[phenixbb] AutoMR error

Erik R. Kish-Trier kishtrier at biochem.utah.edu
Thu Feb 17 17:00:37 PST 2011


Hi,

I am getting the following error from AutoMR, which I am fairly certain is due to the deficiencies of my machine:

Python(2624) malloc: *** mmap(size=1665024000) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

While using the prior release of phenix, I was able to get a similar job to complete, which makes me curious.

I am running phenix 1.7-650 (GUI) on an Intel Mac with 4GB of RAM and OS 10.6.6.

Any suggestions?

Thanks!

Erik


On Feb 17, 2011, at 11:29 AM, <phenixbb-request at phenix-online.org<mailto:phenixbb-request at phenix-online.org>> <phenixbb-request at phenix-online.org<mailto:phenixbb-request at phenix-online.org>> wrote:

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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" <machius at med.unc.edu<mailto:machius at med.unc.edu>>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] At what percentage of saturated peaks is
       acceptable?
Message-ID: <91F63968-BF15-47B4-A15E-FB73279AD18C at med.unc.edu<mailto:91F63968-BF15-47B4-A15E-FB73279AD18C at med.unc.edu>>
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 <epozh001 at umaryland.edu<mailto:epozh001 at umaryland.edu>>
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] At what percentage of saturated peaks is
       acceptable?
Message-ID: <1297907147.30587.17.camel at 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
======================


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

Message: 3
Date: Thu, 17 Feb 2011 08:52:26 +0100
From: Ina Lindemann <lindema2 at staff.uni-marburg.de<mailto:lindema2 at staff.uni-marburg.de>>
To: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Cc: heinea at mailer.uni-marburg.de<mailto:heinea at mailer.uni-marburg.de>
Subject: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID:
       <20110217085226.106944rzydtyujeo at home.staff.uni-marburg.de<mailto:20110217085226.106944rzydtyujeo at home.staff.uni-marburg.de>>
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 <folmerf at gmail.com<mailto:folmerf at gmail.com>>
To: PHENIX user mailing list <phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>>
Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID:
       <AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw at mail.gmail.com<mailto:AANLkTimXZUDZQMxf70jRSMPxi+=9dFKHB6OAoVV6wGuw at mail.gmail.com>>
Content-Type: text/plain; charset=ISO-8859-1

Dear Ina

Have a look here (from the CCP4BB)

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg19631.html

Best regards,
Folmer Fredslund

2011/2/17 Ina Lindemann <lindema2 at staff.uni-marburg.de>:

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

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

Message: 5
Date: Thu, 17 Feb 2011 10:23:58 +0200
From: Felix Frolow <mbfrolow at post.tau.ac.il>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Cc: heinea at mailer.uni-marburg.de
Subject: Re: [phenixbb] Unrealistic number of waters found by phenix?
Message-ID: <D3ACED80-CB0C-4043-BB4A-CF8E8A936195 at post.tau.ac.il>
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: mbfrolow at post.tau.ac.il
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
phenixbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb



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

Message: 6
Date: Thu, 17 Feb 2011 16:23:16 +0100
From: Daniele de Sanctis <de.sanctisd at gmail.com>
To: phenixbb at phenix-online.org
Subject: [phenixbb] EMBO 2011 Practical Course - Exploiting Anomalous
       Scattering - ESRF - 6 - 10 June 2011
Message-ID:
       <AANLkTikigUeBYgzF9wuJg7z5jTkZcKO0sh8j+AGUWDf6 at mail.gmail.com>
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 <gborgstahl at gmail.com>
To: phenixbb at phenix-online.org
Subject: [phenixbb] IUCr Travel Fellowships Available
Message-ID:
       <AANLkTik3EecaF_MB8avPPs5jZbVWjoA+s__6k067mDAD at mail.gmail.com>
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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