[ccp4bb] Maprot question.

[Niu Tou]

Dear Colleagues,

Does anybody know if the definition of rotation parameters in Maprot are
different from that of Coot? I used Coot to superimpose a model A to model
B, to get a new model A* and rotation parameters (Euler angles and
translations), howerver when I used these parameters to move the original
map with Maprot, the new map did not fit with model A*. I tried the 3x3
matrix and translations, it did not work either. I wonder if there is any
different from these two prgrams?

Thanks!
Niu

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Allan Pang]

If the information is out there and had been published, then I do not  
see the point why it cannot be used to get your story out. I assumed  
that you will cite their Acta F paper.


You might ended up waiting for a long time to get your structure out,  
so why wait? It also depends whose project is it. If it is a project  
of a PhD student (like me), getting it published as soon as possible  
(and even if it is a low impact) is important career stepping stone. I  
do agree though that contacting the (competing) authors of the Acta F  
is the best advised.


Also, not because you published your structure means the other group  
cannot published their structure.


Allan

Quoting "Lukacs, Christine" :


I'd like to get a community opinion on something.

If a group has published crystallization and diffraction data (Acta   
Cryst F style crystallization report), and you happen to have the   
same crystal form and have solved the structure, is there an   
unspoken rule that you don't publish, or an amount of time that you   
wait to allow the other group to publish before you do?  I am not   
talking about a high impact structure with a race to publish.


Just looking for a general consensus.

Thanks
Christine

Christine Lukacs, Ph.D.
Principal Scientist
Roche
christine.luk...@roche.com
This message is intended for the use of the named recipient(s) only   
and may contain confidential and/or proprietary information. If you   
are not the intended recipient, please contact the sender and delete  
 this message. Any unauthorized use of the information contained in   
this message is prohibited.







--
Allan Pang

PhD Student

G35 Joseph Priestley Building
Queen Mary University of London
London
E1 4NS

Phone number: 02078828480

Twitter: @xerophytes

Re: [ccp4bb] Direct crystallization of Lysozyme from eggs

[Jacob Keller]

Alhtough perhaps a little more macabre--maybe you could crystallize
hemoglobin or myoglobin from blood or muscle (meat?). I recollect some
story of whale myo- or hemo-globin crystallizing on the salty decks of a
whaling ship...

Jacob



On Tue, Sep 25, 2012 at 11:59 AM, David Smith  wrote:

> Dear crystallographers,
>
> I am working on an outreach program through the APS to get motivated high
> school students some/more research experience.  As I work at a
> crystallography beamline (LS-CAT), we are trying to get a
> crystallographically centered experiment in place that will be interesting
> to a high school student.  Among other ideas, I had mentioned to the
> teacher the possibility of crystallizing lysozyme directly from egg
> whites.  The teacher picked up on this idea as the one he and his students
> would like to pursue.  I have done a bit of reseach and I have found the
> Alderton and Fevold paper from '46 about direct crystallization from egg
> whites.  However I am unable to find any papers that refine or expand upon
> this experiment.  While there appears to be some literature about lysozyme
> and crystallizing the same, these papers do not use lysozyme directly from
> hen egg whites.  Do any of you know of any more recent papers or procedures
> that would be relevant or easily adapted to an high school environment?
>
> Our goal is to get diffraction quality crystals, expose the crystals at
> the beamline, and present a poster of the experience.
>
> Cheers and thanks,
>
> David Smith
>
> --
> David W Smith
> Research Scientist
> LS-CAT
> APS, Argonne IL
> W:(630)343-9811
> F:(630)252-4664
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] Direct crystallization of Lysozyme from eggs

[David Smith]

Dear crystallographers,

I am working on an outreach program through the APS to get motivated high
school students some/more research experience.  As I work at a
crystallography beamline (LS-CAT), we are trying to get a
crystallographically centered experiment in place that will be interesting
to a high school student.  Among other ideas, I had mentioned to the
teacher the possibility of crystallizing lysozyme directly from egg
whites.  The teacher picked up on this idea as the one he and his students
would like to pursue.  I have done a bit of reseach and I have found the
Alderton and Fevold paper from '46 about direct crystallization from egg
whites.  However I am unable to find any papers that refine or expand upon
this experiment.  While there appears to be some literature about lysozyme
and crystallizing the same, these papers do not use lysozyme directly from
hen egg whites.  Do any of you know of any more recent papers or procedures
that would be relevant or easily adapted to an high school environment?

Our goal is to get diffraction quality crystals, expose the crystals at the
beamline, and present a poster of the experience.

Cheers and thanks,

David Smith

-- 
David W Smith
Research Scientist
LS-CAT
APS, Argonne IL
W:(630)343-9811
F:(630)252-4664

Re: [ccp4bb] Joining two atoms to display in pymol

[Christopher Browning]

Hi,

Yeah, thanks for the help. I've noticed that it needs to be for the
chain object, so I'll just modify the PDB accordingly,

Cheers,

C 



On Tue, 2012-09-25 at 18:49 +0200, Sabine Schneider wrote:
> Hi Chris,
> 
> If you select the two atoms in 'editing mode' and type 'bond' at the 
> command line, pymol should draw a bond between them (if they are in the 
> same object that is).
> 
> Sabine
> 
> 
> On 09/25/2012 06:36 PM, Christopher Browning wrote:
> > Hi,
> >
> > I have a question about how to join two atoms together so that in Pymol
> > a bond is drawn between them. I have 2 sugar molecules that are
> > covalently bound, but in the the PDB they are separate sugar molecules
> > and they need to be joined together by a single bond. Do I have to
> > annotate the PDB file with something like "CONNECT" or "JOIN" or "LINK"?
> > These are the two atoms I'd like to join.
> >
> >
> > ATOM  19317  C2  SIA Y   1  20.503  35.557  43.691  1.00 22.97
> > C
> > ATOM  19387  O9  SLB Z   1  21.630  36.539  45.311  1.00 28.53
> > O
> >
> >
> > Thanks,
> >
> > Chris
> >
> >
> >
> 

-- 
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Switzerland
Tel: 0041 (0) 02 16 93 04 40

[ccp4bb] Joining two atoms to display in pymol

[Christopher Browning]

Hi,

I have a question about how to join two atoms together so that in Pymol
a bond is drawn between them. I have 2 sugar molecules that are
covalently bound, but in the the PDB they are separate sugar molecules
and they need to be joined together by a single bond. Do I have to
annotate the PDB file with something like "CONNECT" or "JOIN" or "LINK"?
These are the two atoms I'd like to join.


ATOM  19317  C2  SIA Y   1  20.503  35.557  43.691  1.00 22.97
C
ATOM  19387  O9  SLB Z   1  21.630  36.539  45.311  1.00 28.53
O


Thanks,

Chris 



-- 
Dr. Christopher Browning
Post-Doctor to Prof. Petr Leiman
EPFL
BSP-416
1015 Lausanne
Switzerland
Tel: 0041 (0) 02 16 93 04 40

[ccp4bb] Open position for protein crystallographer at Bayer in Berlin, Germany

[Roman Hillig]

Dear all,

We have an open position in our Structural Biology department at Bayer in 
Berlin. All details can be found in the job advertisement under the following 
link:

https://mybayerjob.bayerbbs.com/sap/bc/webdynpro/sap/hrrcf_a_posting_apply?param=cG9zdF9pbnN0X2d1aWQ9MDA1MDU2ODkwMEI0MUVEMjgwOUE0Qjg2NUVFNDQ5QTMmY2FuZF90eXBlPUVYVA%3d%3d&sap-client=005&sap-language=EN¶ms=cG9zdF9pbnN0X2d1aWQ9MDA1MDU2ODkwMEI0MUVEMjgwOUE0Qjg2NUVFNDQ5QTM%3d

If you are interested, please do not reply to me but submit your application at 
www.myBayerjob.de quoting the Reference Code: 
042823, see also the link above.

Best wishes,
Roman



Dr. Roman Hillig
Senior Scientist, Structural Biology

Bayer HealthCare Pharmaceuticals
Bayer Pharma AG
Structural Biology, Lead Discovery
Muellerstr. 178, Building S110/03/710
13353 Berlin, Germany
Phone +49 30 468 18451
Fax +49 30 468 98451


E-Mail: roman.hil...@bayer.com
Web: http://www.bayerpharma.com

Vorstand: Andreas Fibig, Vorsitzender | Hartmut Klusik, Manfred Vehreschild
Vorsitzender des Aufsichtsrats: Richard Pott
Sitz der Gesellschaft: Berlin | Eintragung: Amtsgericht Charlottenburg HRB 283 B
_

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Oganesyan, Vaheh]

Herman,

I don't know which early days you refer to, but from late 80s until structural 
genomics era there were relatively few crystallization reports. May be I didn't 
see them, and then I apologize. But crystallization reports in large started in 
late 90s through early 21st century and Acta F has been created to accommodate 
them. As far as my understanding goes, you publish crystallization results only 
if you're sure the structure will be solved or is already solved but not ready 
for different reasons to be published.
Some time ago I was in position similar to Christine's. And I waited and waited 
until I decided to contact the authors of the notes. Sure enough, they intended 
to publish structure but the postdoc left and nobody else was able to do the 
work.
Christine, you have got good advises already. Contact the authors and if they 
are reasonable publish back to back, if they are not - you do not have any 
legal/moral obligations to wait.

My two drams,

 Vaheh




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
herman.schreu...@sanofi.com
Sent: Tuesday, September 25, 2012 11:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Etiquette on publishing if there is a crystallization 
report from someone else.

In the very early days, solving a protein structure was an enormous amount of 
work and since hardly any protein structures were solved there was a huge pool 
of unsolved structures. Under these circumstances, it was a waste of resources 
if two groups would work on the same protein.  To prevent this, people would 
publish crystallization notes so other groups could choose another protein to 
work on and this is what usually happened. Also, the purpose of scientific 
publications is that other people can use this information to progress their 
results.

Unless unethical actions were involved (holding up referee reports, making 
shortcuts to publish before the competition) I do not see a reason why you 
could not publish your paper. As Jürgen suggested, you may want to contact the 
other group to see if you could publish back to back.

my two cents,
Herman


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lukacs, 
Christine
Sent: Tuesday, September 25, 2012 3:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Etiquette on publishing if there is a crystallization report 
from someone else.
I'd like to get a community opinion on something.

If a group has published crystallization and diffraction data (Acta Cryst F 
style crystallization report), and you happen to have the same crystal form and 
have solved the structure, is there an unspoken rule that you don't publish, or 
an amount of time that you wait to allow the other group to publish before you 
do?  I am not talking about a high impact structure with a race to publish.

Just looking for a general consensus.

Thanks
Christine

Christine Lukacs, Ph.D.
Principal Scientist
Roche
christine.luk...@roche.com
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Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Herman . Schreuder]

In the very early days, solving a protein structure was an enormous amount of 
work and since hardly any protein structures were solved there was a huge pool 
of unsolved structures. Under these circumstances, it was a waste of resources 
if two groups would work on the same protein.  To prevent this, people would 
publish crystallization notes so other groups could choose another protein to 
work on and this is what usually happened. Also, the purpose of scientific 
publications is that other people can use this information to progress their 
results.
 
Unless unethical actions were involved (holding up referee reports, making 
shortcuts to publish before the competition) I do not see a reason why you 
could not publish your paper. As Jürgen suggested, you may want to contact the 
other group to see if you could publish back to back.
 
my two cents,
Herman




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
Lukacs, Christine
Sent: Tuesday, September 25, 2012 3:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Etiquette on publishing if there is a crystallization 
report from someone else.



I'd like to get a community opinion on something. 

 

If a group has published crystallization and diffraction data (Acta 
Cryst F style crystallization report), and you happen to have the same crystal 
form and have solved the structure, is there an unspoken rule that you don't 
publish, or an amount of time that you wait to allow the other group to publish 
before you do?  I am not talking about a high impact structure with a race to 
publish.

 

Just looking for a general consensus.

 

Thanks

Christine

 

Christine Lukacs, Ph.D. 
Principal Scientist 
Roche 
christine.luk...@roche.com 

This message is intended for the use of the named recipient(s) only and 
may contain confidential and/or proprietary information. If you are not the 
intended recipient, please contact the sender and delete this message. Any 
unauthorized use of the information contained in this message is prohibited.

 

[ccp4bb] Postdoctoral position at the European Institute of Oncology, Milano

[Marina Mapelli]

Postdoctoral research position in Structural Biology

A postdoctoral research position is available in the group of Marina Mapelli at 
the European Institute of Oncology in Milano 
(http://www.ifom-ieo-campus.it/research/mapelli.php).
The main interest of the group focuses on the molecular mechanisms underlying 
asymmetric cell divisions, with emphasis on the role of mitotic spindle 
coupling to cortical polarity. To study these processes we use a combination of 
X-ray crystallography, biochemistry and cell biology.

I am seeking a motivated and enthusiastic postdoctoral fellow who enjoys 
working as part of a collaborative, fun, and multidisciplinary team. The ideal 
candidate should have a PhD in protein structure, biochemistry or an equivalent 
qualification, and extensive experience in protein expression and 
characterization. Experience in protein structure determination would be an 
advantage. 

The Structural Biology Department of the IFOM-IEO Campus is equipped with the 
state-of-the-art apparatus for protein purification and crystallization, 
including
a nanodrop crystallization robot and an automated imaging system, and has good 
access to the synchrotron beamlines. Successful candidates will benefit from a 
stimulating
and collaborative environment within the Campus 
(http://www.ifom-ieo-campus.it/).

Postdoc applicants should send their enquiries by e-mail to Marina Mapelli 
(marina.mape...@ieo.eu). They should also ask two referees to send letters of 
recommendation at the same electronic address.

With my kind regards,
Marina


---
  Marina Mapelli, PhD
  Department of Experimental Oncology
  European Institute of Oncology
  Via Adamello 16, 20139 Milan, Italy
  tel:  +39-02-94375018
  email: marina.mape...@ieo.eu
  web: http://www.ifom-ieo-campus.it/research/mapelli.php
---

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Edwin Pozharski]

Tim,

On 09/25/2012 09:51 AM, Tim Gruene wrote:

I would assume that someone who publishes crystallisation conditions has
given up solving the structure or some other reason to encourage others
to pick up the project


there could be several situations when this is not so.  Sometimes a 
crystallization report and preliminary structure may be needed for 
another publication.  Also, current NIH rules disallow proposal updates 
other than reference to an accepted manuscript, and so this may be a way 
to get information to reviewers.  It may also be a gambit to dissuade 
your competition, although that may backfire if such competition already 
has the structure done and was simply procrastinating.


With that said, I personally see no ethical issue here other than one 
absolutely must acknowledge the existence of published crystallization 
report.


Cheers,

Ed.

Re: [ccp4bb] low-resolution refinement

[Pete Meyer]

3)  Activating map sharpening results in mtz files that look just normal 
and open in coot after the typical map calculation break, but no maps 
are displayed.  This is independent of the sharpening factor I choose 
(between 5 and 60).


I haven't used coot for map sharpening, but using the ranges I'd usually 
have to use (in cad) to seen an effect are more in the 80-120 range. 
You might want to start with an unrealistically large value just to 
ensure that things are working, then back off to a better value.


Pete

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Peter Moody]

Its not always the case that the project has been abandoned or died, some
labs will push crystallisation notes to give a student paper-writing
experience, and could have invested a significant effort since in the
project. They could be waiting for e.g. the complex that makes it
interesting. Or the PI could be slow and inefficient (like me)!

If its a simple MR task, and the other groups crystals are the same as
yours, then its perhaps  unlikely they would not have solved it.

In the old days the thing to do would be to contact the other group and see
what their plans are. But this requires people to be nice to each other,
and I'm not sure that works anymore, even in crystallography.

Peter


On 25 September 2012 15:03, Nat Echols  wrote:

> On Tue, Sep 25, 2012 at 6:51 AM, Tim Gruene 
> wrote:
> > I would assume that someone who publishes crystallisation conditions has
> > given up solving the structure or some other reason to encourage others
> > to pick up the project, i.e., no, I don't see much point NOT
> > publishing your data.
>
> I always assumed that the point of publishing crystallization
> conditions was to establish priority, and apparently there was once
> such an unspoken rule about publishing the structure.  Or so I'm told;
> from what I've seen it's long abandoned.
>
> A bit of historical perspective (about a very high-profile project):
>
> http://www.sciencemag.org/content/285/5436/2048.full
>
> -Nat
>

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Bosch, Juergen]

It could also be salami-tactic, the least-publishable unit.

@Christine,
since you are at a company and worry about somebodies PhD I would contact the 
person from that Acta F paper and simply inform them that you would like to 
publish that. There are many scenarios that might follow, one of them would be 
co-publish back-to-back, another one add the PhD student as second author and 
the PI somewhere else on the same paper if they contribute additional data, or 
publish alone.

During my PhD I had that offer, we decided to not co-publish and let the others 
take the "fame" (don't take that too serious, it's a low cited paper).

Jürgen

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu






On Sep 25, 2012, at 9:51 AM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Christine,

I would assume that someone who publishes crystallisation conditions has
given up solving the structure or some other reason to encourage others
to pick up the project, i.e., no, I don't see much point NOT
publishing your data.
Cheers,
Tim

On 09/25/2012 03:32 PM, Lukacs, Christine wrote:
I'd like to get a community opinion on something.

If a group has published crystallization and diffraction data
(Acta Cryst F style crystallization report), and you happen to have
the same crystal form and have solved the structure, is there an
unspoken rule that you don't publish, or an amount of time that you
wait to allow the other group to publish before you do?  I am not
talking about a high impact structure with a race to publish.

Just looking for a general consensus.

Thanks Christine

Christine Lukacs, Ph.D. Principal Scientist Roche
christine.luk...@roche.com This message is 
intended for the use of
the named recipient(s) only and may contain confidential and/or
proprietary information. If you are not the intended recipient,
please contact the sender and delete this message. Any
unauthorized use of the information contained in this message is
prohibited.



- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQYbbIUxlJ7aRr7hoRAo54AJ9VezGSlgF3JATdN+kNDs3OrxNFugCgnJro
Hh4ZMkUtBbCWn19cHjKUqEo=
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Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Nat Echols]

On Tue, Sep 25, 2012 at 6:51 AM, Tim Gruene  wrote:
> I would assume that someone who publishes crystallisation conditions has
> given up solving the structure or some other reason to encourage others
> to pick up the project, i.e., no, I don't see much point NOT
> publishing your data.

I always assumed that the point of publishing crystallization
conditions was to establish priority, and apparently there was once
such an unspoken rule about publishing the structure.  Or so I'm told;
from what I've seen it's long abandoned.

A bit of historical perspective (about a very high-profile project):

http://www.sciencemag.org/content/285/5436/2048.full

-Nat

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Christine,

I would assume that someone who publishes crystallisation conditions has
given up solving the structure or some other reason to encourage others
to pick up the project, i.e., no, I don't see much point NOT
publishing your data.
Cheers,
Tim

On 09/25/2012 03:32 PM, Lukacs, Christine wrote:
> I'd like to get a community opinion on something.
> 
> If a group has published crystallization and diffraction data
> (Acta Cryst F style crystallization report), and you happen to have
> the same crystal form and have solved the structure, is there an
> unspoken rule that you don't publish, or an amount of time that you
> wait to allow the other group to publish before you do?  I am not
> talking about a high impact structure with a race to publish.
> 
> Just looking for a general consensus.
> 
> Thanks Christine
> 
> Christine Lukacs, Ph.D. Principal Scientist Roche 
> christine.luk...@roche.com This message is intended for the use of 
> the named recipient(s) only and may contain confidential and/or 
> proprietary information. If you are not the intended recipient, 
> please contact the sender and delete this message. Any
> unauthorized use of the information contained in this message is
> prohibited.
> 
> 

- -- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQYbbIUxlJ7aRr7hoRAo54AJ9VezGSlgF3JATdN+kNDs3OrxNFugCgnJro
Hh4ZMkUtBbCWn19cHjKUqEo=
=7j/9
-END PGP SIGNATURE-

[ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

[Lukacs, Christine]

I'd like to get a community opinion on something.

If a group has published crystallization and diffraction data (Acta Cryst F 
style crystallization report), and you happen to have the same crystal form and 
have solved the structure, is there an unspoken rule that you don't publish, or 
an amount of time that you wait to allow the other group to publish before you 
do?  I am not talking about a high impact structure with a race to publish.

Just looking for a general consensus.

Thanks
Christine

Christine Lukacs, Ph.D.
Principal Scientist
Roche
christine.luk...@roche.com
This message is intended for the use of the named recipient(s) only and may 
contain confidential and/or proprietary information. If you are not the 
intended recipient, please contact the sender and delete this message. Any 
unauthorized use of the information contained in this message is prohibited.

[ccp4bb] suggestions for good yet cost-effective pipettes

[sreetama das]

Dear all,
  We are planning to buy electronic dispensing pipette (single 
channel) and mechanical multi-channel pipette (8 channel) in the range 0.5 - 10 
ul in our lab.

Currently, we are considering IKA PRECISION pipettes.

It will be helpful if we can get feedback on how these pipettes work from labs 
which have used them, or any other relevant comments.

We are also open to looking at other options, provided they cost about 600 USD 
or less.

Thanks,
sreetama

Re: [ccp4bb] low-resolution refinement

[Robert Nicholls]

Hi Andreas,

In your case, it sounds like a reasonable strategy would be to use external 
restraints for a few rounds of refinement (as you have done), but then release 
them and instead use jelly-body restraints. This two-stage process will help to 
initially hold your model in a sensible conformation using external restraints, 
but then gently release the structure in order to reduce further bias in later 
rounds. The immediate subsequent use of jelly-body restraints after external 
restraints will ensure that the model won't deviate too far from that sensible 
conformation, unless the data suggests otherwise.

Of course, if certain regions lose their sensible conformations in subsequent 
rounds of refinement, you can continue to use external restraints just in these 
regions.

> I substantially rebuilt a surface loop that I don't want to restrain by the 
> model.


In this case, I would recommend re-generating the external restraints, this 
time telling ProSMART not to generate restraints for these particular 
residues/regions. This can be done using the -restrain and -restrain_rm 
keywords, as described in the documentation (let me know off-board if you want 
help with this).

If you enable map sharpening then the single output MTZ file should be the 
sharpened map… I'm not sure why you are finding that the map is not displayed… 
do you see any difference between enabling/disabling map sharpening?

Cheers,
Rob


On 25 Sep 2012, at 11:19, Andreas Förster wrote:

> Dear all,
> 
> I'm making first steps in the desolate world of low-resolution refinement.  
> With dodgy 3.8A data, the magic of Phaser was able to solve the structure of 
> a complex by MR with its components as MR models. Jelly-body refinement does 
> wonders for R free.  There are three issues that I would like to get some 
> advice on:
> 
> 1)  Using external restraints calculated with ProSMART improved the structure 
> further, but I'm worried that using restraints derived from the structures 
> used for MR gets me into a sinkhole of model bias. Should it be either 
> molecular replacement or homology restraints?
> 
> 2)  Do I recalculate restraints at each round of refinement?  In particular, 
> I substantially rebuilt a surface loop that I don't want to restrain by the 
> model.
> 
> 3)  Activating map sharpening results in mtz files that look just normal and 
> open in coot after the typical map calculation break, but no maps are 
> displayed.  This is independent of the sharpening factor I choose (between 5 
> and 60).
> 
> Thanks for your help.
> 
> 
> Andreas
> 
> 
> -- 
>Andreas Förster, Research Associate
>Paul Freemont & Xiaodong Zhang Labs
> Department of Biochemistry, Imperial College London
>http://www.msf.bio.ic.ac.uk

[ccp4bb] low-resolution refinement

[Andreas Förster]

Dear all,

I'm making first steps in the desolate world of low-resolution 
refinement.  With dodgy 3.8A data, the magic of Phaser was able to solve 
the structure of a complex by MR with its components as MR models. 
Jelly-body refinement does wonders for R free.  There are three issues 
that I would like to get some advice on:


1)  Using external restraints calculated with ProSMART improved the 
structure further, but I'm worried that using restraints derived from 
the structures used for MR gets me into a sinkhole of model bias. 
Should it be either molecular replacement or homology restraints?


2)  Do I recalculate restraints at each round of refinement?  In 
particular, I substantially rebuilt a surface loop that I don't want to 
restrain by the model.


3)  Activating map sharpening results in mtz files that look just normal 
and open in coot after the typical map calculation break, but no maps 
are displayed.  This is independent of the sharpening factor I choose 
(between 5 and 60).


Thanks for your help.


Andreas


--
Andreas Förster, Research Associate
Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
http://www.msf.bio.ic.ac.uk

[ccp4bb] Joint EMBL-CCP4 training course in macromolecular crystallography

[eugene . krissinel]

Dear All,

This is a reminder that the application deadline for the joint EMBL-CCP4 
training course "European School for Macromolecular Crystallography (ESMAX)" is 
now just a week ahead (October 1st).

The Course will take place at the EMBL Hamburg Outstation, the DESY synchrotron 
site during the period:

Monday November 19th to Monday November 26th, 2012. 

The ESMAX-2012 school will build upon the traditions of the forefront of 
training in structural biology – the M2M workshops and the CCP4 crystallography 
schools and will include a range of activities addressing essential steps in 
determining biomolecular structures. In particular, the courses will have 
practicals on the use of synchrotron radiation and beamline equipment, sample 
handling and carrying out an experiment, followed by an intense course on data 
processing, structure solution, model building and validation using top-ranked 
software packages.

Speakers and tutors include G. Bourenkov (Hamburg), C. Carolan (Hamburg), M. 
Cianci (Hamburg), Z. Dauter (Argonne), K. Diederichs (Konstanz), W. Kabsch 
(Heidelberg), J. Kallio (Hamburg), R. Keegan (Harwell), E. Krissinel (Harwell), 
V. Lamzin (Hamburg), A. Lebedev (Harwell), B. Lohkamp (Stockholm), W. Minor 
(Charlottesville), G. Murshudov (Cambridge), S. Panjikar (Melbourne), N. Pannu 
(Leiden), H. Powell (Cambridge), T. Schneider (Hamburg), T. Schwede (Basel), T. 
Wiegels (Hamburg).

The number of places is restricted to 20. Applications can be made 
electronically via the link 

http://www.embl-hamburg.de/training/events/2012/ESMAX-12/index.html

The deadline for applications is October 1st, 2012.

The organising committee - Michele Cianci, Johanna Kallio, Ronan Keegan, Eugene 
Krissinel, Victor Lamzin, Andrey Lebedev, Thomas Schneider



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