to say, I basically
>>   agree.
>>   A.
>>
>> I suggest also ensuring that it includes
>> electronic tools that actually help. Two examples
>> from PiMS are primer design, and automatically
>> uploading and interpreting results from the
>> Caliper GX instrument.
>>
>> It must allow round trips with spreadsheets, i.e.
>> dump ELN data as a spreadsheet, edit it, upload it
>> again. Despite their substantial disadvantages,
>> some scientists will not give them up. It should
>> also allow crossreferencing with paper note books.
>> Some will continue to use a lab notebook. When
>> they discover that the ELN serves as a searchable
>> index to it, they will warm to the ELN.
>>
>> I suggest aiming for "no paper" at your lab
>> progress meetings within say 12 months. When you
>> reach that point, everything important is in the
>> ELN. Before then, the ELN is not giving real
>> value.
>>
>> You will need someone who is keen on the
>> introduction of the ELN, to customise it, provide
>> first line user support, and act as a single point
>> of contact with the supplier. This might be a
>> scientist or an IT person. I have also seen this
>> done well by a technician, Delphine Chesnel when
>> she was at the EMBL Hamburg. If you can't find
>> such a "champion", then introduction will not be
>> successful.
>>
>> Some of the problem here is an "own goal" by the
>> community: scientists are trained to use paper
>> during their degrees, so ELNs are a controversial
>> change of practice. 

[ccp4bb] Coot on an SGI

[Clayton, Gina]

Hi there

we are trying to install Coot onto one of our old SGIs and so we installed Coot 
0.0.33 (IRIX). However when starting Coot,  such as in the Coot (install) 
directory,  we get an error message stating thatlib "libgcc_s.so is required 
but can not be found. We have the sgi freeware gcc_lib installed (the link on 
the Coot page to sgi.freeware, is dead ) but can only find libgcc_a in our 
gcc_lib. 

Can someone tell us how we can get hold of the right library?

Thanks so much for any help
Gina 


NOTICE: This email message is for the sole use of the intended recipient(s) and 
may contain confidential and privileged information. Any unauthorized review, 
use, disclosure or distribution is prohibited. If you are not the intended 
recipient, please contact the sender by reply email and destroy all copies of 
the original message.

Re: [ccp4bb] No diffraction

[Kevin Jin]

Maybe, you can adjust the ion strength of your condition.




On Thu, Jan 26, 2012 at 8:32 AM, Kevin Jin  wrote:
> For crystallization:
>
> Your xtal may come out a little bit fast. If the condition contain
> alcohol,  such as IPA, you may have to modify it.
>
> If you let people know the condition, it may be more helpful.
>
> Also, please check the purity of your protein.
>
> Kevin
>
> On Thu, Jan 26, 2012 at 7:33 AM, Theresa H. Hsu  wrote:
>> Dear crystallographers
>>
>> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch 
>> and vapor diffusion method in 24 hours but no diffraction at home source. 
>> Dissolved crystals was confirmed to be the protein with mass spec.
>>
>> Any suggestions to improve diffraction would be welcome.
>>
>> Thanking you in advance.
>>
>> Theresa

Re: [ccp4bb] No diffraction

[Kevin Jin]

For crystallization:

Your xtal may come out a little bit fast. If the condition contain
alcohol,  such as IPA, you may have to modify it.

If you let people know the condition, it may be more helpful.

Also, please check the purity of your protein.

Kevin

On Thu, Jan 26, 2012 at 7:33 AM, Theresa H. Hsu  wrote:
> Dear crystallographers
>
> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch 
> and vapor diffusion method in 24 hours but no diffraction at home source. 
> Dissolved crystals was confirmed to be the protein with mass spec.
>
> Any suggestions to improve diffraction would be welcome.
>
> Thanking you in advance.
>
> Theresa

Re: [ccp4bb] Introducing an ELN

[Phoebe Rice]

As the proud owner of a carefully organized, highly annotated VMS backup tape 
(reel-to-reel, of course), my main concern is that paper is the only format 
that we'll be able to count on reading a decade (or more) from now.

=
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp


 Original message 
>Date: Thu, 26 Jan 2012 16:50:04 +0100
>From: CCP4 bulletin board  (on behalf of Anastassis 
>Perrakis )
>Subject: Re: [ccp4bb] Introducing an ELN  
>To: CCP4BB@JISCMAIL.AC.UK
>
>   I think that all these points are interesting and
>   valid. 
>   On Jan 25, 2012, at 10:37, Chris Morris wrote:
>
> Tassos reports:
>
>   1. None of the twenty test-users was satisfied
>   with any of the two
>
>   solutions - and each was annoyed for a different
>   reason.
>
> This suggests that the choice of ELN is not the
> most difficult part of the adoption process. Maybe
> the test users at the NKI were annoyed by the idea
> of using an ELN at all.
>
>   That would surely apply to some users. Some were
>   actually very keen, and thats why they signed up for
>   it. 
>
> In my experience, the hardest part is ensuring
> that it provides benefits to the people who have
> to enter the data, and provides them early. The
> fact that it will make information retrieval
> easier in three years is not enough.
>
> I suggest focussing on electronic support for
> housekeeping: booking time on an instrument,
> finding the files the instrument created, ordering
> oligos, recording when you use the last of a
> reagent. Scientists work very independently in
> most respects, but they do have certain
> obligations that flow from sharing the lab space.
> You can make use of these to encourage compliance
> with the ELN. If you do, then most of the science
> will get recorded in passing.
>
>   I think that this was exactly one of the problems.
>   The ELNs we tested had no option for booking
>   instruments, no way to find files from instruments
>   let alone read them (it would support only TIF,
>   JPEG, Doc, XLS, PDF), and would not do stock
>   keeping: all these are thought to be out of the ELN
>   scope. And that makes an ELN inherently less useful.
>   Lack of instrument support is another issue: a
>   machine that would allow us to import real
>   chromatograms to ELN would be cool - alas, the
>   solution that was suggested to us is to save as PDF
>   or XLS and reload ...! (it took 3 weeks to come back
>   with this great plan!)
>   For the rest I have nothing much to say, I basically
>   agree.
>   A.
>
> I suggest also ensuring that it includes
> electronic tools that actually help. Two examples
> from PiMS are primer design, and automatically
> uploading and interpreting results from the
> Caliper GX instrument.
>
> It must allow round trips with spreadsheets, i.e.
> dump ELN data as a spreadsheet, edit it, upload it
> again. Despite their substantial disadvantages,
> some scientists will not give them up. It should
> also allow crossreferencing with paper note books.
> Some will continue to use a lab notebook. When
> they discover that the ELN serves as a searchable
> index to it, they will warm to the ELN.
>
> I suggest aiming for "no paper" at your lab
> progress meetings within say 12 months. When you
> reach that point, everything important is in the
> ELN. Before then, the ELN is not giving real
> value.
>
> You will need someone who is keen on the
> introduction of the ELN, to customise it, provide
> first line user support, and act as a single point
> of contact with the supplier. This might be a
> scientist or an IT person. I have also seen this
> done well by a technician, Delphine Chesnel when
> she was at the EMBL Hamburg. If you can't find
> such a "champion", then introduction will not be
> successful.
>
> Some of the problem here is an "own goal" by the
> community: scientists are trained to use paper
> during their degrees, so ELNs are a controversial
> change of practice. One person who, unusually,
> began with an ELN told me how inconvenient it is
> now she works in a paper-based lab.
>
> PepTalk 2012 had a workshop on this topic. The
> recording and notes are here:
>
> http://www.structuralbiology.eu/support/forums/networks/pims/why-dont-scientists-use-limselns
>
> regards,
> Chris
> 
> Chris Morris  
> chris.mor...@stfc.ac.uk   
> Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
> Mobile: 07921-717915
> Skype: chrishgmorris
> http://pims.structuralb

Re: [ccp4bb] No diffraction

[Patrick Shaw Stewart]

Theresa

You should also try microseeding into *random screens *by making a seed
stock with the crystals that you have, to use with both microbatch and
vapor diffusion experiments.  You will often pick up new and better
conditions and you're more likely to get well-formed crystals right out of
the screens.

I hope it works

Patrick

_

Refs: Allan D’Arcy, Frederic Villarda, May Marsh. An automated microseed
matrix-screening method for protein crystallization.  Acta
Crystallographica section D 63 (2007), 550–554.

Galina Obmolova,* Thomas J. Malia, Alexey Teplyakov, Raymond Sweet and Gary
L. Gilliland. 'Promoting crystallization of antibody–antigen complexes via
microseed matrix screening.' Acta Crystallographica Section D 66 (2010)
927–933.  Open-access at
http://journals.iucr.org/d/issues/2010/08/00/bw5361/bw5361.pdf

A. G. Villaseñor, A. Wong, A. Shao, A. Garg, A. Kuglstatter and S. F.
Harris. 'Acoustic matrix microseeding: improving protein crystal growth
with minimal chemical bias.' Acta Crystallographica Section D 66 (2010)
568-576.

Gregory Ireton and Barry Stoddard.  'Microseed matrix screening to improve
crystals of yeast cytosine deaminase'.  Acta Crystallographica section D60
(2004) 601–605.

Patrick D. Shaw Stewart, Stefan A. Kolek, Richard A. Briggs, Naomi E.
Chayen and Peter F.M. Baldock. 'Random Microseeding: A Theoretical and
Practical Exploration of Seed Stability and Seeding Techniques for
Successful Protein Crystallization'. Cryst. Growth Des., 2011, 11 (8), pp
3432–3441. On-line at http://pubs.acs.org/doi/abs/10.1021/cg2001442.  * If
you don't have a subscription to Crystal Growth and Design, click
**here*
* to obtain a free copy (we're limited to 50 downloads in the first year).*



On 26 January 2012 15:33, Theresa H. Hsu  wrote:

> Dear crystallographers
>
> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch
> and vapor diffusion method in 24 hours but no diffraction at home source.
> Dissolved crystals was confirmed to be the protein with mass spec.
>
> Any suggestions to improve diffraction would be welcome.
>
> Thanking you in advance.
>
> Theresa
>



-- 
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
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Re: [ccp4bb] No diffraction

[Roger Rowlett]

  
  
As other have/surely will suggest, by all means
  try RT collection to establish if your crystals really diffract
  OK, or if your cryo conditions are killing them. We have lots of
  experience in our lab getting "beamstop" diffraction with certain
  samples when subjected to cryoprotection. Depending on the
intensity of your home source (and its life-cycle age), small
crystals may not be large enough to produce usable or visible
diffraction. With our home source, we really need 0.3 mm crystals
(larger if thin plates) to get usable diffraction.

Cheers,

___
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu

On 1/26/2012 10:33 AM, Theresa H. Hsu wrote:

  Dear crystallographers

I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and vapor diffusion method in 24 hours but no diffraction at home source. Dissolved crystals was confirmed to be the protein with mass spec.

Any suggestions to improve diffraction would be welcome.

Thanking you in advance.

Theresa


  

Re: [ccp4bb] No diffraction

[George Sheldrick]

It depends a lot on which home source and which synchrotron, there are 
enormous differences. Goettingen is uniquely well placed because we can 
reach four synchrotrons in a few (3-7) hours by high speed train and in 
theory at least five more with a longer train journey, trains are very 
convenient for transporting crystals. Two of these synchrotrons do not 
give a higher resolution than our home system, but at least they can 
vary the wavelength. However if we think we can see at least two 
reflections at home, of course we take the crystal to a (suitable) 
synchrotron.


George

On 01/26/2012 04:54 PM, Francis E Reyes wrote:

Ditto to Poul's advice.

I've had many many many cases where crystals diffract poorly (or not at all) on 
home sources only to show excellent diffraction at a synchrotron. (Whether or 
not a home source is properly calibrated is probably the biggest issue, but 
that's for another discussion).



On Jan 26, 2012, at 8:33 AM, Theresa H. Hsu wrote:


Dear crystallographers

I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and 
vapor diffusion method in 24 hours but no diffraction at home source. Dissolved 
crystals was confirmed to be the protein with mass spec.

Any suggestions to improve diffraction would be welcome.

Thanking you in advance.

Theresa



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] No diffraction

[Francis E Reyes]

Ditto to Poul's advice. 

I've had many many many cases where crystals diffract poorly (or not at all) on 
home sources only to show excellent diffraction at a synchrotron. (Whether or 
not a home source is properly calibrated is probably the biggest issue, but 
that's for another discussion). 



On Jan 26, 2012, at 8:33 AM, Theresa H. Hsu wrote:

> Dear crystallographers
> 
> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch 
> and vapor diffusion method in 24 hours but no diffraction at home source. 
> Dissolved crystals was confirmed to be the protein with mass spec.
> 
> Any suggestions to improve diffraction would be welcome.
> 
> Thanking you in advance.
> 
> Theresa



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] No diffraction

[Edward Snell]

And ambient if you were using cryo ...

Edward Snell Ph.D.
Assistant Prof. Department of Structural Biology, SUNY Buffalo,
Senior Scientist, Hauptman-Woodward Medical Research Institute
700 Ellicott Street, Buffalo, NY 14203-1102
Phone: (716) 898 8631 Fax: (716) 898 8660
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz

Heisenberg was probably here!

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Poul 
Nissen
Sent: Thursday, January 26, 2012 10:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] No diffraction

But first of all: try to add a synchrotron to the crystals

Poul
On 26/01/2012, at 16.48, Katherine Sippel wrote:


Might I suggest consulting the CCP4 user community wiki on the topic:

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality

Good luck,

Katherine

On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu 
mailto:theresah...@live.com>> wrote:
Dear crystallographers

I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and 
vapor diffusion method in 24 hours but no diffraction at home source. Dissolved 
crystals was confirmed to be the protein with mass spec.

Any suggestions to improve diffraction would be welcome.

Thanking you in advance.

Theresa

Re: [ccp4bb] Introducing an ELN

[Anastassis Perrakis]

I think that all these points are interesting and valid.

On Jan 25, 2012, at 10:37, Chris Morris wrote:


Tassos reports:


1. None of the twenty test-users was satisfied with any of the two
solutions - and each was annoyed for a different reason.


This suggests that the choice of ELN is not the most difficult part  
of the adoption process. Maybe the test users at the NKI were  
annoyed by the idea of using an ELN at all.




That would surely apply to some users. Some were actually very keen,  
and thats why they signed up for it.


In my experience, the hardest part is ensuring that it provides  
benefits to the people who have to enter the data, and provides them  
early. The fact that it will make information retrieval easier in  
three years is not enough.


I suggest focussing on electronic support for housekeeping: booking  
time on an instrument, finding the files the instrument created,  
ordering oligos, recording when you use the last of a reagent.  
Scientists work very independently in most respects, but they do  
have certain obligations that flow from sharing the lab space. You  
can make use of these to encourage compliance with the ELN. If you  
do, then most of the science will get recorded in passing.


I think that this was exactly one of the problems. The ELNs we tested  
had no option for booking instruments, no way to find files from  
instruments let alone read them (it would support only TIF, JPEG, Doc,  
XLS, PDF), and would not do stock keeping: all these are thought to be  
out of the ELN scope. And that makes an ELN inherently less useful.


Lack of instrument support is another issue: a machine that would  
allow us to import real chromatograms to ELN would be cool - alas, the  
solution that was suggested to us is to save as PDF or XLS and  
reload ...! (it took 3 weeks to come back with this great plan!)


For the rest I have nothing much to say, I basically agree.


A.

I suggest also ensuring that it includes electronic tools that  
actually help. Two examples from PiMS are primer design, and  
automatically uploading and interpreting results from the Caliper GX  
instrument.


It must allow round trips with spreadsheets, i.e. dump ELN data as a  
spreadsheet, edit it, upload it again. Despite their substantial  
disadvantages, some scientists will not give them up. It should also  
allow crossreferencing with paper note books. Some will continue to  
use a lab notebook. When they discover that the ELN serves as a  
searchable index to it, they will warm to the ELN.


I suggest aiming for "no paper" at your lab progress meetings within  
say 12 months. When you reach that point, everything important is in  
the ELN. Before then, the ELN is not giving real value.


You will need someone who is keen on the introduction of the ELN, to  
customise it, provide first line user support, and act as a single  
point of contact with the supplier. This might be a scientist or an  
IT person. I have also seen this done well by a technician, Delphine  
Chesnel when she was at the EMBL Hamburg. If you can't find such a  
"champion", then introduction will not be successful.


Some of the problem here is an "own goal" by the community:  
scientists are trained to use paper during their degrees, so ELNs  
are a controversial change of practice. One person who, unusually,  
began with an ELN told me how inconvenient it is now she works in a  
paper-based lab.


PepTalk 2012 had a workshop on this topic. The recording and notes  
are here:

   
http://www.structuralbiology.eu/support/forums/networks/pims/why-dont-scientists-use-limselns

regards,
Chris

Chris Morris
chris.mor...@stfc.ac.uk
Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
Mobile: 07921-717915
Skype: chrishgmorris
http://pims.structuralbiology.eu/
http://www.citeulike.org/blog/chrishmorris
Daresbury Lab,  Daresbury,  Warrington,  UK,  WA4 4AD




P please don't print this e-mail unless you really need to
Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member
Department of Biochemistry (B8)
Netherlands Cancer Institute,
Dept. B8, 1066 CX Amsterdam, The Netherlands
Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791

Re: [ccp4bb] No diffraction

[Poul Nissen]

But first of all: try to add a synchrotron to the crystals

Poul
On 26/01/2012, at 16.48, Katherine Sippel wrote:

> Might I suggest consulting the CCP4 user community wiki on the topic: 
> 
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality
> 
> Good luck,
> 
> Katherine
> 
> 
> On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu  wrote:
> Dear crystallographers
> 
> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch 
> and vapor diffusion method in 24 hours but no diffraction at home source. 
> Dissolved crystals was confirmed to be the protein with mass spec.
> 
> Any suggestions to improve diffraction would be welcome.
> 
> Thanking you in advance.
> 
> Theresa
> 

Re: [ccp4bb] No diffraction

[Katherine Sippel]

Might I suggest consulting the CCP4 user community wiki on the topic:

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality

Good luck,

Katherine


On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu wrote:

> Dear crystallographers
>
> I have a protein of 90 kDa forming dimers. Crystals formed with microbatch
> and vapor diffusion method in 24 hours but no diffraction at home source.
> Dissolved crystals was confirmed to be the protein with mass spec.
>
> Any suggestions to improve diffraction would be welcome.
>
> Thanking you in advance.
>
> Theresa
>

[ccp4bb] No diffraction

[Theresa H. Hsu]

Dear crystallographers

I have a protein of 90 kDa forming dimers. Crystals formed with microbatch and 
vapor diffusion method in 24 hours but no diffraction at home source. Dissolved 
crystals was confirmed to be the protein with mass spec.

Any suggestions to improve diffraction would be welcome.

Thanking you in advance.

Theresa

Re: [ccp4bb] Problem with getting Rfree and Rf down

[Eleanor Dodson]

It is a bit of a mystery to me why two structures of supposedly similar 
resolution with equally acceptable maps can give very different r 
factors - one sticks in the low 20s and another gives a smug 17% ..


I guess one could go back and analyse the model against the data and time..
Eleanor

 On 01/25/2012 09:05 AM, Miguel Ortiz Lombardía wrote:

Le 24/01/12 21:18, Dale Tronrud a écrit :

On 01/24/12 11:52, Miguel Ortiz Lombardia wrote:

El 24/01/12 18:56, Greg Costakes escribió:

Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
redundancies.



But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded. This is not at all unusual. In
the absence of a deep understanding of refinement, intuition suggests
that degraded data should produce degraded models. If Rwork and Rfree
are measuring anything useful they should go up redundancy in those
not-so-unusual cases. Or intuition is misguiding me again.



Yes, if one has a poorer quality data set one expects the Rw and Rf to
be higher, but this is not necessarily a correlation to high redundancy.
Surely if you have high redundancy and know the crystal is decaying you
have to flexibility to not use the decayed data in the merge.  I would
expect that decayed data would only be merged with the early data if
the redundancy was so low that you had to just to get a full data set.

Dale Tronrud



I agree. I would also expect so... unless the user simply runs the data
reduction software and does not check the log files to see, among other
important issues, at what point the data starts degrading due to a
decaying crystal. If the software is clever enough to decide by itself,
it will be all right or sort of, which is, I suppose, a good point for
automation. Unfortunately, there are many users of black boxes, which
is, I presume, a danger of automation. My answer was kind of a caveat
for such type of users.