[ccp4bb] Position BIO0014 at Merck

[Stein, ND (Norman)]

Posted on behalf of Jim Kennedy at Merck.

Please apply via the web. Do not email replies to me.



Merck & Co. Inc., established in 1891, is a global research-driven
pharmaceutical company dedicated to putting patients first. 
 
Join us and experience our culture first-hand - one of strong ethics &
integrity, diversified experiences and a resounding passion for
improving human health. As part of our global team, you'll have the
opportunity to collaborate with talented and dedicated colleagues while
developing and expanding your career. 


Plans, executes, and provides strategic and scientific, technical and
administrative direction to highly complex research and development
projects in the field of Structural Biology.  Participates in program
design and discusses with the Vice President the implementation of
existing programs and advises him/her in the formulation and planning of
new research proposals.  Consults with the Vice President and advises
him/her on progress and results but otherwise proceeds with
independence.  Plays a key role in assuring the Company's continued
competitive position in Structural Biology.  Directs the work of a staff
of Senior Research Scientists across multiple sites and coordinates
activities throughout the Research Division as appropriate.
Particularly maintains close contact with those responsible for the
chemical synthesis and molecular modeling of compounds, development of
biochemical assays and high throughput screening

PhD in Biochemistry/Biophysics and 8+ years directly relevant experience
in biochemistry/biophysics research.  Candidates having directly
relevant experience in the drug development or providing similar
guidance on large scale project developmental and organizational
strategies in an academic setting preferred.

Consistently cited as a great place to work, we discover, develop,
manufacture and market a wide range of vaccines and medicines to address
unmet medical needs. Each of our employees is joined by an extraordinary
sense of purpose - bringing Merck's finest achievements to people around
the world.
 
We offer an excellent salary and an industry-ranked benefits program,
including tuition reimbursement, work-life balance initiatives and
developmental programs at all levels. Merck's retirement package
includes a pension plan and one of the best 401(k) plans in the nation.
To be considered for this position, please visit our career site at
www.merck.com/careers to create a profile and submit your resume for
requisition # BIO0014--. Merck is an equal opportunity employer, M/F/D/V
- proudly embracing diversity in all of its manifestations.
 
Our work is someone's hope. Join us.
Where patients come first - Merck
 
Search Firm Representatives 
 
Please Read Carefully: 
Merck is not accepting unsolicited assistance from search firms for this
employment opportunity. Please, no phone calls or emails. All resumes
submitted by search firms to any employee at Merck via-email, the
Internet or in any form and/or method without a valid written search
agreement in place for this position will be deemed the sole property of
Merck. No fee will be paid in the event the candidate is hired by Merck
as a result of the referral or through other means.

Re: [ccp4bb] Error with scala after combat

[Stein, ND (Norman)]

Hi Paola

This looks like a bug in Scala to me. The error message should only be printed 
out if the Relative Length Error exceeds 0.03 or the Angle error exceeds 0.5, 
whereas in your case both errors are zero. The relevant lines of code are a new 
addition in 6.0.2, which explains why you didn't have the problem with 6.0.1. 

If you can send me your Scala input files and details of the commands you used 
to run Scala (e.g command line script or com file from ccp4i), I will look into 
it further.

Norman

Norman Stein
CCP4
Daresbury Laboratory


-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
Paola Llinas
Sent: 26 April 2007 15:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Error with scala after combat


Hi everybody,

I process data with XDS, then I use Combat to import XDS ASCII data from
CORRECT in order to scale whit Scala but it doesn't work. The message error
is:

 * Wavelength and cell extracted from Batch headers, with rms variation:
* Wavelength:  1.008000  Cell: 91.71093.670   103.36090.000
90.00090.000
*   rms0.00   rms   0.000 0.000 0.000 0.000
0.000 0.000

ERROR: cell deviates too much from constraint 
Relative length error0.000  Angle error 0.00

  >>> Cell constraints:

 Scala:  *** Error in batch cell dimensions ***

I changed ccp4 version from 6.0.1 to 6.0.2 this week and I has this problem
only with 6.0.2 version. (I verified with files that worked with the older
version and I have the same error).
Does somebody know how can I fix this problem?
 
Thanks,
Paola

Re: [ccp4bb] unstable performance of refmac. any suggestions?

[Stein, ND (Norman)]

This looks like it might be a problem with opening temporary files on
Windows. Can you try replacing the refmac5.exe file in your $CCP4/bin
directory with the following:

ftp://ftp.ccp4.ac.uk/nds/windows/refmac5.exe

(It is probably worth keeping the old refmac5.exe under a different
name, just in case you want to revert to it). The modified executable
has two goes at opening a temporary file - if the ordinary Windows
method fails it will try another method. 

Norman

Norman Stein
CCP4
Daresbury Laboratory
Warrington
UK

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
fang sheng
Sent: 21 May 2007 19:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unstable performance of refmac. any suggestions?

Dear all,

I got some strange problems with the refmac. The whole ccp4 package was
newly downloaded to my laptop( window, off-line installation),including
ccp4mg and coot.

First, refmac randomly fails to complete task( as shown as below). 
"randomly" means it failed one time, but will run through and complete
the task the other time, I have got no control over it.

Second, Even after the tasks are finished and I see the output pdb and
map files, (so far I have run SFcheck and refmac,) it does not show"
finished" 
but "running". It only switches to "finished" after I shut down ccp4 and
restart.

Overally ccp4 works on my laptop, but the unstable performance is kind
of nagging me down. If you could offer your suggestions, I appreciate it
very much.

river-lake fang






---

CGMAT cycle number =  3


$TEXT:Warning: $$ comment $$
WARNING: CCPOPN Logical name C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1
has no associated file name $$
Open failed: Unit:   8, File: C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1 
(logical: C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1)
Refmac_5.2.0019:   Open failed: File: 
C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1
Times: User:   0.0s System:0.0s Elapsed: 0:58



***
* Information from CCP4Interface script

***
The program run with command: refmac5 XYZIN
"C:/Ccp4Temp/M5/new_m5_refmac1-coot-2.pdb" XYZOUT
"C:/Ccp4Temp/m5_14_4_pdb_1.tmp" HKLIN "C:/Ccp4Temp/M5/m5_3_1_.mtz"
HKLOUT "C:/Ccp4Temp/m5_14_6_mtz_1.tmp" LIBIN
"C:/Ccp4Temp/M5/m5_3_50_lib.cif" 
LIBOUT "C:/Ccp4Temp/M5/m5_14_lib.cif"
has failed with error message
Last system error message: Permission denied
Refmac_5.2.0019:   Open failed: File: 
C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1

***


#CCP4I TERMINATION STATUS 0 Last system error message: Permission denied

Refmac_5.2.0019:   Open failed: File: 
C:\Ccp4Temp\\refmac5_temp1.03096_REFSCR_1
#CCP4I TERMINATION TIME 20 May 2007  19:35:09 #CCP4I MESSAGE Task failed

_
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[ccp4bb] Postdoc at University of Texas Medical Branch

[Stein, ND (Norman)]

A post-doctoral position is available in Dr. Choi's laboratory at University of 
Texas Medical Branch for an X-ray crystallographer to study the structure and 
mechanism of viral replication complexes.  We use a combination of X-ray 
crystallography, cryo-electron microscopy, protein chemisty, and bioinformatics 
to determine the structure of viral replication machinery and to develop 
antiviral therapeutics.  Experience in all aspects of X-ray crystallography is 
required.
 
The X-ray crystallography resources include two X-ray area detector systems, a 
Phoenix crystallization robot, a Minstrel crystal imaging robot, and an 
Alchemist liquid handling robot.  The cryoEM facility includes two JOEL 200 keV 
cryoEM microscopes for high-resolution imaging work, FEI vitrobot, and a BSL-3 
room for viral and pathogen work.
 
Interested parties should send a CV and a list of 2-3 references to Dr. Kyung 
(Kay) Choi at 301 University Blvd, 6.614 Basic Science Building, Galveston, 
Texas 77555-0647, or via e-mail at [EMAIL PROTECTED]

Re: [ccp4bb] Pseudo-merohedral twinning and Molecular replacement

[Stein, ND (Norman)]

Yes, as the twinning fraction increases from 0 to 0.5, the cumulative
intensity distribution curve changes in a continuous way from untwinned
to perfectly twinned. The exact way in which it does this was calculated
by Rees (Acta A 36, 578 (1980)). Note that the variation is markedly
non-linear - if the plot is 'a little off' the untwinned plot the
twinning fraction may be rather more than you think, whereas if the plot
is 'a little off' the perfectly twinned plot, the twinning fraction will
still be very close to 0.5. 

The usual caveats apply - for example the shape of the cumulative
intensity distribution can be affected by pseudosymmetry as well as
twinning, so while the cumulative intensity distribution can indeed be
used to detect partial as well as perfect twinning, it is important to
consider other measures (e.g. moments) as well.

Norman 

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Bryan W. Lepore
Sent: 30 October 2007 17:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Pseudo-merohedral twinning and Molecular
replacement

On Mon, 29 Oct 2007, Iain Kerr wrote:
> The cumulative intensity distribution plot from crystal A did suggest 
> partial twinning (attached, doesn't look too bad though..)

notwithstanding other plots/statistics, does the cum. intens. dist. plot
(e.g. from truncate) really show a continuum from untwinned to twinned?

i.e, if the plots are 'overlapped in the middle', no question - twinned.

but, if the plots are 'a little off, but not in the middle' can this
result (alone) really mean the data is - as we want to say - partially
twinned?  i.e. is the plot robust only for the detection of perfect
twinning?

-bryan

[ccp4bb] PhD position in Graz

[Stein, ND (Norman)]

Job PhD position

Institution Institute of Biophysics and Nanosystems Research
Austrian Academy of Sciences, Graz

Topic   Molecular structure of apolipoproteins

Duration3 years

Salary  According to the salary schemes of the
Austrian FWF


Starting date   March 2008

Contact Univ.Doz.Dr. Ruth Prassl
([EMAIL PROTECTED])



Project summary

The aim of this project is to explore the three dimensional domain
structure of lipid-free apolipoprotein B100 (apo-B100), which is the
only protein moiety of the primary human cholesterol carrier low density
lipoprotein (LDL), and of defined fragments thereof, as well as of avian
apo-VLDL-II, which is the most effective endogeneous inhibitor of the
important enzyme lipoprotein lipase known. 

Detailed information on www.fwf.ac.at  project-database /project number
P20455.

Job description

We are looking for a highly motivated student to meet the challenge to
solve the structure of human apolipoproteins and to tackle a demanding
but fascinating topic. Focus of work is on protein purification,
biophysical characterisation, crystallisation, low resolution structure
determination by small angle X-ray scattering and X-ray protein
crystallography.


Requirements

The candidate must hold a MSc degree and should have a sound background
in biochemistry, laboratory experience, computer skills and should be
conversant with concepts of lipoproteins and/or lipid membranes. 

Re: [ccp4bb] Molrep fails to run

[Stein, ND (Norman)]

Dear Xishan
 
Can you tell me what version of CCP4 you are running and on which
platform? Have you been able to run other programs through ccp4i
successfully?
Does the molrep job fail immediately or does it produce any output
before failing? If the latter, it would be very useful to see all the
output.
 
Norman Stein
CCP4 



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Mike Xishan
Sent: 25 February 2008 11:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molrep fails to run


Dear all
sorry if this query has already been asked. Whenever, I run a job for
molecular replacement in Molrep program using ccp4i, it fails to run and
shows the following error.
Child killed: segementation violation
 
I would appreciate for suggestions to fix this eror.
 
xishan

Re: [ccp4bb] SC program in CCP4 - No radius found for residue G atom P

[Stein, ND (Norman)]

Hi Rosemary
 
SC has stopped because P is not in its list of atomic radii. This list
is located at
 
$CCP4/lib/data/sc_radii.lib
 
You will need to edit this file to add a value for P ( and possibly some
of the other atoms in your RNA fragment). The format is fairly
self-explanatory, with asterisks being used for wildcards. Alternatively
you can use your own dictionary of atomic radii, and specify its
location using the SCRADII command
 
e.g. SC XYZIN .pdb SCRADII mydictionary.lib
 
Norman Stein
CCP4
Daresbury Laboratory



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Rosemary Harrison
Sent: 27 February 2008 06:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SC program in CCP4 - No radius found for residue G
atom P


Hi, 

I have been trying to run SC on a pdb file with an RNA fragment.
I get the answer below.  There appears to be a problem with the P in the
RNA backbone.

Has anyone else had this problem and/or suggestions to fix it

Thanks in advance,
Rose Harrison


 Parameter values
 
 Dot density  :15.00 per square Angstrom
 Interface separation : 8.00 Angstroms
 Trim width   : 1.50 Angstroms
 Probe radius : 1.70 Angstroms
 Weight factor: 0.50 per square Angstrom
 No radius found for
 Residue G   Atom P   

 SC:   S/r assign_r: no radius for residue/atom
 SC:   S/r assign_r: no radius for residue/atom

Re: [ccp4bb] Revise

[Stein, ND (Norman)]

Dear Sajid

It sound as though you are running Revise through CCP4i. If you do this,
the first thing you normally select is your mtz file. The buttons
labelled 'FPH+1' and 'FPH-1' in the gui then default to the same thing.
You need to click on at least one of these buttons and select a
different label. You should then no longer get duplicate column labels
in your output file.

Norman

Norman Stein
CCP4
Daresbury Laboratory
Warrington
WA4 4AD
UK  

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
sajid akthar
Sent: 15 April 2008 19:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Revise

Dear All

I'm trying to locate heavy atoms. SO I started with Revise from CCP4.
But it fails with error message

#CCP4I TERMINATION STATUS 0 " REVISE:  Duplicate column labels in output
file"
#CCP4I TERMINATION TIME 15 Apr 2008  14:50:34 #CCP4I MESSAGE Task failed


Any help pls

Thanks
Sajid


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[ccp4bb] X-ray crystallographer position, Zaragoza

[Stein, ND (Norman)]

Call for the Recruitment of a Researcher in the Area of Structural
Biology: Resolution of Three-dimensional Structures of Biological
Macromolecules by X-ray Crystallography

The Institute for Biocomputation and Physics of Complex Systems (BIFI), 
University of Zaragoza,
(Spain), looks for a researcher with proved experience in the technique of 
X-ray crystallography
applied to biological macromolecules. The candidate has to be interested in 
competing for one of the
positions summoned by the government of Aragon (Aragon I+D) for recruitment of 
researchers.

The BIFI institute will support the application of candidates with credited 
experience in:
1.- Methods in the production of monocrystals of proteins and nucleic acids.
2.- X-ray diffraction collection in conventional systems in laboratory and 
using synchrotron facilities.
3.- Handling of software packages for the resolution of three-dimensional 
structures from X-ray data
(data processing, phases determination, molecular replacement, refinement, 
modelling, model
validation ...)
4.- Any further relevant experience will be also considered an asset: capacity 
in the application for
public and private funds, experience with crystallisation robots and in the 
resolution of proteinprotein
and protein:ligand complex structures, as well as knowledge in cloning, 
expression and
protein purification.

It offers:
1.- An scientific work environment. The working place will be the BIFI 
laboratories, located in a new
building, in the "Rio Ebro" Campus, University of Zaragoza
2.-A recently acquired X-ray diffractometer. This equipment is provided with 
all necessary systems
and devices for x-ray diffraction of macromolecules.
3.- Linux work stations including all software necessary for structure 
resolution from X-ray diffraction
data.
4.- Crystallization laboratories with controlled temperature (4 and 18 ºC) and 
with all material
required for crystal growing and visualizing.
5.- Preparative laboratories for production and manipulation of proteins and 
nucleic acids.
6.- Permanent collaborations with the established research lines of the 
Structural Biology section of
BIFI; proteins stability and folding, protein-protein, protein-DNA and 
protein-ligand interactions.

It is expected that the selected candidate will:
1- Develop his/her own projects
2- Collaborates with the ongoing research lines at BIFI
3- Participates in setting up the protein crystallization and X-ray diffraction 
laboratories in the new
BIFI building

Candidates interested please send an email with CV (including list of 
publications) plus three
reference letters before 15th July of 2008 to:

Dra. Marta Martínez: [EMAIL PROTECTED]; Phone: +34976762841
Dra. Milagros Medina: [EMAIL PROTECTED]; Phone: +34976762476
Dr. Javier Sancho: [EMAIL PROTECTED]; Phone: +34976761286

If you wish further information please contact us or check our web page 
http://bifi.unizar.es


Call for the recruitment of researchers. Gobierno de Aragón

Aragon I+D has launched a new call for applications to fill 8 research 
positions in different
areas. The call for applications is open to any candidate that fills the 
requirements of academic
background as well as a significant postdoctoral experience, irrespective of 
nationality.
However, only very strong candidates with excellent leadership capabilities and 
an outstanding
research record will be considered. Applications must be downloaded from this 
site and
submitted by email to [EMAIL PROTECTED] before 14.00 h (GMT) of September 26th 
2008.
(Please see the requirements below)

Characteristics of the positions:

8 full-time positions will be offered, and it is generally expected that the 
successful candidates will become permanent staff of Aragon I+D,
and will work along with teams from university or other research centres in 
Aragon in the premises of these cooperating institutions (please
see the institutions below). Arago I+D researchers are expected to make a 
substantial contribution to their own areas of research and be
active members of the Aragon science-technology system.The performance of the 
researchers will be periodically subjected to external
evaluation.

Salaries will be in line with those paid at Aragon university and will be 
commensurate with the experience and potential of the candidates
and will therefore be negotiated individually. Start-up research packages may 
also be arranged in certain cases.
For foreign nationals, Aragon I+D will assist with visa and work permit 
procedures. The contract will be effective only when the selected
candidates are able to work legally in Spain.

The selection of applicants will take into consideration the objectives of the 
Aragon Government's Research and Innovation Plan, which
prioritizes certain areas (see the list below). However, applications from 
outstanding researchers in any area of knowledge may also be
considered.

Requisites for the candidates:

The candidates are expected to have a minimum of 6 yea

[ccp4bb] Post-doctoral and PhD position : Structure-function of chemokine receptors

[Stein, ND (Norman)]

Post-doctoral and PhD position :
Structure-function of chemokine receptors



Corinne Vivès, Eva Pebay-Peyroula and Franck Fieschi, Institut de Biologie 
Structurale, UMR5075 CEA-CNRS-Univ. J.Fourier, 41, rue Jules Horowitz, F38027 
Grenoble cedex 1, FRANCE 
In collaboration with Jean-Luc Popot, C.N.R.S./Université Paris-7 UMR 7099, 
Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 
Paris, FRANCE


CXCR4 and CCR5 are chemokine receptors and belong to the 7 transmembrane 
G-Protein coupled receptor (GPCR) family. Besides their physiological 
functions, they have attracted the scientific community by their role in HIV 
internalization. So far the identification of HIV inhibitory molecules has been 
mainly empirical, as their rational design would request the structural 
characterization of the HIV co-receptors. Structural studies of membrane 
proteins are highly limited by the bottleneck of their production in quantities 
compatible with structural studies. In this context we have been involved in a 
collaboration to develop a method for the high level production of GPCRs in 
E.coli, taking CXCR4 and CCR5 as a working model. E.coli has proved to be an 
amazing machinery for protein recombinant expression but is not compatible with 
the functional expression of eukaryotic membrane proteins. To overcome the 
problem we address our proteins to inclusion bodies and are now able to produce 
mg quantities of purified receptors under denaturing conditions. Preliminary 
tests have already proven the feasibility of the protein refolding. 

We do provide two positions (one post-doctoral and one PhD) to work jointly on 
the refolding procedure optimisation using either classical detergent solutions 
or non-natural surfactants. A biochemical characterisation of the refolded 
proteins will be required (ligand binding capacity, stability) with the 
final goal to achieve structural investigations. We have also developed in 
parallel a functional expression system that does not allow expression yield 
compatible with structural research but that will enable structure/function 
studies.

The PhD position proposed requires a european student (except French) with a 
strong biochemistry and/or structural biology knowledge. The 3 year European 
funding could start before the end of 2008. For the post-doctoral project, we 
are looking for a graduate student with strong biochemical background, specific 
skills related to membrane protein biochemistry would be appreciated. A grant 
from the French National Research Agency will allow an 18 months funding and 
could start as soon as possible. The research will take place in one of the 
groups of the Membrane Protein Laboratory headed by Eva Pebay-Peyroula in the 
IBS (Structural Biology Institute) located within Grenoble scientific polygone 
ranked in the top european research centers. If you are interested, feel free 
to contact us to discuss the project to the following address. Do not hesitate 
to refer to our web sites.





[EMAIL PROTECTED]

http://www.ibs.fr/content/ibs_eng/home/

http://www.ibs.fr/content/ibs_eng/presentation/lab/lpm/

Re: [ccp4bb] problem about Chainsaw

[Stein, ND (Norman)]

Hi
 
This is a problem that occasionally cropped up if there were large gaps in the 
alignment between target and model.  It has been fixed in the ccp4-6.0.99d test 
release. You can either download and install the test release, or if you let me 
know what operating system you are using, I will try to create a binary for you.
 
Norman
 
Norman Stein
CCP4
Daresbury Laboratory 
Warrington
WA4 4AD



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Xiang Liu
Sent: 25 June 2008 03:45
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] problem about Chainsaw


Dear all,

I have used chainsaw for several times and no problem happened before yesterday.
When I used it last evening, the chainsaw couldn't run as usual. I checked the 
log file and saw the error message as follow " CHAINSAW:  Chainsaw is having 
trouble reconciling input pdb with sequence ". In fact, the pdb file I used for 
model was just being downloaded for PDB database.

So I wonder what happened or what I should do to manage this problem.
ps: To do the work by chainsaw manually is terrible .
Thank you for your attention.


Xiang Liu
the third year Ph.D candidate
lab of structural biology, college of life science
Peking University, Beijing, P.R.China
100871
Tel:86-10-62755714


   





雅虎邮箱，您的终生邮箱！  

Re: [ccp4bb] Missing space group in ?.mtz file

[Stein, ND (Norman)]

Dear Petr

In your $CCP4/src/dev_tools_ directory there is a small utility named
readmtz.cpp which I created for use in a situation like this. You will
need to compile it by typing

g++ -o readmtz readmtz.cpp

Then type

./readmtz .mtz

The data will be written out as an ascii file called output.txt. You can
read this back in using the CCP4 program F2MTZ, which allows you to
supply the spacegroup.

Norman

Norman Stein
CCP4
Daresbury Laboratory
  

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Petr Kolenko
Sent: 08 July 2008 09:54
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Missing space group in ?.mtz file

Dear colleagues,
I have a ?.mtz file from integration with missing info about the space
group in the SYMINFO. I tried to modify the file with combat and
mtzutils, but it always ends up in reading the original file with this
message:

 Failed to find spacegroup in SYMINFO!
 MTZUTILS:  Fatal error in ccp4spg_register_by_symops
 MTZUTILS:  Fatal error in ccp4spg_register_by_symops

Here is report from mtzdump:
 Failed to find spacegroup in SYMINFO!
 MTZDUMP:  Fatal error in ccp4spg_register_by_symops

I know the correct space group, but I do not know how to supply the .mtz
file. Any suggestion, please? Thanks for all of them.

Best Regards,
Petr

Petr Kolenko
[EMAIL PROTECTED]

Re: [ccp4bb] mtz library in windows

[Stein, ND (Norman)]

Dear Alex
 
The exact form taken by the external symbols depends on the compiler
settings. The Compaq Fortran 6.6 compiler defaulted to adding an @ to
the function name, followed by a number which was the sum of the sizes
in bytes of the function arguments. This practice was not followed in
later versions of the compiler, after the rights to it had been bought
by Intel. We currently use the Intel 10 compiler to build the suite. You
need to adjust your Project properties to get the external symbols
right. Go to
 
Project, Properties, Fortran, External Procedures
 
and try adjusting the Calling Convention entry. 'C, Reference' is
probably the one to use. (At least this is what you do with later
versions of the compiler. It's a few years since I last used CVF6.6 so
you might need to make minor modifications to these instructions. I
assume you are running through the gui. If you are running CVF 6.6 from
the command line, please get back to me and I'll try to dig out the
command line way of doing this).
 
Norman Stein
CCP4
 


From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Alex XIE
Sent: 01 October 2008 03:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mtz library in windows


Dear all,
 
I am using CCP4 mtz library and other libraries to develop a program.
Because
I am using a PC at home, I am actually using the CCP4 in windows.
 
However, when I link the mtz library(hence libccp4c.lib), it happens
that the
compiler complains
 
error LNK2001: unresolved external symbol [EMAIL PROTECTED]
 
and some other functions that should be in libccp4c not found. I checked
the project setting(I am using compaq visual fortran 6.6), I have
included
libccp4c, libccp4f in the library, and library path in
/link/input/Additional
Library Path, so I don't understand why the compiler still cannot
resolve
the functions.
 
Can anybody help, please? Your suggestion is greatly appreciated.
 
Alex

[ccp4bb] ccp4bb subscriber approval

[Stein, ND (Norman)]

Subscription requests to ccp4bb have to be manually approved by a member
of the CCP4 staff. Unfortunately we have been unable to access the
machine on which the requests are stored since Saturday 25th October,
when it was switched off to allow the power supply to the whole of the
Daresbury Laboratory to be changed. This situation is likely to persist
until Wednesday 5th November. 

In the meantime, please address any urgent requests to delete subscibers
or change subscription details, to the CCP4 helpdesk at [EMAIL PROTECTED]

Norman Stein
CCP4

Re: [ccp4bb] ccp4 6.0.99e test release -problems with xplot84driver on 64bit ubuntu

[Stein, ND (Norman)]

Hi Hari
 
Can you send me your yjchotmp_2_1.plt file and I will look into it.
 
Norman
 
Norman Stein
CCP4
Daresbury Laboratory



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
hari jayaram
Sent: 07 November 2008 21:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ccp4 6.0.99e test release -problems with xplot84driver
on 64bit ubuntu


Sorry for resending this message but I may have sent it to the wrong
address the first time


Hello ccp4-ers
I have been happily running ccp4-6.0.99e,  which I self compiled on an
Ubuntu 64bit ( Version 8.04) box

Things have been going smoothly till I noticed a segmentation fault when
I tried to get a postscript file using xplot84driver .
The binary run from  a shell and the ccp4i gui give the following error 

FROM SHELL
[EMAIL PROTECTED]:~/ccp4-6.0.99e/x-windows/XCCPJIFFY$ ./xplot84driver
~/yjchotmp/yjchotmp_2_1.plt 
Warning: Representation size 1 must match superclass's to override
useStringInPlace
Segmentation fault

FROM CCP4 GUI
[EMAIL PROTECTED]:~$ Warning: Representation size 1 must match superclass's
to override useStringInPlace

Any ideas on how to overcome this

I am attaching the Makefile I used to compile this xplot84driver binary
on my system
Thank you for your help 
Hari 



On Fri, Jul 25, 2008 at 11:54 AM, Martyn Winn <[EMAIL PROTECTED]> wrote:


Dear All

the latest test version is on the ccp4 ftp server.

ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-core-src.tar.gz<-
core ccp4, rapper, clipper
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-phaser-src.tar.gz  <-
cctbx and phaser
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-balbes_db.tar.gz   <-
balbes database only

There is also the dependency of PyXML if you want to run balbes
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-PyXML.tar.gz

for the first 3 tarballs unpack into the same directory, then
configure...make...make install.
For the PyXML, follow the instructions in the PyXML-0.8.4
directory.

Major changes:
refmac5.5 built by default.  This gives twinning and sad
refinement.
dbhandler. Many optimisations, so this should be much more
responsive.

For other updates see the CHANGES file.

Still to come:
downloads pages (under internal testing).
documentation updates (lots of)

Feedback to the usual locale ([EMAIL PROTECTED])

Thanks

Charles and the rest of us here at DL.


--

***
*
*
*   Dr. Martyn Winn
*
*
*
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD,
U.K.   *
*   Tel: +44 1925 603455E-mail: [EMAIL PROTECTED]
*
*   Fax: +44 1925 603825Skype name: martyn.winn
*
* URL: http://www.ccp4.ac.uk/martyn/
*

***

Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066

[Stein, ND (Norman)]

Just to add to that, Windows users can download a Refmac 5.5.0070 binary
from the CCP4 prerelease page.

www.ccp4.ac.uk/prerelease

Norman

Norman Stein
CCP4
Daresbury Laboratory


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Pavol Skubak
Sent: 19 December 2008 22:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac 5.5.063 vs. 5.5.066

The latest version with all the bugfixes will of course appear in
CCP4-6.1.1. Until then, the latest binaries and source codes are
available on the mentioned webpage.

Pavol

Re: [ccp4bb] Refmac5.scripts error -

[Stein, ND (Norman)]

Hi Jon

There's no point applying the patch; it should have been incorporated
into all versions of CCP4 subsequent to  5.0.2 already. The problem
seems to be that a spacegroup has not been set in your input mtz file. I
would try editing the file to set the spacegroup, using the SFTOOLS
program included in CCP4.

Norman 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jonathan Marvin Caruthers
Sent: 31 January 2009 00:08
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac5.scripts error -

All:


I'm trying to get the latest version of Refmac up and running - the one
bundled into ccp4 6.1.0 - and have come across an error I've never seen
before:

#CCP4I TERMINATION STATUS 0 Error from script
/usr/local/ccp4-6.1.0/ccp4-6.1.0/ccp4i/scripts/refmac5.script: can't
read "space_group": no such variable #CCP4I TERMINATION TIME 29 Jan 2009
18:23:02 #CCP4I TERMINATION OUTPUT_FILES
/home/caruthej/bo3/ccp4/bo3A_71_Unspecified.refmac.cif bo3A #CCP4I
MESSAGE Task failed

I found that this error is mentioned on the problems page for ccp4
version 5.0 - 5.0.2 and the suggested fix is to apply the following
patch:

ftp://ftp.ccp4.ac.uk/ccp4/5.0.2/patches/CCP4_utils-25Aug2004.tcl.diff

to the scripts directory.  


Does anyone know if the same patch can be used to fix this error for the
latest version of Refmac5 that's bundled into ccp4 6.1.0 as well as the
version that was available in 2004 when the patch was created?  Sorry
for the simplistic question, but I don't have permission to install or
modify programs on the system I'm using so I can't readily perform the
experiment and the IT guy wants to know if anybody has any experience
using this patch with the latest version of Refmac5 before he starts
monkeying around with it.


thanks,


Jon Caruthers
Stowell Lab
University of Colorado

Re: [ccp4bb] Problem with setting up ccp4 gui

[Stein, ND (Norman)]

Hi Jan

If they exist, could you please send me any of the .log files in the
following directory:

~/.CCP4/

In particular the file dbhandler.log. These should help to fix the
problem.

Thanks

Norman Stein
CCP4
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jan Jensen
Sent: 03 March 2009 17:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with setting up ccp4 gui

Hi all,
I have been struggling with installing the new CCP4 package. I run
RedHat Enterprise 4 and have previously used older packages with
success. After I untar and run ./install as root everything seems to
install just fine. When I run ccp4i -c to configure I think something
goes wrong or extensions get misdirected. If I try to run all the
scripts to test, they all seem to execute fine.
I have had luck starting the GUI as root or user but when you get to the
part where projekt directories are setup the GUI stops working and
cannot be restarted (showing the message below)

Error in startup script: wrong # args: should be "dbccp4i_open_project
project args"
while executing
"dbccp4i_open_project"
("eval" body line 1)
invoked from within
"eval dbccp4i_open_project $project $args"
(procedure "DbLoadFile" line 12)
invoked from within
"DbLoadFile $project"
(procedure "DbOpenDatabase" line 13)
invoked from within
"DbOpenDatabase $project"
(procedure "DbOpen" line 30)
invoked from within
"DbOpen -init"
(procedure "DbInitialise" line 19)
invoked from within
"DbInitialise"
(procedure "task" line 14)
invoked from within
"task"
("configure" arm line 6)
invoked from within
"switch  $system(RUN_MODE) \
  script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def
file

source [file join $env(CCP4I_..."
(file "/opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl" line 163)
invoked from within
"source [file join $env(CCP4I_TOP) bin ccp4i.tcl]"
(file "/opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i" line 5)


Can anyone help me?

Thanks,

Jan K Jensen, Pl-R, Ph.D. 
Post doctoral fellow at University of Illinois at Chicago (UIC)
Laboratory of Peter GW Gettins Department of Biochemistry and Molecular
Genetics MBRB Room 1260 900 S Ashland Chicago Il, 60607
Phone: 312 996 7664 or 773 574 9276 (mobile)
Email: j...@uic.edu
Homepage: http://www.epernicus.com/jkj


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Nadir T. Mrabet
Sent: Monday, February 16, 2009 12:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB protein strucutrues as screen saver


Hi,
You may want to have a look at
http://www.luminorum.com/html/luminorum_ltd___extras.html.
hth
Nadir

--

Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax:   +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr



Jayashankar wrote:
> Dear Scientists,
>
> It may be too much...
>
> But as a biophysics student I would like to appreciate and feel happy 
> to have pdb structures as my computers screen savers than to have some

> funny and fancy stuffs.
> And it may help me as a motivator to solve my own structures in
future
>
> I want to ask is there any existing script that grep strucutres one by

> one with one line definition of that structure.
>
>
>
>
> S.Jayashankar
> Research Student
> Institute for Biophysical Chemistry
> Hannover Medical School
> Germany.

Re: [ccp4bb] ccp4i / refmac issue

[Stein, ND (Norman)]

Hi Jan

Changes have been made to the Refmac interface in 6.1.1 which are not
backwardly compatible. This means that if you try to rerun an old refmac
job, it will give the error you see. The solution is to run a new refmac
job and fill in the input fields from scratch.

Norman Stein
CCP4 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jan Abendroth
Sent: 06 March 2009 06:41
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ccp4i / refmac issue

Hi all,
I keep on getting the following error message when I try to start a
refmac job through ccp4i with ccp4 version 6.1.1. This initially only
happened in a linux installation, now all of a sudden appeared in a osx
installation as well. The interface hangs when starting the job.  
It also occurs for files that refined w/o any problems before. Any ideas
what is going on here?

Thanks for any input.

Jan

~~~

Top level CCP4 directory is /usr/local/ccp4-6.1.1 Using CCP4 programs
from /usr/local/ccp4-6.1.1/bin can't set "ATOM(0)": variable isn't array
 while executing
"set [subst $root]([subst $indx0]) """
 (procedure "ExecuteScript" line 50)
 invoked from within
"ExecuteScript $system(SCRIPT)"
 ("script" arm line 8)
 invoked from within
"switch  $system(RUN_MODE) \
   script {

 source [file join $env(CCP4I_TOP) src execute.tcl]
 source [file join $env(CCP4I_TOP) src job_utils..."
 (file "/usr/local/ccp4-6.1.1/share/ccp4i/bin/ccp4ish.tcl" line 145)
 invoked from within
"source [file join $env(CCP4I_TOP) bin ccp4ish.tcl]"
 (file "/usr/local/bin/ccp4ish" line 12)

--
Jan Abendroth
deCODE biostructures
Seattle / Bainbridge Island WA, USA
work: JAbendroth_at_decode.is
home: Jan.Abendroth_at_gmail.com

Re: [ccp4bb] Refmac failed at the end of run

[Stein, ND (Norman)]

Hi Joe
 
The problem is that your dataset name contains colons, which Windows
does not like. This is probably because your original mtz file was
generated using scalepack2mtz or dtrek2mtz and you did not explicitly
set a dataset name, so that a default was chosen based on the date and
time and using colons as separators.  You can get round this by
switching off Data harvesting when you run Refmac, or by changing the
dataset name using CAD.
 
Norman
 
Norman Stein
CCP4
Daresbury Laboratory

 


From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
JOE CRYSTAL
Sent: 20 March 2009 17:33
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac failed at the end of run


Hi all, 

I am using refmac in ccp4i 6.1.1 (installed in windows). It runs well
when using automatic weight, but failed when using user-specified weight
(0.12 in this case). I attach the error message as follow. Your help is
very much appreciated. 



.. 
 18   0.2064   0.2348   0.846407628.   21897.0   0.0075  0.318
1.170  0.502   0.076 
 19   0.2065   0.2343   0.846407625.   21896.4   0.0075  0.318
1.169  0.501   0.076 
 20   0.2065   0.2347   0.846407629.   21897.3   0.0075  0.318
1.167  0.501   0.076 
$$ 

$TEXT:Warning: $$ comment $$ 
WARNING: CCPOPN Logical name
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac has no asso 
$$ 
Open failed: Unit:   9, File:
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac (logical:
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac) 
Refmac_5.5.0072:   Open failed: File:
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac
Times: User:   0.0s System:0.0s Elapsed:27:38  
 

*** 
* Information from CCP4Interface script 

*** 
The program run with command: refmac5 XYZIN
"C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/472cr8c10_v1-coot-4_refmac1.p
db" XYZOUT "C:/Ccp4Temp/47crc10_3_2_pdb_1.tmp" HKLIN
"C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/472cr8nsls_refmac1.mtz"
HKLOUT "C:/Ccp4Temp/47crc10_3_3_mtz_1.tmp" LIBIN
"C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/libcheck_C10.cif" TLSIN
"C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/472cr8c10_v1-coot-4_edit_tls1
_refmac1.tls" TLSOUT "C:/Ccp4Temp/47crc10_3_4_tls_1.tmp" LIBOUT
"C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/47crc10_3_lib.cif" 
has failed with error message 
Last system error message: Unknown error 
Refmac_5.5.0072:   Open failed: File:
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac

*** 


#CCP4I TERMINATION STATUS 0 Last system error message: Unknown error
Refmac_5.5.0072:   Open failed: File:
C:/Chen/Xtal/cvir/472cr8_c10/work2/refmac/DepositFiles/472cr8nsls/unknow
n211008:17:49:34.refmac
#CCP4I TERMINATION TIME 20 Mar 2009  13:23:28 
#CCP4I MESSAGE Task failed 






-- 
Best regards,

Joe

Re: [ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a dataset_name?

[Stein, ND (Norman)]

Hi Francis 

There is a fix for this on the CCP4 problems page:

http://www.ccp4.ac.uk/problems.php#6.1.1-ccp4i

(item 7).

Norman

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Francis E Reyes
Sent: 17 April 2009 18:55
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] In CCP4 6.1.1 import_scaled isn't reading a
dataset_name?

Despite setting a dataset name in the dialog box, i get the following in
the log file.



  $TEXT:Warning: $$ comment $$
  WARNING:  PROJECTNAME not assigned
  $$

  $TEXT:Warning: $$ comment $$
  WARNING:  CRYSTALNAME not assigned
  $$

  $TEXT:Warning: $$ comment $$
  WARNING:  DATASETNAME not assigned
  $$


Which ultimately fails in...


#CCP4I TERMINATION STATUS 0 Error from script /sw/share/xtal/
ccp4-6.1.1/ccp4i/scripts/import_scaled.script: can't read
"dataset_name": no such variable
#CCP4I TERMINATION TIME 17 Apr 2009  11:49:17 #CCP4I MESSAGE Task failed



Despite the fact that http://www.ccp4.ac.uk/dist/html/
scalepack2mtz.html says :

Specify the project, crystal and dataset names for the output MTZ file.
It is strongly recommended that this information is given.  
Otherwise, the default project, crystal and dataset names are "unknown",
"unknown" and "unknown" respectively (where  is the
date, with no spaces).


So there seems to be two broken things here.


Any ideas?

Thanks

FR

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

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] molrep can't find *_trfn_scr.crd

[Stein, ND (Norman)]

Hi Francis

This is a known problem. Molrep is prepending the path name twice to the
file name, which means that when it subsequently looks for the file, it
cannot find it. You can fix the problem by downloading the latest source
code version of molrep from Alexei's site:

http://www.ysbl.york.ac.uk/~alexei/molrep.html#installation

Alternatively you can pick up a Molrep 10.2.31 binary for Linux from

ftp://ftp.ccp4.ac.uk/nds/molrep_10.2.31/molrep  

Norman Stein
CCP4

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Francis E Reyes
Sent: 29 June 2009 18:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] molrep can't find *_trfn_scr.crd

When doing a multi-copy search, after the first rotation is done it
seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp
directory that it can't find just prior to doing the "first monomer
search".

Anyone have any ideas?
thanks

FR

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

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D
--
Scanned by iCritical.

[ccp4bb] Equipment

[Stein, ND (Norman)]

Posted on behalf of Wolfram Saenger:

X-ray equipment to give away

Since I am close to retirement, the equipment I have will be given away
at no cost except for transport. The equipment are two mar research
image plates, 345 and 250 mm diameter, the first running under PC, the
secondhas an interface for an SGI workstation.

Also available are two rotating anodes (FR591) from enraf Nonius, a CAD4
diffractometer, and a FAST detector, also from Enraf Nonius, several
precesion cameras from Enraf Nonius and STOE, goniometer heads fitting
to all these equipments, etc., etc.

Please contact Prof. Wolfram Saenger, Tel. +49-30-83853412,
Fax +49-30-83856702, e-mail: saen...@chemie.fu-berlin.de

Prof. Dr. Wolfram Saenger
Institut fuer Kristallographie
Freie Universitaet Berlin
Takustr.6
14195 Berlin
Germany

phone (+49)-30-838-53412
fax (+49)-30-838-56702
e-mail saen...@chemie.fu-berlin.de
 
--
Scanned by iCritical.

Re: [ccp4bb] ctruncate problems

[Stein, ND (Norman)]

Dear Justin

I have been unable to reproduce either of these problems. Perhaps
something went wrong during the self compilation process? Something odd
seems to have gone on even in the logfiles you classify as good. For
example, in

http://dev.gentooexperimental.org/~jlec/paste/good.log.html

there are nan's in the L test data and the cumulative intensity
distribution, and the acentric moments of E all seem to be exactly 1.

Note that if your input mtz file contains anomalous data, you will get
different results depending on whether or not you specify '-colano'. If
you do specify it, F(+) and F(-) will be calculated from I(+) and I(-)
respectively, and FMEAN will be calculated from FMEAN = 0.5*[F(+) +
F(-)]; if you don't FMEAN will be calculated from IMEAN. 

You can download a linux binary for the latest ctruncate (including the
patch) from

ftp://ftp.ccp4.ac.uk/nds/bin/ctruncate

Best wishes

Norman

Norman Stein
CCP4
Daresbury Laboratory






-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Justin Lecher
Sent: 08 July 2009 07:57
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] ctruncate problems

Dear all,

I have two problems with ctruncate. I tested two versions, the "old" one
from the 6.1.1 binary distro and a self compiled version including the
patch.
As dataset I used data/mtz/X13089.mtz from the test-framework, which
should be a twinned dataset.

problem 1:
The new version isn't able to detect the twinning anymore.

problem 2:
When running from ccp4i the used command is /usr/bin/ctruncate -mtzin
data/mtz/X13089.mtz -mtzout out.mtz -colin "/*/*/[IMEAN,SIGIMEAN]"
-colano "/*/*/[I(+),SIGI(+),I(-),SIGI(-)]"
Either running it from the interface or the shell it works fine but the
resulting mtz[2] is broken.
>From the manpage it says that those -colin or -colan are the default
values and passing them should give no difference compared to without.
But it actually does.
If I run the command like it is used in the test-framework
/usr/bin/ctruncate -mtzin data/mtz/X13089.mtz -mtzout out.mtz the
resulting mtz is fine [1].

Does anybody experienced similar problems?

These are the links to the mtzdumps and build.logs of the different
runs.

[1]
mtzdump from "unbroken" mtz
http://dev.gentooexperimental.org/~jlec/paste/mad.html

[2]
mtzdump from "broken" mtz
http://dev.gentooexperimental.org/~jlec/paste/good.html

[3]
_binary_
/usr/bin/ctruncate -mtzin data/mtz/X13089.mtz -mtzout out.mtz -colin
"/*/*/[IMEAN,SIGIMEAN]" -colano "/*/*/[I(+),SIGI(+),I(-),SIGI(-)]"

http://dev.gentooexperimental.org/~jlec/paste/old.bad.html

/usr/bin/ctruncate -mtzin data/mtz/X13089.mtz -mtzout out.mtz

http://dev.gentooexperimental.org/~jlec/paste/old.good.html

[4]
_compiled_
/usr/bin/ctruncate -mtzin data/mtz/X13089.mtz -mtzout out.mtz -colin
"/*/*/[IMEAN,SIGIMEAN]" -colano "/*/*/[I(+),SIGI(+),I(-),SIGI(-)]"

http://dev.gentooexperimental.org/~jlec/paste/bad.log.html

/usr/bin/ctruncate -mtzin data/mtz/X13089.mtz -mtzout out.mtz

http://dev.gentooexperimental.org/~jlec/paste/good.log.html


Thanks justin


--
Justin Lecher
Institute for Neuroscience and Biophysics
ISB3 - structural biochemistry
Research Centre Juelich GmbH,
52425 Juelich,Germany
phone: +49 2461 61 5385



--
Scanned by iCritical.

[ccp4bb] Senior Research Scientist position, University 0f Wisconsin-Milwaukee

[Stein, ND (Norman)]

THE UNIVERSITY OF WISCONSIN - MILWAUKEE

Senior Research Scientist (equivalent to Research Assistant Professor)

The Department of Physics at the University of Wisconsin - Milwaukee
seeks outstanding applicants for a senior scientist position (equivalent
to research assistant professor). Candidates must have: a Ph.D. in
physics or closely related field, and at least two years of postdoctoral
research experience in one or more of the following fields: theory of
electron or X-ray scattering, advanced imaging algorithms, and/or
numerical methods.  Exceptional candidates from related fields will also
be considered. A strong record of independent research evidenced by
publications is required.

Responsibilities include research in structure determination by
scattering methods, development of advanced noise-robust algorithms for
structure recovery and reconstruction, and leading research associates.


Applicants should submit their resume (curriculum vitae), summary of
relevant research experience, publications and patents lists, and names
of three referees. To apply, please see
www.jobs.uwm.edu/applicants/Central?quickFind=51047 .  Review of
applications will begin on September 1, 2009 and continue until the
position is filled.  As an equal opportunity/affirmative action
employer, the University of Wisconsin - Milwaukee promotes excellence
through diversity and encourages all qualified individuals to apply. 

For further information contact: Professor Abbas Ourmazd, Department of
Physics, ourm...@uwm.edu University of Wisconsin-Milwaukee, P.O. Box
413, Milwaukee, WI 53201.

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Re: [ccp4bb] refmac failed message

[Stein, ND (Norman)]

Hi Elad
 
You don't say which version of Refmac you are using but I think the first thing 
to do would be to try the latest version (5.5.0102). You can pick this up from
 
ftp://ftp.ccp4.ac.uk/nds/windows/refmac_5.5.0102/refmac5.exe
 
Copy this exe file to the bin subdirectory of your CCP4 installation. (Probably 
wise to make a backup copy of the existing refmac5.exe first).
 
Best wishes
 
Norman Stein
CCP4



From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Elad 
Binshtien
Sent: 30 July 2009 11:50
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refmac failed message


Dear all,


I am refining a structure in Refmac at 2.2 A in win OS.  However, Refmac failed 
and send this message:forrtl: error (72): floating overflow  

Thank you in advance for your any helpful suggestions.  


Best,
Elad


Elad Binshtein
Ph.D student 
Department of Life Science 
Ben Gurion University of the Negev
Ph: 972-8-6461325

‎ 

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