Re: [ccp4bb] PLEASE I NEED YOUR HELP.

[Bernhard Rupp]

Try unrestrained refinement first.

BR

 

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ming
Zhou
Sent: Friday, December 04, 2009 12:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [Bulk] [ccp4bb] PLEASE I NEED YOUR HELP.

 

Dear,

How are you today? May this emergency appeal finds you well,i am sorry i do
not inform you about my travel to Africa for a program. The program is
taking place in three major Countries in Africa which includes Ghana,Nigeria
and South Africa. It has been a very sad and bad moment for me that the
condition i found myself is so intoxicated to explain.I am stranded in
Nigeria because I forgot my little bag in a taxi where my Atm card,all the
money i have with me and some important documents are,i am so confussed
right now that i do not know what to do or where to go.Please i need your
urgent help to send some money to me so that i could be able to come back
home.
 
Please i need the sum of $1,500USD as a loan to enable me sort-out myself
and confirm my Basic Travelling Allowance fees back home,but if you cannot
come up with all the requested amount due to the short notice, kindly go
ahead and send me any amount you can and email me the transfer details. I
will be so grateful to receive it and i promise to pay back the money to you
as soon as am back home.
 
Kindly understand that i am in a very tight and horrible situation at the
moment that i could not even afford to take a good meal due to the fact that
i do not have a cent with me. I know you will never disappoint me and that
is why i have to contact you in this regard and please as you endeavor to
help me with this money i don't mean you should disclose my predicament to
anybody for my personal reasons till when am successfully back home.
However,it is not compulsory you will send me the money but if my situation
and our good relationship touches you quickly proceed to any of the western
union money transfer local 
stores or post office around you and transfer me the money as soon as you
have received this emergency appeal.

Western union money transfer is the most convenience and safety way to
receive money here without any delay or problem. 
 
Below is my information where to send the money to me through western union.

Receivers Name: Ming Zhou
 
Address: 45 Awolowo Road Ikoyi 
City: Lagos Island
State: Lagos
Zip Code:23401
 
Country: Nigeria
 
After you have sent the money, kindly email me the western union transfer
details such as:

MTCN(Money transfer control number)
Test Question: What is your year of birth?
Answer: 1954
Amount Needed: $1,500USD
 
I will check my email soonest to pick up the western union transfer details
to enable me come back home with the next available flight and i will need
the transfer # MTCN (money transfer control number) as soon as possible.
 
Thanks,
Ming 

 

  _  

Chat with Messenger straight from your Hotmail inbox. Check it out
 

Re: [ccp4bb] PLEASE I NEED YOUR HELP.

[Partha Chakrabarti]

He needs to be refined in dual space with different weights and
gradients.. (whip round and spam reporting).

Considering the space time anomaly.. Ming Zhou is stuck in Nigeria,
speaking English but no physics.. and it is not even 1st April..

If you wish, you can report such emails to ab...@hotmail.com /
report_s...@hotmail.com

Cheers, Partha



On Fri, Dec 4, 2009 at 2:18 PM, David Briggs  wrote:
> Given he "is so intoxicated to explain" I suggest that more slightly
> more restrained refinement might be in order
>
> Forward Fee 419 scam FAIL.
>
> He didn't even offer me the sum of $100,000,000 (ONE HUNDRED MILLION
> US DOLLAR) as a sweetener to the deal...
>
> I really don't see the motivation in sending this guy the cash - still
> - we could have a whip 'round at ccp4 workshop in Jan?
>
> (A Physics pal of mine had more fun baiting FF419ers -
> http://www-zeus.desy.de/~lightwd/ff419.html )
>
> D
>
> 2009/12/4 Bernhard Rupp :
>> Try unrestrained refinement first.
>>
>> BR
>>
>>
>>
>> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ming
>> Zhou
>> Sent: Friday, December 04, 2009 12:24 AM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [Bulk] [ccp4bb] PLEASE I NEED YOUR HELP.
>>
>>
>>
>> Dear,
>>
>> How are you today? May this emergency appeal finds you well,i am sorry i do
>> not inform you about my travel to Africa for a program. The program is
>> taking place in three major Countries in Africa which includes Ghana,Nigeria
>> and South Africa. It has been a very sad and bad moment for me that the
>> condition i found myself is so intoxicated to explain.I am stranded in
>> Nigeria because I forgot my little bag in a taxi where my Atm card,all the
>> money i have with me and some important documents are,i am so confussed
>> right now that i do not know what to do or where to go.Please i need your
>> urgent help to send some money to me so that i could be able to come back
>> home.
>>
>> Please i need the sum of $1,500USD as a loan to enable me sort-out myself
>> and confirm my Basic Travelling Allowance fees back home,but if you cannot
>> come up with all the requested amount due to the short notice, kindly go
>> ahead and send me any amount you can and email me the transfer details. I
>> will be so grateful to receive it and i promise to pay back the money to you
>> as soon as am back home.
>>
>> Kindly understand that i am in a very tight and horrible situation at the
>> moment that i could not even afford to take a good meal due to the fact that
>> i do not have a cent with me. I know you will never disappoint me and that
>> is why i have to contact you in this regard and please as you endeavor to
>> help me with this money i don't mean you should disclose my predicament to
>> anybody for my personal reasons till when am successfully back home.
>> However,it is not compulsory you will send me the money but if my situation
>> and our good relationship touches you quickly proceed to any of the western
>> union money transfer local
>> stores or post office around you and transfer me the money as soon as you
>> have received this emergency appeal.
>>
>> Western union money transfer is the most convenience and safety way to
>> receive money here without any delay or problem.
>>
>> Below is my information where to send the money to me through western union.
>>
>> Receivers Name: Ming Zhou
>>
>> Address: 45 Awolowo Road Ikoyi
>> City: Lagos Island
>> State: Lagos
>> Zip Code:23401
>>
>> Country: Nigeria
>>
>> After you have sent the money, kindly email me the western union transfer
>> details such as:
>>
>> MTCN(Money transfer control number)
>> Test Question: What is your year of birth?
>> Answer: 1954
>> Amount Needed: $1,500USD
>>
>> I will check my email soonest to pick up the western union transfer details
>> to enable me come back home with the next available flight and i will need
>> the transfer # MTCN (money transfer control number) as soon as possible.
>>
>> Thanks,
>> Ming
>>
>>
>>
>> 
>>
>> Chat with Messenger straight from your Hotmail inbox. Check it out
>
>
>
> --
> 
> Science knows it doesn't know everything...otherwise it would stop.
>  - Dara O'Briain
> 
> David C. Briggs PhD
> Father & Crystallographer
> http://drdavidcbriggs.googlepages.com/home
> Skype: DocDCB
> 
>

[ccp4bb] HKL2000 def.site file for ID14-4

[raz zarivach]

Dear CCP4 members

Can anyone please send me a  HKL2000 def.site file for ESRF ID14-4?

Thanks Raz
‎ 
 
Raz Zarivach, Ph.D. 


Department of Life Sciences and the NIBN
Ben-Gurion University of the Negev
POB 653
Zip code 84105
Beer-Sheva
Israel


Home page: http://lifeserv.bgu.ac.il/wb/zarivach/
tel: +972-8-6461999
fax: +972-8-6472970
skype: zarivach
ra...@yahoo.com
 


  

Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5

[Kay Diederichs]

Ian,

I cannot reproduce that bug on my x86_64 CentOS 5.4 system:

di...@turn29:-/tmp% cat temp.f90
  CHARACTER A(2)*2
  DATA A/2*'.A'/
  CALL CA(A)
  STOP 1
  END

  SUBROUTINE CA(A)
  CHARACTER A(2)*2
  DO 1 I=1,2
! With given data, the condition "A(I)(2:).NE.'A'" is always FALSE,
! so we should never execute the 'STOP 1' here:
1   IF(A(I)(2:).NE.'A' .AND. A(I).NE.'..') RETURN
! Should always drop through to here:
  STOP 2
  END

di...@turn29:-/tmp% ifort temp.f90
di...@turn29:-/tmp% ./a.out
2
di...@turn29:-/tmp% file a.out
a.out: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for 
GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 
2.6.9, not stripped

di...@turn29:-/tmp% ifort -m32 temp.f90
di...@turn29:-/tmp% ./a.out
2
di...@turn29:-/tmp% file a.out
a.out: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for 
GNU/Linux 2.6.9, dynamically linked (uses shared libs), for GNU/Linux 
2.6.9, not stripped

di...@turn29:-/tmp% ifort -v
Version 11.1
di...@turn29:-/tmp% ifort --vv
ifort: command line warning #10006: ignoring unknown option '-fvv'
ifort: command line error: no files specified; for help type "ifort -help"
di...@turn29:-/tmp% ifort -V
Intel(R) Fortran Intel(R) 64 Compiler Professional for applications 
running on Intel(R) 64, Version 11.1Build 20091012 Package ID: 
l_cprof_p_11.1.059

Copyright (C) 1985-2009 Intel Corporation.  All rights reserved.
FOR NON-COMMERCIAL USE ONLY

di...@turn29:-/tmp% uname -a
Linux turn29.biologie.uni-konstanz.de 2.6.18-164.6.1.el5 #1 SMP Tue Nov 
3 16:12:36 EST 2009 x86_64 x86_64 x86_64 GNU/Linux


best,

Kay

Ian Tickle schrieb:

Before you all go away and install the latest Intel compilers to fix
this bug - don't bother!  We just installed the latest version (ifort
11.3) and it has the same bug!  We plan to file a bug report with Intel.

In case anyone is interested, this is the code snippet which exhibits
the buggy behaviour (this was pruned down from s/r CHK_ALT in Refmac):

  CHARACTER A(2)*2
  DATA A/2*'.A'/
  CALL CA(A)
  STOP 1
  END

  SUBROUTINE CA(A)
  CHARACTER A(2)*2
  DO 1 I=2
C With given data, the condition "A(I)(2:).NE.'A'" is always FALSE,
C so we should never execute the 'STOP 1' here:
1   IF(A(I)(2:).NE.'A' .AND. A(I).NE.'..') RETURN
C Should always drop through to here:
  STOP 2
  END

It fails using -O2, -O3 and -Os, i.e. it only gives the right answer
using -O0 & -O1.

I should say that this is the first time we've ever encountered a bug in
the Intel compilers - I wish I could say the same for g77 & gfortran!

Cheers

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk 
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle

Sent: 28 November 2009 13:22
To: Garib Murshudov; john.pas...@jefferson.edu
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] Bad geometry for alt. conformation 
refined in Refmac5


I think I've finally squashed this particular bug which had been
annoying me for quite some time!  It appears that Intel Fortran v11.0
has an optimisation bug in s/r CHK_ALT (i.e. checking alternate atom
codes), & possibly also 10.x - I don't have those to test - 
though v9.1

& possibly earlier seem to be bug-free (at least this bug anyway!).
Possibly this is fixed in the current version of ifort (11.1), again I
don't have it to test, maybe someone who does can try it.  
This affects
compilations using optimisation levels -O2, -Os and -O3, but 
-O0 and -O1

are unaffected.

So my solution is to recompile with -O1.  The CCP4 6.1.2 distribution
uses -O2 so you need either to fix the makefile, or download Garib's
source code and make sure the makefile you use has the 
appropriate flag

settings.

As was pointed out earlier, having to use the 
gfortran-compiled code is

an issue, because at least for the OS I'm using (Centos 4.6),
gfortran-compiled code runs ~ 300% slower than the ifort code!!

Hope this helps!

-- Ian


-Original Message-
From: owner-ccp...@jiscmail.ac.uk 
[mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of Garib Murshudov

Sent: 25 November 2009 16:27
To: john.pas...@jefferson.edu
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Bad geometry for alt. conformation 
refined in Refmac5


Could you please try the version from York:

www.ysbl.york.ac.uk/refmac/latest_refmac.html

I think probkem you mention is related with compilation or 
something.  
At least I cannot repat it on my computer


regards
Garib

On 25 Nov 2009, at 16:18, John Pascal wrote:


Hello All,

We are trying to refine ARG residues with two conformations in  
Refmac5, and the
refined atom positions in the output PDB file are all over the  
place, as if the

geometry restraints are not well defined.

We've tried several different formats for the input file, 
based on  

previous
postings to the bulletin board and the PDB standard (two 
examples  

below), but
the result is always the 

Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5

[Kay Diederichs]

Ian Tickle schrieb:

Before you all go away and install the latest Intel compilers to fix
this bug - don't bother!  We just installed the latest version (ifort
11.3) and it has the same bug!  We plan to file a bug report with Intel.



Ian,

I just checked my older versions of ifort:  ifort 11.0.081 (January 
2009) indeed shows the bug.


I also tried 11.1.056 and that (as the latest 11.1.059; see my last 
email) does not show the bug. So it was fixed sometime in the 11.1 series.


Which "11.3" do you mean - not even 11.2 is announced?

best,

Kay
--
Kay Diederichshttp://strucbio.biologie.uni-konstanz.de
email: kay.diederi...@uni-konstanz.deTel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

This e-mail is digitally signed. If your e-mail client does not have the
necessary capabilities, just ignore the attached signature "smime.p7s".



smime.p7s
Description: S/MIME Cryptographic Signature

[ccp4bb] Map averaging question

[Simon Kolstoe]

Hi,

 

I have 20 identical monomers in my asu of a 2.5A structure. We have
previously model built all twenty monomers and used strict NCS in the
refinement, however I would like to compare this with the maps generated by
building one monomer into an averaged map and then replicating it nineteen
times for the refinement. On a previous structure with just two monomers I
did this to good effect using coot to make my average map and then pymol to
replicate the second monomer, however with twenty monomers things are a bit
more complicated. So:

 

1.   Can the map averaging function in coot cope with averaging across
twenty monomers or is there another better program to use?

2.   What program can I use to generate the nineteen NCS symmetry
operators and then apply them to the monomer I am building? I'm guessing
I'll need a script to do this - is there a webpage/tutorial that explains
how to do what I imagine must be a fairly common procedure?

 

Thanks,

 

Simon 

Re: [ccp4bb] Map averaging question

[Vellieux Frederic]

Simon Kolstoe wrote:


Hi,

I have 20 identical monomers in my asu of a 2.5A structure. We have 
previously model built all twenty monomers and used strict NCS in the 
refinement, however I would like to compare this with the maps 
generated by building one monomer into an averaged map and then 
replicating it nineteen times for the refinement. On a previous 
structure with just two monomers I did this to good effect using coot 
to make my average map and then pymol to replicate the second monomer, 
however with twenty monomers things are a bit more complicated. So:


1. Can the map averaging function in coot cope with averaging across 
twenty monomers or is there another better program to use?


2. What program can I use to generate the nineteen NCS symmetry 
operators and then apply them to the monomer I am building? I’m 
guessing I’ll need a script to do this - is there a webpage/tutorial 
that explains how to do what I imagine must be a fairly common procedure?


Thanks,

Simon


Hi Simon,

NCS symmetry operators:

It all depends on the averaging program you want to use. For dm, I've 
used superpose (in ccp4i). For DEMON/ANGEL, I use the program SUPPOS 
(provides matrices and vectors in the correct format).


Fred.

Re: [ccp4bb] Map averaging question

[Kevin Cowtan]

Simon Kolstoe wrote:
1.   Can the map averaging function in coot cope with averaging 
across twenty monomers


Yup. Just tries it with 1c9s (22-fold ncs)
The 'all' button is handy for turning off the 19 maps you aren't 
interested in, then turning on the one you are.

The averaged density will appear over the A chain.


or is there another better program to use?


:)

2.   What program can I use to generate the nineteen NCS symmetry 
operators and then apply them to the monomer I am building? I’m guessing 
I’ll need a script to do this - is there a webpage/tutorial that 
explains how to do what I imagine must be a fairly common procedure?


Coot'll do it all for you - no script or matrices required.

Extensions/NCS/Copy NCS chain.

Kevin


p.s. Coot 0.6 out today!!!

[ccp4bb] Post-Doctroal position

[santiago ramon]

An opening for a Post-doctoral position is available starting January 
15th in the Structural Basis of Genome Integrity Group at the Spanish 
National Cancer Research Centre in Madrid (CNIO).


The ideal candidate should have a PhD in structural biology, 
biochemistry or a related field and should have experience in 
molecular biology, protein expression and purification. Additional 
experience in macromolecular X-ray crystallography and/or 
single-particle electron microscopy is highly desirable. Experience 
with protein expression in eukaryotic systems is an advantage. 
Fluency in English required.


The research focuses on structural and functional aspects of genome 
integrity, with particular emphasis on employing X-ray 
crystallography and single-particle electron microscopy to elucidate 
the structures and understand the function of large macromolecular 
complexes involved in DNA recombination and repair.


The candidate will work with a team of highly motivated structural 
biologists and biochemists and collaborate with cell biology and 
computational groups at the CNIO. The Structural Basis of Genome 
Integrity Group is a newly established research group led by Dr. 
Santiago Ramon-Maiques who recently moved to the CNIO from the 
Institute of Biomedicine of Valencia, and previously worked in the 
group of Dr. Wei Yang at the National Institutes of Health, in 
Bethesda.


We offer: 
o	An appointment for a period of one year with the possibility 
of extension up to five years.

o   A competitive salary and an attractive benefits package.
o	Access to state-of-the-art facilities for X-ray 
crystallography and electron microscopy.
o	The opportunity to be part of a European Cancer Research 
Centre of excellence that successfully combines basic and applied 
research.


Applications can be sent at any time, preferably before 1st of 
January 2010. Applicants should submit a CV, a statement of research 
interests, and the names and contact information of two references to 
Santiago Ramon-Maiques (sra...@ibv.csic.es). All enquiries and 
applications will be treated confidentially.

Re: [ccp4bb] Minimum hardware requirement of Mac OSX for CCP4

[William G. Scott]

Hi Sergei:

No.  That is the real beauty of it.  It is completely passive.  In  
fact I am using it now just as a regular display hooked into my  
laptop. It comes with a pair of glasses that are essentially identical  
to the ones they give away in 3D movie theaters.  You start up the  
program, pop on the glasses, and you have stereo.  No emitter or any  
other special hardware, and no special video card (my laptop doesn't  
even HAVE a separate video card).  I think the picture is as good as  
what I had with my $14K SGIs, but no headache from the flicker.


The latest versions of O, coot and pymol (in inverse chronological  
order) all work, and there are probably others.  It is operating- 
system independent as well.


There is a great description on Warren DeLano's PyMOL site:

http://pymol.org/zalman/

In the US at least you can get it for about $300.

As a "normal" monitor is is about 90% as good as an Apple LCD.

All the best,

Bill



William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott



On Oct 28, 2009, at 10:20 AM, Sergei Strelkov wrote:


Dear Bill,

please excuse my ignorance but
I have assumed that this Zalman thing
does require an emitter and stereoglasses
in addition, and hence I ask myself:
where do you hook up the emitter? (I thought
than it must be plugged into the graphics card).

Thank you,
Sergei







On Tue, Oct 27, 2009 at 02:13:48PM +0100, Dirk Kostrewa wrote:



I agree with Ronnie Berntsson and Roger Rowlett. The only thing
that you
can't do on those machines is to work with Coot in stereo 3D.
Currently,
you would need a MacPro and a special Nvidia Quadro graphics card
(and
stereo glasses & emitter) for that.



He could buy a Zalman 3d LCD and hook it up to the external video
port on
the iMac.  It works fine with Coot, PyMOL, Chimera, etc.




O also now works on OS X with the Zalman monitor. (Thank you,  
Alwyn!!!).


No special hardware -- it (and CCP4,etc) even works fine with my
wife's first-generation macbook and the mac mini.

I haven't managed yet to get ccp4 and friends working on the ipod.

Bill

[ccp4bb] Positions available in Membrane Protein Structural Biology

[Said Eshaghi (Vg Assoc Prof)]

The School of Biological Sciences at Nanyang Technological University in 
Singapore is seeking outstanding scientists for functional and structural 
studies of integral membrane proteins. The School hosts a number of research 
groups specialized in working with membrane proteins using methodologies 
including X-ray crystallography, NMR spectroscopy, Surface Plasmon Resonance 
and electrophysiology. The research groups have access to state-of-the-art 
instrumentations and robotics to facilitate high-throughput protein expression 
and purification, as well as further protein characterizations. The target 
proteins include membrane proteins from bacteria, viruses as well as human with 
high medical impact. The studies are performed on both individual proteins, but 
also include protein-protein interactions within important signalling and 
enzymatic pathways.

The positions are available at various levels including postdoctoral fellows, 
research associates and graduate students. The applicants must have relevant 
and strong background in at least one of the following areas, in order to be 
considered:

* Membrane protein expression and purification
* Protein complex analysis and characterizations
* Drug-screening and interaction studies
* High-throughput protein production
* Recombinant molecular biology
* Biophysics (SPR, ITC, AUC, etc)
* X-ray crystallography
* NMR spectroscopy
* Electrophysiology


The positions are initially for 2 years with the possibility of extension. 
Competitive salaries are offered based on individual merits. The applicants 
should state their interest and what kind of position they are applying for in 
a cover letter and send their applications, along with their CV and the name 
and contact information of three references, by 15 January 2010 to: 
position@gmail.com 

NB! Only applications sent to the above mentioned address will be considered. 
Direct reply to this email account WILL NOT be considered!

The research groups are headed by:
Professor Pär Norldund
Associate Professor Jaume Torres
Associate Professor Konstantin Pervushin
Associate Professor Julien Lescar
Associate Professor Said Eshaghi
Assistant Professor Tobias Cornvik

CONFIDENTIALITY: This email is intended solely for the person(s) named. The 
contents may be confidential and/or privileged. If you are not the intended 
recipient, please delete it, notify us, and do not copy or use it, nor disclose 
its contents. Thank you.

Towards A Sustainable Earth: Print Only When Necessary

[ccp4bb] Memory allocation error in phaser - Mac os

[Narayanan Ramasubbu]

Dear All:
How to increase the memory size (?) to avoid the following error?

***
* Information from CCP4Interface script
***
The program run with command: /sw/share/xtal/ccp4-6.1.1/bin/phaser
has failed with error message
phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error code=3)
phaser(1393) malloc: *** error: can't allocate region
phaser(1393) malloc: *** set a breakpoint in szone_error to debug
phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error code=3)
phaser(1393) malloc: *** error: can't allocate region
phaser(1393) malloc: *** set a breakpoint in szone_error to debug
***

Thanks
Subbu

Re: [ccp4bb] Memory allocation error in phaser - Mac os

[Vellieux Frederic]

Hi Subbu,

Vaguely rings a bell. From years ago.

Try the command "limit" in tcsh or csh (I think it's ulimit in bash, 
don't use bash myself).

[Mac OS X is a Unix system (BSD) so it should be similar if not identical].

I get here on a Linux box:

limit (followed by carriage return)
cputime  unlimited
filesize unlimited
datasize unlimited
stacksizeunlimited
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 32 kbytes
maxproc  32736

and make sure that memoryuse is unlimited

You add a line in your .cshrc or .tcshrc file:

limit memoryuse unlimited

Of course this will apply if the problem is due to your system not allocating 
enough
memory for the process.
If it's something else, I wouldn't know.

HTH,

Fred.

Narayanan Ramasubbu wrote:

Dear All:
How to increase the memory size (?) to avoid the following error?

*** 


* Information from CCP4Interface script
*** 


The program run with command: /sw/share/xtal/ccp4-6.1.1/bin/phaser
has failed with error message
phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error 
code=3)

phaser(1393) malloc: *** error: can't allocate region
phaser(1393) malloc: *** set a breakpoint in szone_error to debug
phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error 
code=3)

phaser(1393) malloc: *** error: can't allocate region
phaser(1393) malloc: *** set a breakpoint in szone_error to debug
*** 



Thanks
Subbu

Re: [ccp4bb] How to reduce free-R factor

[Lionel Mourey]

Lionel Mourey
Institut de Pharmacologie et de Biologie Structurale
CNRS - Université de Toulouse
205 route de Narbonne
31077 Toulouse
France
Tél : 05 61 17 54 36
Mobile : 06 73 50 95 51
Fax : 05 61 17 59 94
E-mail : lionel dot mourey at ipbs dot fr

- Message d'origine -
De: Pankaj Chauhan 
Env: vendredi 4 décembre 2009 06:07
À: CCP4BB@JISCMAIL.AC.UK
Objet: [ccp4bb] How to reduce free-R factor



[Le message original intégral n'est pas inclus]

Re: [ccp4bb] PLEASE I NEED YOUR HELP.

[Sanishvili, Ruslan]

Best story I've heard on scamming the scammers appeared on BBC some
years ago. Fortunately, it was easy to find it. Take a look at
http://news.bbc.co.uk/2/hi/africa/3887493.stm

Enjoy,
Nukri

Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
David Briggs
Sent: Friday, December 04, 2009 2:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PLEASE I NEED YOUR HELP.

Given he "is so intoxicated to explain" I suggest that more slightly
more restrained refinement might be in order

Forward Fee 419 scam FAIL.

He didn't even offer me the sum of $100,000,000 (ONE HUNDRED MILLION
US DOLLAR) as a sweetener to the deal...

I really don't see the motivation in sending this guy the cash - still
- we could have a whip 'round at ccp4 workshop in Jan?

(A Physics pal of mine had more fun baiting FF419ers -
http://www-zeus.desy.de/~lightwd/ff419.html )

D

2009/12/4 Bernhard Rupp :
> Try unrestrained refinement first.
>
> BR
>
>
>
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Ming
> Zhou
> Sent: Friday, December 04, 2009 12:24 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [Bulk] [ccp4bb] PLEASE I NEED YOUR HELP.
>
>
>
> Dear,
>
> How are you today? May this emergency appeal finds you well,i am sorry
i do
> not inform you about my travel to Africa for a program. The program is
> taking place in three major Countries in Africa which includes
Ghana,Nigeria
> and South Africa. It has been a very sad and bad moment for me that
the
> condition i found myself is so intoxicated to explain.I am stranded in
> Nigeria because I forgot my little bag in a taxi where my Atm card,all
the
> money i have with me and some important documents are,i am so
confussed
> right now that i do not know what to do or where to go.Please i need
your
> urgent help to send some money to me so that i could be able to come
back
> home.
>
> Please i need the sum of $1,500USD as a loan to enable me sort-out
myself
> and confirm my Basic Travelling Allowance fees back home,but if you
cannot
> come up with all the requested amount due to the short notice, kindly
go
> ahead and send me any amount you can and email me the transfer
details. I
> will be so grateful to receive it and i promise to pay back the money
to you
> as soon as am back home.
>
> Kindly understand that i am in a very tight and horrible situation at
the
> moment that i could not even afford to take a good meal due to the
fact that
> i do not have a cent with me. I know you will never disappoint me and
that
> is why i have to contact you in this regard and please as you endeavor
to
> help me with this money i don't mean you should disclose my
predicament to
> anybody for my personal reasons till when am successfully back home.
> However,it is not compulsory you will send me the money but if my
situation
> and our good relationship touches you quickly proceed to any of the
western
> union money transfer local
> stores or post office around you and transfer me the money as soon as
you
> have received this emergency appeal.
>
> Western union money transfer is the most convenience and safety way to
> receive money here without any delay or problem.
>
> Below is my information where to send the money to me through western
union.
>
> Receivers Name: Ming Zhou
>
> Address: 45 Awolowo Road Ikoyi
> City: Lagos Island
> State: Lagos
> Zip Code:23401
>
> Country: Nigeria
>
> After you have sent the money, kindly email me the western union
transfer
> details such as:
>
> MTCN(Money transfer control number)
> Test Question: What is your year of birth?
> Answer: 1954
> Amount Needed: $1,500USD
>
> I will check my email soonest to pick up the western union transfer
details
> to enable me come back home with the next available flight and i will
need
> the transfer # MTCN (money transfer control number) as soon as
possible.
>
> Thanks,
> Ming
>
>
>
> 
>
> Chat with Messenger straight from your Hotmail inbox. Check it out



-- 

Science knows it doesn't know everything...otherwise it would stop.
 - Dara O'Briain

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
Skype: DocDCB

[ccp4bb] Postdoctoral position at the Goethe University Frankfurt- Institute of Biochemistry

[pos]

Post-doc Position at the Institute of Biochemistry at the Goethe University
Frankfurt, Germany

 

I am looking for an experienced crystallographer at the post-doctoral level
with interest to work on structures of membrane transport machineries, in
particular multidrug efflux proteins.

The lab is well-equipped including robotics to facilitate overproduction and
crystallization of membrane proteins and is embedded in the Cluster of
Excellence Frankfurt "Macromolecular Complexes" ( 
www.cef-mc.de).

The Institute of Biochemistry is located in the Biocenter on a young and
vibrant campus at the outskirts, yet near to the city of Frankfurt. 

 

For more information, please visit the web page:

http://www.biochem.uni-frankfurt.de/index.php?id=7

 

Interested candidates can send their CV (closing date 04.01.2010) to:
 p...@em.uni-frankfurt.de

 

 



Klaas Martinus Pos, Ph.D.

Professor of Membrane Transport Machineries

Cluster of Excellence Frankfurt - Macromolecular Complexes

Institute of Biochemistry

Goethe-University Frankfurt am Main

Max-von-Laue-Str. 9

D-60438 Frankfurt am Main

Germany

Tel: +49-69-798 29251

Fax: +49-69-798 29201

E-Mail:   p...@em.uni-frankfurt.de

Website:  
http://www.biochem.uni-frankfurt.de/index.php?id=7


http://www.sfb807.de/index.php?id=pos



 

Re: [ccp4bb] Refining residues as rigid bodies

[Pavel Afonine]

You can do it in phenix.refine. The prototype is:


for trial in trials:
 phenix.refine model.pdb data.mtz main.random_seed=random_value 
modify_start_model.adp.shake=true output.prefix=str(random_value)


where each refinement will start with the original B-factors that are 
shaken by a certain value.


Pavel.

PS> You can use phenix.pdbtools to do any manipulations on your model, 
such as shaking, setting, shifting of coordinates, b-factors, 
occupancies, etc.




On 12/3/09 4:05 AM, MARTYN SYMMONS wrote:
Discussing with Fred Vellieux offlist I suggested the following: would 
it be useful to have a sort of 'simulated annealing' of the B-factor 
values? - in refinement I often try resetting them to higher values 
(Moleman has a function for this I think) and then see which ones 
refine back down nicely - but it would be good to have some sort of 
randomization method - that would be a test of how much the values are 
inherited from the modelling early on - say from the MR probe model 
for example. 

We could do multiple B-factor refinements with different starting 
kicks to the values and look for the best final Rfree or some measure 
of map quality?


Martyn

Martyn F. Symmons
Cambridge
'Chan fhiosrach mur feòraich.' Gaelic proverb - Nothing asked, nothing 
learned.


 





*From:* Pavel Afonine 
*To:* CCP4BB@JISCMAIL.AC.UK
*Sent:* Wednesday, 2 December, 2009 22:52:45
*Subject:* Re: [ccp4bb] Refining residues as rigid bodies

Hi,

you can do similar thing (that is resulting in similar outcome) in 
phenix.refine by increasing the weight on ADP restraints term. 
Example: increase "wu" or decrease "wxu_scale". Although I believe a 
regular refinement of individual isotropic ADPs should normally work 
just fine at 3A resolution in phenix.refine.


Pavel.


On 12/1/09 11:18 PM, Frederic VELLIEUX wrote:

If the problem is B-factor refinement, you can do that easily at low resolution 
with CNS. You just give tight restraints.

You modify the file bindividual.inp

This section:
{* target sigma values for restrained B-factor refinement *}

{* mainchain bonds *}
{===>} bsig_main=1.5;
{* mainchain angles *}
{===>} asig_main=2.0;

{* sidechain bonds *}
{===>} bsig_side=2.0;
{* sidechain angles *}
{===>} asig_side=2.5;

I cannot remember in which direction the values have to go. I think up. I have 
done this with a very low resolution structures (4.5 A?) a few years ago, you 
get smoothly varying B values, very tightly restrained. I do not think we 
published that structure, we obtained a higher resolution structure later (I 
don't think the referees would have been very happy seeing B factor refinement 
at low resolution). But it worked.

Fred.

  

Message du 01/12/09 23:51
De : "Jason C Porta" 
A : CCP4BB@JISCMAIL.AC.UK
Copie à : 
Objet : Re: [ccp4bb] Refining residues as rigid bodies



Basically my reasoning for doing this is a low data-to-parameter ratio, which 
makes B-factor refinement unfeasible. So far I have had nice results with 
breaking the complex into rigid subdomains. So i was basically just thinking of 
a way I could refine the structure best, without using too many parameters.


I see now how this can be done in Phenix. I will give it a try.

Thanks for all of your suggestions!
  

[ccp4bb] Structural Biologist - permanent position in Central London

[Andrew Turnbull]

Structural Biologist - permanent position

Central London, UK

 

Cancer Research Technology (CRT) is a specialist oncology company which
advances discoveries arising from Cancer Research UK and other
prestigious oncology focused organizations into potential therapies for
the benefit of cancer patients.

 

CRT is seeking to recruit a highly motivated protein scientist /
structural biologist to join our X-ray structure determination team.
The team has access to state-of-the-art data collection and
crystallization facilities within the School of Crystallography,
Birkbeck College, London and is adjacent to CRT's Discovery Laboratories
within the Wolfson Institute of Biomedical Research, University College
London.

 

The successful candidate should have experience in one or more of the
following areas:

 

- Production and characterization of crystallization-grade protein for
structural analysis

- Crystallization screening and optimization of protein-ligand complexes

- X-ray data collection and structure determination

 

You should ideally be qualified to PhD level or equivalent. In addition,
you will possess excellent communication and organisation skills, and
will be able to contribute positively to interactive collaborations
within CRT, Cancer Research UK laboratories and other external
organisations.  Previous involvement in projects relating to oncology
and experience within a pharmaceutical environment would be desirable.

 

This is a permanent position with significant opportunity to influence
the development of new cancer therapeutics and will suit a highly
talented individual with strong interpersonal skills.

 

Please note that applications will only be accepted from candidates who
have proof of their right to work in the U.K.

 

To apply, please send a copy of your CV and a covering letter, quoting
the reference number XR1209, to the Head of Medicinal Chemistry by email
to crtrecruitm...@cancertechnology.com
 

 

  

No Agencies

Closing Date: 8th January 2010

CRT is an equal opportunities employer

 

 

 

Andrew Turnbull, PhD

Structural Biologist

 

Cancer Research Technology Ltd

Birkbeck College

University of London

Malet Street

London

WC1E 7HX

UK

 

 

Tel:  +44 (0)20 7631 6837
Fax: +44 (0)20 7631 6803 

 

 


This communication is from Cancer Research Technology Limited. Our website is 
at www.cancertechnology.com. We are a company registered in England & Wales 
under number 1626049 and wholly owned by Cancer Research UK (registered charity 
no. 1089464). Our registered address is Sardinia House, Sardinia Street, London 
WC2A 3NL England. Our central telephone number is +44 (0) 20 7269 3640.

This communication and any attachments contain information which is 
confidential and may also be privileged.   It is for the exclusive use of the 
intended recipient(s).  If you are not the intended recipient(s) please note 
that any form of disclosure, distribution, copying or use of this communication 
or the information in it or in any attachments is strictly prohibited and may 
be unlawful.  If you have received this communication in error, please notify 
the sender and delete the email and destroy any copies of it.

E-mail communications cannot be guaranteed to be secure or error free, as 
information could be intercepted, corrupted, amended, lost, destroyed, arrive 
late or incomplete, or contain viruses.  We do not accept liability for any 
such matters or their consequences.  Anyone who communicates with Cancer 
Research Technology Limited by e-mail is taken to accept the risks in doing so.
 
The views, opinions, and judgements expressed in this message are solely those 
of the author, and are neither given nor endorsed by Cancer Research Technology 
Limited

[ccp4bb] postdoc position in Cambridge

[Matthew Higgins]

A Medical Research Council funded post doctoral position is available to 
work with Dr Matt Higgins in the Cambridge University Department of 
Biochemistry on the structural biology and biochemistry of malarial cell 
surface proteins. This will involve the production and characterisation of 
malarial proteins, the development of interaction assays and structural 
analysis by protein crystallography and nuclear magnetic resonance 
spectroscopy. Experience in NMR and/or crystallography would be of great 
benefit. This post will be available for up to 36 months in the first 
instance and will start early in 2010.


Applications should include a covering letter describing relevant research
experience to date, a CV, completed PD18 form (Part 1 and 3) (The form PD 
18 can
be downloaded from 
http://www.admin.cam.ac.uk/offices/personnel/forms/pd18) and

the names and addresses of two referees. These should be sent quoting the
reference PH06012 by email by 18th December 2009 to j...@bioc.cam.ac.uk or 
post to The Personnel Secretary, Department of Biochemistry, Building O, 
Downing Site, Tennis

Court Road, Cambridge, UK, CB2 1QW.

* Limit of tenure: 36 months

[ccp4bb] LG announces 3D display

[David J. Schuller]

http://www.pcworld.com/article/183644/lg_announces_3d_high_definition_lcd_displays.html

"LG Announces 3D High Definition LCD Displays"

23", "full HD" (which I think means 1920 x 1080)
No mention of connectors or ports,
No mention of compatibility with existing products (e.g. nVidia 3D
Vision)
"No target release date was announced," and no price mentioned.

In short, a rather useless article. But tantalizing.


-- 
===
You can't possibly be a scientist if you mind people
thinking that you're a fool. - Wonko the Sane
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

[ccp4bb] Electron density improvement with resolution graphic

[Brad Bennett]

Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6 to
3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
the ability to model side chains of alpha helices at higher resolutions and
the other a simpler graphic of a tyrosine aromatic ring showing the electron
density hole in the middle of the ring once near atomic resolution maps are
obtained. Does anyone have, in their teaching notes or a textbook or
presentation, a graphic which displays this? I need it for a talk this
weekend and Google searches have come up blank. If all else fails, I can
generate it myself...(lazy sigh)

Thanks in advance-
Brad

Re: [ccp4bb] Electron density improvement with resolution graphic

[Jim Fairman]

You can find one here on the Cambridge X-ray crystallography course website:
 http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html

On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett wrote:

> Hi all-
> I recall seeing a long time ago a figure which showed the progressive
> improvement of electron density as one increases resolution, say from 6 to
> 3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
> the ability to model side chains of alpha helices at higher resolutions and
> the other a simpler graphic of a tyrosine aromatic ring showing the electron
> density hole in the middle of the ring once near atomic resolution maps are
> obtained. Does anyone have, in their teaching notes or a textbook or
> presentation, a graphic which displays this? I need it for a talk this
> weekend and Google searches have come up blank. If all else fails, I can
> generate it myself...(lazy sigh)
>
> Thanks in advance-
> Brad
>



-- 
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Electron density improvement with resolution graphic

[Jonathan Winger]

James Holton has a great little movie showing how electron density  
changes with decreasing resolution:  http://ucxray.berkeley.edu/~jamesh/movies/resolution.mpeg


Jon

On Dec 4, 2009, at 5:37 PM, Jim Fairman wrote:

You can find one here on the Cambridge X-ray crystallography course  
website:  http://www-structmed.cimr.cam.ac.uk/Course/Fitting/fittingtalk.html


On Fri, Dec 4, 2009 at 8:25 PM, Brad Bennett  
 wrote:

Hi all-
I recall seeing a long time ago a figure which showed the  
progressive improvement of electron density as one increases  
resolution, say from 6 to 3.5 to 2A. I believe I've seen two  
versions- one a larger scale pic showing the ability to model side  
chains of alpha helices at higher resolutions and the other a  
simpler graphic of a tyrosine aromatic ring showing the electron  
density hole in the middle of the ring once near atomic resolution  
maps are obtained. Does anyone have, in their teaching notes or a  
textbook or presentation, a graphic which displays this? I need it  
for a talk this weekend and Google searches have come up blank. If  
all else fails, I can generate it myself...(lazy sigh)


Thanks in advance-
Brad



--
Jim Fairman, Ph D.
Post-Doctoral Fellow
National Institutes of Health - NIDDK
Cell: 1-865-748-8672
Lab: 1-301-594-9230
E-mail: fairman@gmail.com james.fair...@nih.gov

Re: [ccp4bb] Electron density improvement with resolution graphic

[Bernhard Rupp]

This could be useful:

 

http://www.ruppweb.org/Xray/resolution.html

 

BR

 

From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Brad
Bennett
Sent: Friday, December 04, 2009 5:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Electron density improvement with resolution graphic

 

Hi all-
I recall seeing a long time ago a figure which showed the progressive
improvement of electron density as one increases resolution, say from 6 to
3.5 to 2A. I believe I've seen two versions- one a larger scale pic showing
the ability to model side chains of alpha helices at higher resolutions and
the other a simpler graphic of a tyrosine aromatic ring showing the electron
density hole in the middle of the ring once near atomic resolution maps are
obtained. Does anyone have, in their teaching notes or a textbook or
presentation, a graphic which displays this? I need it for a talk this
weekend and Google searches have come up blank. If all else fails, I can
generate it myself...(lazy sigh)

Thanks in advance-
Brad

[ccp4bb] Warren Obituary

[Bernhard Rupp]

To the Warren Memorial raffle donators: Thank you for your support
and please read the obituary accessible from my site.

http://www.ruppweb.org/Garland/Warren_raffle.htm

Thx,BR
-
Bernhard Rupp
US National Academy of Sciences Committee for Crystallography
001 (925) 209-7429
+43 (676) 571-0536
b...@qedlife.com
b...@ruppweb.org
http://www.ruppweb.org/
-
The hard part about playing chicken
is to know when to flinch
-