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Today's Topics:

  1. Re: At what percentage of saturated peaks is acceptable?
     (Mischa Machius)
  2. Re: At what percentage of saturated peaks is acceptable?
     (Ed Pozharski)
  3. Unrealistic number of waters found by phenix? (Ina Lindemann)
  4. Re: Unrealistic number of waters found by phenix?
     (Folmer Fredslund)
  5. Re: Unrealistic number of waters found by phenix? (Felix Frolow)
  6. EMBO 2011 Practical Course - Exploiting Anomalous Scattering
     - ESRF - 6 - 10 June 2011 (Daniele de Sanctis)
  7. IUCr Travel Fellowships Available (Gloria Borgstahl)


----------------------------------------------------------------------

Message: 1
Date: Wed, 16 Feb 2011 20:42:55 -0500
From: "Mischa Machius" <[email protected]>
To: "PHENIX user mailing list" <[email protected]>
Subject: Re: [phenixbb] At what percentage of saturated peaks is
       acceptable?
Message-ID: <[email protected]>
Content-Type: text/plain; charset=us-ascii

I would recommend taking two passes; a low-resolution pass with short exposures and a high-resolution pass with longer exposures. Then merge the two, and you've got a complete dataset. If applicable, take three or more passes. MM

On Feb 16, 2011, at 8:39 PM, Jason wrote:

Hi,

I have a technical question that is not related to phenix, but I hope some expertise around may help me out.

I am intending to increase the exposure time to gain some resolution. At the same time I do not want too many over exposed peak.  The question comes to at what percentage of the saturated peaks is acceptable? Many thanks.

======================

Jason

Structural Biology Department

University of Pittsburgh

======================

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------------------------------

Message: 2
Date: Wed, 16 Feb 2011 20:45:47 -0500
From: Ed Pozharski <[email protected]>
To: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] At what percentage of saturated peaks is
       acceptable?
Message-ID: <1297907147.30587.17.camel@thunderclap>
Content-Type: text/plain; charset="UTF-8"

If you start losing completeness at low resolution, just collect a low
resolution pass (i.e. exactly the same frames but with short exposures).
Be mindful of radiation damage though.

On Wed, 2011-02-16 at 20:39 -0500, Jason wrote:

Hi,

I have a technical question that is not related to phenix, but I hope

some expertise around may help me out.

I am intending to increase the exposure time to gain some resolution.

At the same time I do not want too many over exposed peak.  The

question comes to at what percentage of the saturated peaks is

acceptable? Many thanks.

======================

Jason

Structural Biology Department

University of Pittsburgh

======================

_______________________________________________

phenixbb mailing list

[email protected]

http://phenix-online.org/mailman/listinfo/phenixbb

------------------------------

Message: 3
Date: Thu, 17 Feb 2011 08:52:26 +0100
From: Ina Lindemann <[email protected]>
To: [email protected]
Cc: [email protected]
Subject: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID:
       <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
       format="flowed"


Hi,

I am refining a crystal structure of a protein with 198 amino acids at
1.59 A resolution.
I have used the function Update waters in phenix. After visual
inspection of the found water molecules I deleted some of them, but
there are still 334 water molecules left which show reasonable
electron density. Many of them interacts just with other water
molecules and not with the protein.
I calculated the average B of water molecules = 26.3 and protein = 12.6.
Now I am wondering if the number of water molecules and their average
B value is to high with respect to the protein and would be very
pleased about your answers.

With best regards,
Ina




Ina Lindemann
Philipps-Universit?t Marburg
Pharmazeutische Chemie
AG Klebe
Marbacher Weg 6
35032 Marburg
Tel.: 06421/2825908



------------------------------

Message: 4
Date: Thu, 17 Feb 2011 09:14:41 +0100
From: Folmer Fredslund <[email protected]>
To: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID:
       <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1

Dear Ina

Have a look here (from the CCP4BB)

http://www.mail-archive.com/[email protected]/msg19631.html

Best regards,
Folmer Fredslund

2011/2/17 Ina Lindemann <[email protected]>:

Hi,

I am refining a crystal structure of a protein with 198 amino acids at 1.59

A resolution.

I have used the function Update waters in phenix. After visual inspection of

the found water molecules I deleted some of them, but there are still 334

water molecules left which show reasonable electron density. Many of them

interacts just with other water molecules and not with the protein.

I calculated the average B of water molecules = 26.3 and protein = 12.6.

Now I am wondering if the number of water molecules and their average B

value is to high with respect to the protein and would be very pleased about

your answers.

With best regards,

Ina

Ina Lindemann

Philipps-Universit?t Marburg

Pharmazeutische Chemie

AG Klebe

Marbacher Weg 6

35032 Marburg

Tel.: 06421/2825908

_______________________________________________

phenixbb mailing list

[email protected]

http://phenix-online.org/mailman/listinfo/phenixbb

------------------------------

Message: 5
Date: Thu, 17 Feb 2011 10:23:58 +0200
From: Felix Frolow <[email protected]>
To: PHENIX user mailing list <[email protected]>
Cc: [email protected]
Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID: <[email protected]>
Content-Type: text/plain; charset=iso-8859-1

Dear Ina Lindemann
These are problems of the rich people...
Be happy and why not, after all your resolution is ~1.6 A
I would say that you have not enough water molecules. In such resolution and such molecular size
I would expect about 2 or even 3 water molecules per residue. So you are missing 198*2-334=62 water molecules.
As a frequent reviewer I would not let a paper describing such structure to pass!  ;-) ;-)

Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: [email protected]
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608

On Feb 17, 2011, at 09:52 , Ina Lindemann wrote:

Hi,

I am refining a crystal structure of a protein with 198 amino acids at 1.59 A resolution.

I have used the function Update waters in phenix. After visual inspection of the found water molecules I deleted some of them, but there are still 334 water molecules left which show reasonable electron density. Many of them interacts just with other water molecules and not with the protein.

I calculated the average B of water molecules = 26.3 and protein = 12.6.

Now I am wondering if the number of water molecules and their average B value is to high with respect to the protein and would be very pleased about your answers.

With best regards,

Ina

Ina Lindemann

Philipps-Universit?t Marburg

Pharmazeutische Chemie

AG Klebe

Marbacher Weg 6

35032 Marburg

Tel.: 06421/2825908

_______________________________________________

phenixbb mailing list

[email protected]

http://phenix-online.org/mailman/listinfo/phenixbb

------------------------------

Message: 6
Date: Thu, 17 Feb 2011 16:23:16 +0100
From: Daniele de Sanctis <[email protected]>
To: [email protected]
Subject: [phenixbb] EMBO 2011 Practical Course - Exploiting Anomalous
       Scattering - ESRF - 6 - 10 June 2011
Message-ID:
       <[email protected]>
Content-Type: text/plain; charset=UTF-8

Deadline in 10 days!!


DEADLINE TO APPLY FEBRUARY 28th


COURSE ANNOUCEMENT

EMBO 2011 Practical Course - Exploiting Anomalous Scattering in
Macromolecular Structure Determination
ESRF-EMBL, Grenoble, France, 6 - 10 June 2011


The EMBO 2011 Practical Course on Exploiting Anomalous Scattering in
Macromolecular Structure Determination will be hosted by the ESRF in
Grenoble, France from 6 to 10, June 2011. The course aims to impart
the theoretical and practical basis for the 3-dimensional structure
determination of bio-macromolecules using Anomalous Dispersion
techniques (SAD & MAD) to young scientists who intend to apply these
methods in macromolecular crystallography.

Through a series of lectures, software demonstrations, practicals on
the ESRF beamlines and tutorials, participants will get insights into
all aspects of the structure determination process including beamline
instrumentation, data collection and processing, heavy atom
substructure determination, phasing and model building. There will
also be sessions focusing on automated structure solution procedures
and newer methods. Additional sessions will include presentations of
distinguished structures solved with these techniques.


Confirmed invited speakers include:
G. Bunkoczi, A. Cameron, D. Chirgadze, Z. Dauter, P. Evans, M.
Grininger, T. Gruene,
W. Kabsch, S. Panjikar, N. Pannu, A. Popov, H. Powell, L. Sazanov, G.
Sheldrick, T. Terwilliger, C. Vonrhein


The number of participants is limited to 20 and the deadline for
application is February 28th, 2011.
Additional information, course programme and instructions to apply to
the course can be found in the course webpages:
http://cwp.embo.org/pc11-03/

--
?????
---------------------------------------
Daniele de Sanctis, PhD

Structural Biology Group
ESRF, Grenoble, France
Tel 33 (0)4 76 88 2869


------------------------------

Message: 7
Date: Thu, 17 Feb 2011 10:42:00 -0600
From: Gloria Borgstahl <[email protected]>
To: [email protected]
Subject: [phenixbb] IUCr Travel Fellowships Available
Message-ID:
       <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"

Please see the attachment
The deadline is 15 days away.


************************************************************************
Gloria Borgstahl
Eppley Institute for Cancer Research and Allied Diseases
987696 Nebraska Medical Center
10732A Lied Transplant Center
Omaha, NE 68198-7696

http://sbl.unmc.edu
Office (402) 559-8578
FAX (402) 559-3739

Professor
Hobbies: ?Protein Crystallography, Cancer, Biochemistry,
DNA Metabolism, Modulated Crystals, ?Crystal Perfection
Interests: ?Manga, Led Zeppelin, Cold Play, piano, BRAN,
RAGBRAI, golf and lately superspace groups
************************************************************************
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