Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

2017-07-11 Thread James Foadi
Hello Frederic. Interesting. Have you got some reference on this to share?
James
 Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

On Tuesday, 11 July 2017, 7:15, Vellieux Frédéric 
<frederic.velli...@ibt.cas.cz> wrote:
 

 Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford <j...@ebi.ac.uk> wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the absolute deviates in the data to form a statistic that is more 
>>> accurate that Rmerge, but also (potentially) less precise.
>>>
>>> Perhaps that is what we are debating here?  Which is better? accuracy or 
>>> precision?  Personally, I prefer to know both.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 7/8/2017 11:02 AM, Frank von Delft 

Re: [ccp4bb] RMSD between unaligned structures

2017-07-03 Thread James Foadi
Hi Eleanor.You do the alignment if you are looking to measure the similarity of 
two molecules after refinement or the similarity of two molecules in general. 
When you do this, like you say, you have to carry out some sort of alignment, 
i.e. you move one of the two structures so to have the highest degree of 
overlapping with the other , without any constraint. This is what most of the 
programs do (and after having done that they compute the RMSD). But I'm looking 
for a program to measure the RMSD of two fixed (un-moved) structures; the 
structures have already been moved (with the symmetry and unit cell origin 
constrain) by CSYMMATCH. Does it make sense to you?
James
 Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

On Monday, 3 July 2017, 11:59, Eleanor Dodson <eleanor.dod...@york.ac.uk> 
wrote:
 

 Dont understand your Q James..
You have to make sort of alignment to get the RMSD surely?
And csymmatch will just apply the symmetry and origin shifts needed for any 
comparisonn?
E

On 3 July 2017 at 11:32, Stéphane Duquerroy <stephane.duquer...@u-psud.fr> 
wrote:

Hi James
LSQMAN can calculate the current RMSD between the 2 models (RMsd_calc mol1 
range1 mol2 range2 [Ltarget])
Be careful it renames the chain names

Stephane

-- -
Duquerroy Stéphane
Structural Virology Unit - PASTEUR INSTITUTE
25 rue du Dr Roux, 75015 Paris, France
lab: +33 (0)1 45 68 82 66
fax: +33 (0)1 45 68 89 93
email: sduq...@pasteur.fr
-- ------



De: "James Foadi" <09daa8ec3774-dmarc- requ...@jiscmail.ac.uk>
À: 
Envoyé: Lundi 3 Juillet 2017 11:47:00
Objet: [ccp4bb] RMSD between unaligned structures

Dear ccp4 tribe,this might have been asked before, but I haven't paid enough 
attention.

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt?
Many thanks, in advance.
James Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell 
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
personal web page: http://www.jfoadi.me.uk




   

[ccp4bb] RMSD between unaligned structures

2017-07-03 Thread James Foadi
Dear ccp4 tribe,this might have been asked before, but I haven't paid enough 
attention.

I'd like to measure the RMSD between two models after molecular replacement. I 
can force the two models to overlap as much as possible within the symmetry and 
origin-shift constraints (using CSYMMATCH). But I don't want the program that 
compute RMSD to align the two structures. Can you suggest what I should use? 
And, perhaps, what keywords I should adopt?
Many thanks, in advance.
James Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell 
Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office 
email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk 
personal web page: http://www.jfoadi.me.uk

Re: [ccp4bb] wavelet application in CCP4

2016-11-28 Thread James Foadi
 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; } Peter Main is retired. Julie works on different stuff now. I'm 
not aware of any application aside what Julie implemented at the end of the 90s.
James


Sent from Yahoo Mail for iPhone


On Monday, November 28, 2016, 4:16 pm, CPMAS Chen  wrote:

Dear, All
I happen to see this paper,

Low-resolution phase extension using wavelet analysis.
Main P1, Wilson J
However, I did not see any application in current structure refinement 
softwares. Maybe I overlooked this function in CCP4/phenix etc?
Also, I did not see much references to this paper?
Could anyone give me some heads-up?
Thanks!
Charles
-- 



***

Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

**







Re: [ccp4bb] Blend not outputting dendogram

2016-11-23 Thread James Foadi
Dear Claire,you have only one dataset in the "group of datasets" being analysed 
by BLEND. No dendrogram is supposed to be generated by BLEND with just one 
dataset.
Concerning your second question, alternative indexing is managed internally by 
POINTLESS, which BLEND calls when preparing merged data from combination of 
datasets, before scaling (carried out by AIMLESS).
Regards,
James
 Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal 
web page: http://www.jfoadi.me.uk 

On Wednesday, 23 November 2016, 0:27, Claire Smith <sclaire7...@gmail.com> 
wrote:
 

 Hello,
I am trying to use blend to merge several datasets. Blend seems to give "normal 
termination" with no errors but no tree file is being output and no clustering 
analysis is being done. Does anyone have an explanation for this? Logfile 
pasted below.
Also a related question - how do I ensure that the different data sets are not 
alternatively indexed - they use the same origin?

Many thanks,Claire
You are now running BLEND in analysis mode.

Reading from file mtz_names.dat .
 Spacegroup information obtained from library file:  Logical Name: SYMINFO   
Filename: /Applications/ccp4-6.4.0/lib/data/syminfo.lib

Loading datasets from all valid reflection files .Loading complete.
Partitioning datasets into groups with same bravais lattice .These 
datasets are partitioned in 1 group.The following crystals are part of bravais 
lattice n. 7: 1  Building summary table listing all crystals .
$TABLE: Summary of type I parameters :$GRAPHS:        Cell Parameters (a,     
b,    c)     : N : 1, 2, 3, 4 :       :        Cell Parameters (alpha, beta, 
gamma) : N : 1, 5, 6, 7 :       :        Cell Volume                          : 
N : 1, 8 :       :        Mosaicity                            : N : 1, 9 
:$$Crystal  a  b  c  alpha  beta  gamma  Cell_Volume  Mosaicity  
Resolution(low)  Resolution(high)  Wavelength             1    96.667   
131.331   131.394    90.00    90.00    90.00  1668095.82    0.10600   54.336    
1.549   0.97949$$
Summary information is included in file BLEND_SUMMARY.txt

 BLEND - Normal Termination                                   


#CCP4I TERMINATION STATUS 1 #CCP4I TERMINATION TIME 18 Nov 2016  20:41:05#CCP4I 
TERMINATION OUTPUT_FILES   /Users/sclaire/Desktop/blend_3#CCP4I MESSAGE Task 
completed successfully

   

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

2016-11-09 Thread James Foadi
 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px 
#715FFA solid !important; padding-left:1ex !important; background-color:white 
!important; }  I totally agree with you, Edward!
James


Sent from Yahoo Mail for iPhone


On Wednesday, November 9, 2016, 5:02 pm, Edward Snell  
wrote:

-- _filtered {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered 
{font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} p.MsoNormal, li.MsoNormal, 
div.MsoNormal {margin:0in;margin-bottom:.0001pt;font-size:12.0pt;}a:link, 
span.MsoHyperlink {color:blue;text-decoration:underline;}a:visited, 
span.MsoHyperlinkFollowed {color:purple;text-decoration:underline;}p 
{margin-right:0in;margin-left:0in;font-size:12.0pt;}span.EmailStyle18 
{color:#1F497D;}span.EmailStyle19 {color:windowtext;}.MsoChpDefault {} 
_filtered {margin:1.0in 1.0in 1.0in 1.0in;}div.WordSection1 {}
As a Brexit and Trumpet affected person having a foot in both countries ,this 
topic is too far off the normal discussion on CCP4 and probably better taken up 
privately.  CCP4 is not a political discussion site. With CCP4 the signal is 
unusually high and the noise low when compared to any discussion board. I for 
one would like to keep it there. Political views aside, we’re all trying to 
achieve the same scientific goals. Let’s remember that and keep that the focus.
 
  
 
Edward Snell Ph.D.
 
President and CEO Hauptman-Woodward Medical Research Institute
 
Assistant Prof. Department of Structural Biology, University at Buffalo
 
700 Ellicott Street, Buffalo, NY 14203-1102
 
Phone: (716) 898 8631 Fax: (716) 898 8660
 
Skype:  eddie.snell Email: esn...@hwi.buffalo.edu 
 

 
Heisenberg was probably here!

  
 
 



Re: [ccp4bb] invalid dataset in BLEND

2015-03-19 Thread James Foadi
Dear Charles,BLEND assumes data to be continuous sweeps, i.e. they should not 
include gaps. A valid data set,for example, could go from image 1 to image 100; 
an invalid one from 1 to 20 and, say, 22 to 100 - forsome reason image 21 has 
gone missing.
This can be annoying, I know, and, indeed, a future version of BLEND will 
eliminate this feature.
A typical case where datasets include gaps is when they are collected with the 
inverse beamstrategy. In this case one should use programs like rebatch 
(keyword REJECT) on two identicalcopies of each dataset and eliminate in turn 
one wedge from them.
There could be other reasons why files are rejected, but I need to look at one 
of your datasets to get moredetails.
J
 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom

office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk

personal web page: http://www.jfoadi.me.uk 


 On Thursday, 19 March 2015, 16:01, CPMAS Chen cpmas...@gmail.com wrote:
   

 Dear All,
when I use BLEND to analyze XDS-POINTLESS processed mtz files, some are 
reported as invalid datasets. Do you guys have some suggestions on what could 
be wrong with the datasets?
I processed these datasets in the same way, XDS and then POINTLESS. I am 
looking the detail of the processing. Meanwhile, I would like to know what 
others could make these datasets invalid as judged by BLEND. 
I have tried to use the XDS_ASCII.HKL, the same invalid datasets.
Thanks!
Charles

-- 
***Charles ChenResearch 
AssociateUniversity of Pittsburgh School of MedicineDepartment of 
Anesthesiology**

  

[ccp4bb] new Nature article on the R platform

2014-12-30 Thread James Foadi
Dear all,I have a long-standing interest on R and would like to share the 
following withthose interested:
    Programming tools: Adventures with R
|   |
|   |  |   |   |   |   |   |
| Programming tools: Adventures with RA guide to the popular, free statistics 
and visualization software that gives scientists control of their own data 
analysis. |
|  |
| View on www.nature.com | Preview by Yahoo |
|  |
|   |

   Happy New Year!

J

Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom

office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk

personal web page: http://www.jfoadi.me.uk

Re: [ccp4bb] merging anisotropic datasets

2014-11-13 Thread James Foadi
BLEND is mainly applicable to cases with many more than 3 data sets. So I would 
say it does notadd anything useful to what already suggested by Matthias. 

I have had positive results when scaling and merging several (unmerged) 
anisotropic data togetherwith POINTLESS / AIMLESS. The main reason for this was 
that the main directions of anisotropy were 
not exactly matching and some reflections intensity became stronger. As a 
result, resolution (as described 
by CC1/2) increased along that specific direction.
I have never tried a similar approach with XSCALE, but I would be interested in 
learning from peoplewho have tried it.
J
 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom

office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk

personal web page: http://www.jfoadi.me.uk 

 On Wednesday, 12 November 2014, 23:18, Antony Oliver 
antony.oli...@sussex.ac.uk wrote:
   

 Would the CCP4 program BLEND be a suitable initial option? And then the 
anisotropic server? 
Tony. 
--- sent from my mobile account ---
On 12 Nov 2014, at 21:29, Robert Keenan bkee...@uchicago.edu wrote:




I have three datasets of varying quality collected from different regions of a 
single crystal. In each case, the data are anisotropic (from Aimless using 
CC1/20.5):
Dataset 1:  3.5, 3.5 5.5 ADataset 2:  4.2, 4.3, 4.8 ADataset 3:  3.7, 3.9, 4.4 A
I initially took a simple-minded approach and processed each dataset at the 
appropriate resolution limit (set 1: 3.5A; set 2: 4.2A; set 3: 3.7A) using 
XDS/XSCALE as implemented in xia2. The resulting merged dataset seems fine 
(albeit with ugly stats in the high-res bins because of the anisotropy), and it 
allowed me to solve the structure (Rfree/Rcryst ~31/26).
Now I am wondering if I can improve the maps further by first applying an 
ellipsoidal truncation (using the UCLA diffraction anisotropy server) and then 
scaling/merging the three datasets together. However, it seems that the UCLA 
anisotropy server only allows input of one dataset at a time, and it outputs 
merged amplitudes. 
Is there some way to obtain the elliptically truncated but unmerged data for 
each of the three datasets? 
More generally, are there preferred strategies for dealing with strongly 
anisotropic data?
Bob

Robert Keenan
Associate Professor
Dept. of Biochemistry  Molecular Biology
GCIS W238
University of Chicago        
929 East 57th Street         
Chicago, IL  60637 
(o)  773.834.2292
(f)   773.834.5416
(e)  bkee...@uchicago.edu
http://keenanlab.bsd.uchicago.edu







   

Re: [ccp4bb] Room temperature data collection

2014-02-06 Thread James Foadi
Dear Enrico,

almost always it will be possible to achieve  
better diffraction using cryogenic data collection.

I would say almost always until now. Times change, instrumentation improves
and data collection techniques are becoming cunning. It's right time people 
start
exploring the new possibilities offered by modern synchrotrons.

All the best,

J

 
Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk


personal web page: http://www.jfoadi.me.uk



On Thursday, 6 February 2014, 11:35, Enrico Stura est...@cea.fr wrote:
 
Dear Joern and other BBers,

While I fully agree that it is important to test a few images at room  
temperature, to know the crystal's
potential, I think that almost always it will be possible to achieve  
better diffraction using cryogenic
data collection.
Those rare cases, as the one you mention below are worthy of critical  
investigation  as
to why there is a loss of order on cryo-cooling:
Unsuitable cryoprotectant is my first guess.
The rate of cooling in liquid N2 is slow, liquid ethane could be a better  
choice.

Enrico


On Thu, 06 Feb 2014 11:19:47 +0100, Joern Krausze jk...@helmholtz-hzi.de  
wrote:

 Dear Theresa,

 We recently collected a room temperature data set from one single  
 crystal at Petra III. The beam line was equipped with a Pilatus  
 detector. Data were good to 2.7 A. In contrast, at 100 K similar  
 crystals diffracted very poorly. So, it is perfectly possible to obtain  
 useful room temperature data sets from synchrotron sources. I have to  
 admit that in our case it certainly helped that the crystal belonged to  
 a high-symmetry space and full completeness was achieved after 40  
 degrees angular range.

 Regards,

 Joern

 Sent from my iPad

 On 06.02.2014, at 10:51, Theresa Hsu theresah...@live.com wrote:

 Dear crystallographers

 Just out of curiosity, is it possible to collect datasets from crystals  
 at room temperature at synchrotron? Are fast detectors like Pilatus  
 useful for this?

 Thank you.

 Theresa


-- 
Enrico A. Stura D.Phil. (Oxon) ,    Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152,                         Tel: 33 (0)1 69 08 9449    Lab
http://www-dsv.cea.fr/ibitecs/simopro/ltmb/cristallogenese
LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette,   FRANCE
http://scholar.google.com/citations?hl=enuser=Kvm06WIoPAsCpagesize=100sortby=pubdate
http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html
e-mail: est...@cea.fr                             Fax: 33 (0)1 69 08 90 71

Re: [ccp4bb] Today ...

2012-12-20 Thread James Foadi
Thank you, Phil!
The same to you!

J


 
Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk


personal web page: http://www.jfoadi.me.uk



 From: Phil Evans p...@mrc-lmb.cam.ac.uk
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Thursday, 20 December 2012, 11:50
Subject: [ccp4bb] Today ...
 
… is 20.12.2012

Happy Christmas everyone!

Phil

Re: [ccp4bb] Rpim and how its related to anomalous signal

2012-11-04 Thread James Foadi


I also think Rpim, as commonly defined, is not directly useful for measuring 
the anomalous signal.
Commenting on its use, though, I find it quite useful to judge whether one is 
adding useful data
to already existing ones. In a multiple crystals context I always look at both 
Rmeas and Rpim.
Suppose a given dataset shows some Rmeas and Rpim. Now add another dataset to 
the first one, in
the hope to increase completeness and redundancy. This, of course, will depend 
on how isomorphic
were the crystals from which the two datasets were collected. If the Rmeas 
stays stationary, or increases 

just a little, and Rpim decreases, this means thatthe crystals had a good 
degree of isomorphism and 

that scaled data will be more precise. This is what one wished for, when 
collecting from multiple crystals.
On the other hand, an increase in Rpim definitely points at something wrong 
with the addition of the
second dataset, quite certainly some form of non-isomorphism.


J

 
Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk


personal web page: http://www.jfoadi.me.uk



 From: Jim Pflugrath jim.pflugr...@rigaku.com
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Friday, 2 November 2012, 19:24
Subject: Re: [ccp4bb] Rpim and how its related to anomalous signal
 

 
In my opinion Rpim is not related directly to anomalous signal, so perhaps that 
is why there is some confusion. 

Also I think some folks confused Rpim with Rrim.  The latter is also called 
Rmeas.  But once again, these are not related directly to anomalous signal.  I 
do not find Rpim very useful for anything since when the data has high 
multiplicity Rpim gets very low, but as Michael Blum told me, Precision does 
not trump accuracy.  I would personally rather have accurate data than highly 
redundant but inaccurate data.

I like to look at the deltaF / sigma(deltaF) value reported by SHELXC and other 
programs, where deltaF is ||F+| - |F-||.
This might also be called d/sig.  There are other things to look at as well.

Jim


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Vijayakumar.B 
[vijaybioscie...@gmail.com]
Sent: Tuesday, September 18, 2012 4:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Rpim and how its related to anomalous signal


Dear CCP4BB users,

I am very much interested to work in Anomalous scattering technique for 
macromolecular structure determination. I have already gone through some 
literature in which they have explained about a parameter called “Rpim”.  I am 
little bit confused about Rpim values.
Can anyone tell me about the use of this parameter in structure determination 
by anomalous techniques and how Rpim is related to anomalous signal?  Thanks in 
advance 

With kind regards

 
B. Vijayakumar

Re: [ccp4bb] adding gaussian noise to an mtz data column

2011-02-04 Thread James Foadi
If you fancy using R (and its endless ways of generating random deviates),
then you could use part of the crystallographic package we are developing here 
(cRy).

Then you would carry out the following in R:

 source(cRy/all_load.R)
 mtz - 
readMTZ(test.mtz)

 # Load data from mtz file
 newF - mtz$reflections$Fnew+rnorm(mean=0,sd=1,n=length(mtz$reflections$H))  
 # 
Add gaussian deviates with mean 0 and standard dev 1
 mtz$reflections$Fnew - 
newF   
 
# Replace new column
writeMTZ(mtz,new_test.mtz)   

  # Write modified file with a different name


If you are interested I can provide you with my R code for doing this.



J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk



- Original Message 
From: Vellieux Frederic frederic.velli...@ibs.fr
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 4 February, 2011 12:40:35
Subject: [ccp4bb] adding gaussian noise to an mtz data column

Before re-inventing the wheel...

Is there anywhere some software (freely available software, I mean) that can 
add 
some Gaussian noise to data. The data is currently stored in a data column in 
an 
mtz (not phase data, but amplitudes, sigma values...) but can be exported 
to 
another format if required.

Before writing a computer program to do this, does anyone know if this can be 
done without writing any code. If it can then obviously I won't write new code.

Thanks,

Fred.






[ccp4bb] rebatch abort

2011-01-17 Thread James Foadi
 detected ***: rebatch terminated
=== Backtrace: =
/lib/libc.so.6(__fortify_fail+0x37)[0x2b06ab2da217]
/lib/libc.so.6(+0xfe0d0)[0x2b06ab2d90d0]
/lib/libc.so.6(+0xfd539)[0x2b06ab2d8539]
/lib/libc.so.6(__printf_fp+0x1541)[0x2b06ab227421]
/lib/libc.so.6(_IO_vfprintf+0x25fe)[0x2b06ab22299e]
/lib/libc.so.6(__vsprintf_chk+0x99)[0x2b06ab2d85d9]
/lib/libc.so.6(__sprintf_chk+0x7f)[0x2b06ab2d851f]
rebatch[0x4220d4]
rebatch[0x4084ef]
rebatch[0x408602]
rebatch[0x4060cb]
rebatch[0x406376]
rebatch[0x42b2ea]
/lib/libc.so.6(__libc_start_main+0xfd)[0x2b06ab1f9c4d]
rebatch[0x402669]
=== Memory map: 
0040-00438000 r-xp  08:11 6701231
/home/james/build/ccp4-6.1.13/bin/rebatch
00638000-00639000 r--p 00038000 08:11 6701231
/home/james/build/ccp4-6.1.13/bin/rebatch
00639000-0063a000 rw-p 00039000 08:11 6701231
/home/james/build/ccp4-6.1.13/bin/rebatch
0063a000-0179d000 rw-p  00:00 0 
032c2000-032e3000 rw-p  00:00 0  [heap]
2b06a9915000-2b06a9935000 r-xp  08:11 5472457
/lib/ld-2.11.1.so
2b06a9935000-2b06a993a000 rw-p  00:00 0 
2b06a9b34000-2b06a9b35000 r--p 0001f000 08:11 5472457
/lib/ld-2.11.1.so
2b06a9b35000-2b06a9b36000 rw-p 0002 08:11 5472457
/lib/ld-2.11.1.so
2b06a9b36000-2b06a9b37000 rw-p  00:00 0 
2b06a9b37000-2b06aa42c000 r-xp  08:11 9209497
/usr/lib/atlas/liblapack.so.3gf.0
2b06aa42c000-2b06aa62b000 ---p 008f5000 08:11 9209497
/usr/lib/atlas/liblapack.so.3gf.0
2b06aa62b000-2b06aa62c000 r--p 008f4000 08:11 9209497
/usr/lib/atlas/liblapack.so.3gf.0
2b06aa62c000-2b06aa631000 rw-p 008f5000 08:11 9209497
/usr/lib/atlas/liblapack.so.3gf.0
2b06aa631000-2b06aa73e000 rw-p  00:00 0 
2b06aa73e000-2b06aa834000 r-xp  08:11 8925829
/usr/lib/libstdc++.so.6.0.13
2b06aa834000-2b06aaa34000 ---p 000f6000 08:11 8925829
/usr/lib/libstdc++.so.6.0.13
2b06aaa34000-2b06aaa3b000 r--p 000f6000 08:11 8925829
/usr/lib/libstdc++.so.6.0.13
2b06aaa3b000-2b06aaa3d000 rw-p 000fd000 08:11 8925829
/usr/lib/libstdc++.so.6.0.13
2b06aaa3d000-2b06aaa53000 rw-p  00:00 0 
2b06aaa53000-2b06aab3e000 r-xp  08:11 8923073
/usr/lib/libgfortran.so.3.0.0
2b06aab3e000-2b06aad3d000 ---p 000eb000 08:11 8923073
/usr/lib/libgfortran.so.3.0.0
2b06aad3d000-2b06aad3e000 r--p 000ea000 08:11 8923073
/usr/lib/libgfortran.so.3.0.0
2b06aad3e000-2b06aad3f000 rw-p 000eb000 08:11 8923073
/usr/lib/libgfortran.so.3.0.0
2b06aad3f000-2b06aad4 rw-p  00:00 0 
2b06aad4-2b06aadc2000 r-xp  08:11 5472443
/lib/libm-2.11.1.so
2b06aadc2000-2b06aafc1000 ---p 00082000 08:11 5472443
/lib/libm-2.11.1.so
2b06aafc1000-2b06aafc2000 r--p 00081000 08:11 5472443
/lib/libm-2.11.1.so
2b06aafc2000-2b06aafc3000 rw-p 00082000 08:11 5472443
/lib/libm-2.11.1.so
2b06aafc3000-2b06aafd9000 r-xp  08:11 5472417
/lib/libgcc_s.so.1
2b06aafd9000-2b06ab1d8000 ---p 00016000 08:11 5472417
/lib/libgcc_s.so.1
2b06ab1d8000-2b06ab1d9000 r--p 00015000 08:11 5472417
/lib/libgcc_s.so.1
2b06ab1d9000-2b06ab1da000 rw-p 00016000 08:11 5472417
/lib/libgcc_s.so.1
2b06ab1da000-2b06ab1db000 rw-p  00:00 0 
2b06ab1db000-2b06ab355000 r-xp  08:11 5472513
/lib/libc-2.11.1.so
2b06ab355000-2b06ab554000 ---p 0017a000 08:11 5472513
/lib/libc-2.11.1.so
2b06ab554000-2b06ab558000 r--p 00179000 08:11 5472513
/lib/libc-2.11.1.so
2b06ab558000-2b06ab559000 rw-p 0017d000 08:11 5472513
/lib/libc-2.11.1.so
2b06ab559000-2b06ab55e000 rw-p  00:00 0 
2b06ab55e000-2b06abcef000 r-xp  08:11 9209496
/usr/lib/atlas/libblas.so.3gf.0
2b06abcef000-2b06abeee000 ---p 00791000 08:11 9209496
/usr/lib/atlas/libblas.so.3gf.0
2b06abeee000-2b06abef3000 r--p 0079 08:11 9209496
/usr/lib/atlas/libblas.so.3gf.0
2b06abef3000-2b06abef9000 rw-p 00795000 08:11 9209496
/usr/lib/atlas/libblas.so.3gf.0
2b06abef9000-2b06abefc000 rw-p  00:00 0 
7fffd6dd9000-7fffd6df4000 rwxp  00:00 0  [stack]
7fffd6df4000-7fffd6df7000 rw-p  00:00 0 
7fffd6dff000-7fffd6e0 r-xp  00:00 0  [vdso]
ff60-ff601000 r-xp  00:00 0  
[vsyscall]
Aborted




J



 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus

[ccp4bb] issues with idiffdisp

2009-05-05 Thread James Foadi
I have tried starting idiffdisp from ccp4i, but got a wish window open and a 
message saying:
Impossible to load Diffraction Image library 
/home/james/build/ccp4-6.1.1/lib/libDiffractionImage.so!! ...

The file is there, though:

 ls -l $CCP4_LIB
.   .   .   .   .   .   .   .   .
.   .   .   .   .   .   .   .   .
.   .   .   .   .   .   .   .   .
-rw-r--r--  1 james james 2974782 2009-02-25 18:14 libDiffImage.a
-rwxr-xr-x  1 james james 773 2009-02-25 18:14 libDiffImage.la
-rw-r--r--  1 james james 3120264 2009-02-25 18:14 lib_DiffractionImage.a
-rw-r--r--  1 james james 3076274 2009-02-25 18:14 libDiffractionImage.a
-rwxr-xr-x  1 james james 901 2009-02-25 18:14 lib_DiffractionImage.la
-rwxr-xr-x  1 james james 894 2009-02-25 18:14 libDiffractionImage.la
lrwxrwxrwx  1 james james  29 2009-02-25 18:14 lib_DiffractionImage.so - 
lib_DiffractionImage.so.0.0.0
lrwxrwxrwx  1 james james  28 2009-02-25 18:14 libDiffractionImage.so - 
libDiffractionImage.so.0.0.0
lrwxrwxrwx  1 james james  29 2009-02-25 18:14 lib_DiffractionImage.so.0 - 
lib_DiffractionImage.so.0.0.0
lrwxrwxrwx  1 james james  28 2009-02-25 18:14 libDiffractionImage.so.0 - 
libDiffractionImage.so.0.0.0
-rwxr-xr-x  1 james james 4042747 2009-02-25 18:14 lib_DiffractionImage.so.0.0.0
-rwxr-xr-x  1 james james 4015515 2009-02-25 18:14 libDiffractionImage.so.0.0.0
.   .   .   .   .   .   .   .   .
.   .   .   .   .   .   .   .   .
.   .   .   .   .   .   .   .   .


I know nothing about Tcl, so I don't know how to solve this issue. Any idea on 
this from somebody else would be very much appreciated.


J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk





Re: [ccp4bb] issues with idiffdisp

2009-05-05 Thread James Foadi
It doesn't work outside the GIU either.
I should tell that I have my CCP4 install compiled from source, it is not a 
binary installation.
Also that I use ActiveTcl 8.4 and my Linux platform is Ubuntu 8 (64 bit). I 
wonder whether
this is a Tcl version issue...

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
web page:





From: Boaz Shaanan bshaa...@bgu.ac.il
To: James Foadi james_fo...@yahoo.co.uk
Sent: Tuesday, 5 May, 2009 12:37:17
Subject: Re: [ccp4bb] issues with idiffdisp

Hi,

I use it routinely with no problem OUTSIDE the gui.

Cheers,

   Boaz 

- Original Message -
From: James Foadi james_fo...@yahoo.co.uk
Date: Tuesday, May 5, 2009 14:02
Subject: [ccp4bb] issues with idiffdisp
To: CCP4BB@JISCMAIL.AC.UK

 I have tried starting idiffdisp from ccp4i, but got a wish 
 window open and a message saying:
 Impossible to load Diffraction Image library 
 /home/james/build/ccp4-6.1.1/lib/libDiffractionImage.so!! ...
 
 The file is there, though:
 
  ls -l $CCP4_LIB
 .   .   .   .   
 .   .   .   .   .
 .   .   .   .   
 .   .   .   .   .
 .   .   .   .   
 .   .   .   .   .
 -rw-r--r--  1 james james 2974782 2009-02-25 18:14 libDiffImage.a
 -rwxr-xr-x  1 james james 773 2009-
 02-25 18:14 libDiffImage.la
 -rw-r--r--  1 james james 3120264 2009-02-25 18:14 
 lib_DiffractionImage.a-rw-r--r--  1 james james 3076274 
 2009-02-25 18:14 libDiffractionImage.a
 -rwxr-xr-x  1 james james 901 2009-
 02-25 18:14 lib_DiffractionImage.la
 -rwxr-xr-x  1 james james 894 2009-
 02-25 18:14 libDiffractionImage.la
 lrwxrwxrwx  1 james james  29 
 2009-02-25 18:14 lib_DiffractionImage.so - 
 lib_DiffractionImage.so.0.0.0lrwxrwxrwx  1 james 
 james  28 2009-02-25 18:14 
 libDiffractionImage.so - libDiffractionImage.so.0.0.0
 lrwxrwxrwx  1 james james  29 
 2009-02-25 18:14 lib_DiffractionImage.so.0 - 
 lib_DiffractionImage.so.0.0.0lrwxrwxrwx  1 james 
 james  28 2009-02-25 18:14 
 libDiffractionImage.so.0 - libDiffractionImage.so.0.0.0
 -rwxr-xr-x  1 james james 4042747 2009-02-25 18:14 
 lib_DiffractionImage.so.0.0.0-rwxr-xr-x  1 james james 
 4015515 2009-02-25 18:14 libDiffractionImage.so.0.0.0
 .   .   .   .   
 .   .   .   .   .
 .   .   .   .   
 .   .   .   .   .
 .   .   .   .   
 .   .   .   .   .
 
 
 I know nothing about Tcl, so I don't know how to solve this 
 issue. Any idea on this from somebody else would be very much 
 appreciated.
 
 J
 
  Dr James Foadi PhD
 Membrane Protein Laboratory
 Diamond Light Source Ltd.
 Diamond House
 Harwell Science and Innovation Campus
 Didcot
 Oxfordshire
 OX11 0DE
 United Kingdom
 
 
 office email: james.fo...@diamond.ac.uk
 alternative email: j.fo...@imperial.ac.uk
 
 
   
 

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan‎ 


  

Re: [ccp4bb] failed compilation for Pointless

2009-05-05 Thread James Foadi
For those of you who have been experiencing my same problem, I have solved it.
It just sufficed downloading and installing the patch (source code bit):
  
http://www.ccp4.ac.uk/updates/

The compilation went too fast for me to be able to read quickly through the 
lines, but I could see that some
of it involved fftw, I suspect the real problem in my failed previous attempt.
I can now run the full Pointless without problems.

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk






[ccp4bb] CAD on multi-record file

2009-04-09 Thread James Foadi
Dear all,
(apologies for those being tired of similar questions...)
I have tried using CAD on an unscaled MTZ from Mosflm.
All I wanted to do was to change crystal name, dataset name and project name.
This is what I got:


-
BFONT COLOR=#FF!--SUMMARY_BEGIN--
html !-- CCP4 HTML LOGFILE --
hr
!--SUMMARY_END--/FONT/B
BFONT COLOR=#FF!--SUMMARY_BEGIN--
pre
 
 ###
 ###
 ###
 ### CCP4 6.1: CAD  version 6.1 : 20/01/09##
 ###
 User: unknown  Run date:  9/ 4/2009 Run time: 16:20:40 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 
760-763.
 as well as any specific reference in the program write-up.

!--SUMMARY_END--/FONT/B
 Data line--- TITLE Changing crystal, dataset and project names
 Data line--- LABIN FILE_NUMBER 1 ALL
 Data line--- DPNAME  FILE_NUMBER 1 New New NONISO
 Data line--- DRENAME FILE_NUMBER 1 New New Insulin_01 Dataset_01
 Data line--- END
 No CTYP lines input for file:  1
Indices output even if all data items flagged missing
 Warning, NOT all LABOUT data lines given

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN1   Filename: exp_01/in1_MS_1_001.mtz 

 * Title:

 Untitled

 * Base dataset:

0 HKL_base
  HKL_base
  HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

1 New
  New
  New
 81.6000   81.6000   33.6000   90.   90.  120.
 0.92000

 * Number of Columns = 18

 * Number of Reflections = 40898

 * Missing value set to NaN in input mtz file

 * Number of Batches = 100

 * Column Labels :

 H K L M/ISYM BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT WIDTH LP MPART 
FLAG BGPKRATIOS

 * Column Types :

 H H H Y B J Q J Q R R R R R R I I R

 * Associated datasets :

 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)

   81.6000   81.6000   33.6000   90.   90.  120. 

 *  Resolution Range :

0.001090.32315 ( 30.345 -  1.759 A )

 * Sort Order :

  0 0 0 0 0

 * Space group = 'H3' (number 146)


 File   1 is a multi-record MTZ file.
 Inputting a multi-record file to CAD is an unmitigated disaster!
 Please use MTZUTILS.

BFONT COLOR=#FF!--SUMMARY_BEGIN--
 CAD:  Input file is unmerged MTZ file.
 CAD:  Input file is unmerged MTZ file.
Times: User:   0.1s System:0.0s Elapsed: 0:00  
/pre
/html
!--SUMMARY_END--/FONT/B
--

So it would appear that CAD is no good for this sort of files. What should I 
use, then?
I have tried looking into mtzutils, but I don't see how to do it.

Anyone for help?

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
web page:






Re: [ccp4bb] CAD on multi-record file

2009-04-09 Thread James Foadi
Many thanks for all your answers!
It appears that using REBATCH is the best option for me, as I'm not planning on 
using SCALA (or POINTLESS) on this unmerged file.

Keywords were as follows (for those who might be interested):

TITLE Change Project, crystals and datasets name_ change batch numbers
BATCH 1 TO 100 PNAME NONISO XNAME Insulin_01 DNAME Dataset_01
END


Best wishes,

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk





[ccp4bb] failed compilation for Pointless

2009-03-31 Thread James Foadi
I am trying compile Pointless from source as this is the only CCP4 bit which 
hasn't compiled on my x86_64 machine (linux Ubuntu 8).
I cd into src/pointless and then try to run configure.sh. This stops at a 
point where it complains that it can't find ccp4_errno.h. That seems
odd, as I have declared all CCP4 environment variables, and could check that 
the file is actually where it should be.

Anyone could help me with this?

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk






Re: [ccp4bb] failed compilation for Pointless

2009-03-31 Thread James Foadi
Ii is commented out in mine as well. But even deleting the # does not help
In fact this is the full log from configuration:

.
.
.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking for gfortran... gfortran
checking for Fortran compiler default output file name... a.out
checking whether the Fortran compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking how to get verbose linking output from gfortran... -v
checking for Fortran libraries of gfortran...  
-L/usr/lib/gcc/x86_64-linux-gnu/4.2.4 
-L/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib -L/lib/../lib 
-L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../.. 
-lgfortranbegin -lgfortran -lm
checking for xlc++... no
checking for CC... no
checking for cxx... no
checking for c++... c++
checking whether we are using the GNU C++ compiler yes
checking whether c++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of c++... gcc3
checking how to run the C++ preprocessor... c++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for ccp4_errno in CCP4... no
configure: error: Failed to find ccp4 libs
.
.
.

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
web page:



- Original Message 
From: James M. Vergis jver...@virginia.edu
To: James Foadi james_fo...@yahoo.co.uk
Sent: Tuesday, 31 March, 2009 14:50:08
Subject: RE: [ccp4bb] failed compilation for Pointless

James,

I checked my pointless configure file from my install (CentOS 5 64-bit machine) 
and the include ccp4_errno.h line is commented out in my configure file.  I 
did not modify the file, that’s how it came.  Maybe that will solve your 
problem.

Good luck!


James M. Vergis, Ph.D.
University of Virginia Molecular Physiology and Biological Physics
KVWEINR 360A Snyder Building
480 Ray C. Hunt Drive
Charlottesville, VA 22908-0886
phone: 434-243-2730   FAX: 434-243-8271
jver...@virginia.edu


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of James 
Foadi
Sent: Tuesday, March 31, 2009 6:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] failed compilation for Pointless

I am trying compile Pointless from source as this is the only CCP4 bit which 
hasn't compiled on my x86_64 machine (linux Ubuntu 8).
I cd into src/pointless and then try to run configure.sh. This stops at a 
point where it complains that it can't find ccp4_errno.h. That seems
odd, as I have declared all CCP4 environment variables, and could check that 
the file is actually where it should be.

Anyone could help me with this?

J

Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk





[ccp4bb] imosflm STARTDIR

2009-03-18 Thread James Foadi
Dear MOSFLM/IMOSFLM people,
when I start the new version of imosflm I expect it to dump files and to search 
all files
starting from the current directory. This doesn't seem to be the case. It 
appears it always
starts from MOSDIR. I my imosflm.tcl the line related to STARTDIR is:

set STARTDIR [pwd]


Perhaps somebody else has written about this, but if this is the case, I have 
missed the thread.

Can somebody help me with this?

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk


 


Re: [ccp4bb] SCALA failed message

2009-02-25 Thread James Foadi
Thank you Graeme.
I have installed ccp4 6.1.1 and ran the same job on SCALA succesfully.

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
web page:



- Original Message 
From: Graeme Winter graeme.win...@googlemail.com
To: James Foadi james_fo...@yahoo.co.uk
Cc: CCP4BB@jiscmail.ac.uk
Sent: Tuesday, 24 February, 2009 18:51:16
Subject: Re: [ccp4bb] SCALA failed message

Hi James,

You are the victim of an epic command line. This has been fixed in the
6.1.1 release, but you will find that using a shorter path (i.e.
noniso rather than non-isomorphism c.) will pull the command line
down to something more sensible.

CCP4i writes this out to allow the job to be rerun in a comment, but
the comment is too long for Scala!

Cheers,

Graeme

2009/2/24 James Foadi james_fo...@yahoo.co.uk:
 Dear all,
 I am running SCALA using ccp4i. The generated command file is:


 


 ***
 /tmp/james/NONISO_insulin_from_liz_6_2_com.tmp
 ***
  title Scale merged insulin_from_liz _ Datasets in1, in2, in3, in4, in5
 run 1 -
INCLUDE batch 1 to 100
 run 2 -
INCLUDE batch 201 to 380
 run 3 -
INCLUDE batch 401 to 522
 run 4 -
INCLUDE batch 601 to 651
 run 5 -
INCLUDE batch 701 to 720
 RUN 2 reference
 name run 1 project New crystal New dataset New
 name run 2 project New crystal New dataset New
 name run 3 project New crystal New dataset New
 name run 4 project New crystal New dataset New
 name run 5 project New crystal New dataset New
 exclude EMAX -
10.0
 partials -
check -
test 0.95 1.05 -
nogap
 intensities INTEGRATED -
PARTIALS
 final PARTIALS
 scales -
rotation SPACING 5 -
secondary 6 -
bfactor ON -
BROTATION SPACING 20
 UNFIX V
 FIX A0
 UNFIX A1
 initial MEAN
 tie surface 0.001
 tie bfactor 0.3
 cycles 10 converge 0.3 reject 2
 output AVERAGE
 print brief nooverlap
 RSIZE 80
 ## This script run with the command   ##
 # /home/james/build/ccp4-6.1.0/bin/scala HKLIN 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/exp_01/in1_in2_in3_in4_in5_MS_1_001.mtz
  HKLOUT /tmp/james/NONISO_insulin_from_liz_6_1_mtz.tmp SCALES 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6.scala
  ROGUES 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogues.log
  NORMPLOT 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_normplot.xmgr
  ANOMPLOT 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_anomplot.xmgr
  PLOT 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_surface_plot.plt
  CORRELPLOT 
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_correlplot.xmgr
  ROGUEPLOT
  
 /home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogueplot.xmgr
 
 

 Unfortunately SCALA stops immediately with the following error message:


 -
  ** Unrecognized keyword **

   RUN command must come before SCALES definition 

  ** Missing or illegal value **
 -

 Any idea on what's wrong? I have to say, I had run this before with similar 
 data (up to 4 runs), and had never this problem.

 Thank you!

 J

  Dr James Foadi PhD
 Membrane Protein Laboratory
 Diamond Light Source Ltd.
 Diamond House
 Harwell Science and Innovation Campus
 Didcot
 Oxfordshire
 OX11 0DE
 United Kingdom


 office email: james.fo...@diamond.ac.uk
 alternative email: j.fo...@imperial.ac.uk
 web page:











[ccp4bb] SCALA failed message

2009-02-24 Thread James Foadi
Dear all,
I am running SCALA using ccp4i. The generated command file is:





***
/tmp/james/NONISO_insulin_from_liz_6_2_com.tmp
***
 title Scale merged insulin_from_liz _ Datasets in1, in2, in3, in4, in5
run 1 -
INCLUDE batch 1 to 100
run 2 -
INCLUDE batch 201 to 380
run 3 -
INCLUDE batch 401 to 522
run 4 -
INCLUDE batch 601 to 651
run 5 -
INCLUDE batch 701 to 720
RUN 2 reference
name run 1 project New crystal New dataset New
name run 2 project New crystal New dataset New
name run 3 project New crystal New dataset New
name run 4 project New crystal New dataset New
name run 5 project New crystal New dataset New
exclude EMAX -
10.0
partials -
check -
test 0.95 1.05 -
nogap
intensities INTEGRATED -
PARTIALS
final PARTIALS
scales -
rotation SPACING 5 -
secondary 6 -
bfactor ON -
BROTATION SPACING 20
UNFIX V
FIX A0
UNFIX A1
initial MEAN
tie surface 0.001
tie bfactor 0.3
cycles 10 converge 0.3 reject 2
output AVERAGE
print brief nooverlap
RSIZE 80
## This script run with the command   ##
# /home/james/build/ccp4-6.1.0/bin/scala HKLIN 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/exp_01/in1_in2_in3_in4_in5_MS_1_001.mtz
 HKLOUT /tmp/james/NONISO_insulin_from_liz_6_1_mtz.tmp SCALES 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6.scala
 ROGUES 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogues.log
 NORMPLOT 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_normplot.xmgr
 ANOMPLOT 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_anomplot.xmgr
 PLOT 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_surface_plot.plt
 CORRELPLOT 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_correlplot.xmgr
 ROGUEPLOT
 
/home/james/gwyndaf/non-isomorphism/data_created/insulin_from_liz/NONISO_insulin_from_liz_6_rogueplot.xmgr



Unfortunately SCALA stops immediately with the following error message:


-
 ** Unrecognized keyword **

  RUN command must come before SCALES definition 

 ** Missing or illegal value **
-

Any idea on what's wrong? I have to say, I had run this before with similar 
data (up to 4 runs), and had never this problem.

Thank you!

J

 Dr James Foadi PhD
Membrane Protein Laboratory
Diamond Light Source Ltd.
Diamond House
Harwell Science and Innovation Campus
Didcot
Oxfordshire
OX11 0DE
United Kingdom


office email: james.fo...@diamond.ac.uk
alternative email: j.fo...@imperial.ac.uk
web page: