Re: [ccp4bb] Fwd: Re: [ccp4bb] reference for true multiplicity?

2013-05-15 Thread Harry Powell
 meant to know this but I'm blanking, so I'll crowdsource  
instead:


Anybody know a (the) reference where it was showed that the best  
SAD data is obtained by collecting multiple revolutions at  
different crystal offsets (kappa settings)?  It's axiomatic now (I  
hope!), but I remember seeing someone actually show this.  I  
thought Sheldrick early tweens, but PubMed is not being useful.


(Oh dear, this will unleash references from the 60s, won't it.)

phx









--
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] iMosflm bug?

2013-06-25 Thread Harry Powell
Hi

As David suggests, this is certainly a problem with fonts - you're getting a 
large variant of Courier; the default font in iMosflm is Helvetica, and it 
looks like your X-display isn't finding it for some reason.

You should be able to re-size the window by dragging out the bottom right hand 
corner of the Processing options window, even if there's no visible handle.

Ubuntu has been becoming less good at having normal Linux things installed by 
default over the last few years - I'm sure Canonical has very good reasons for 
this, but it has put me off recommending it.

On 25 Jun 2013, at 10:08, David Waterman wrote:

 This might be a problem with fonts. On my laptop the menu items use a sans 
 serif font and that particular window is just wide enough to fit all the 
 items. The font also looks more attractive and readable than your screenshot. 
 I'm guessing (from your desktop background!) that you also use Ubuntu. 
 Unfortunately I can't remember how I set fonts up on my machine, but it may 
 help to:
 
 1) install the ttf-mscorefonts-installer package
 2) ensure the package gsfonts-x11 is *not* installed (this causes an 
 incorrect mapping of unicode symbols so you get things like the registered 
 trademark symbol appearing - an effect apparently known as mojibake...)
 
 Cheers
 
 -- David
 
 
 On 25 June 2013 03:46, Thomas Cleveland thomas.clevel...@gmail.com wrote:
 Has anyone else encountered this?  When I go to processing options in 
 iMosflm 1.0.7, many of the parameters on the right hand side of the window 
 are cut off, and there is no way to scroll over so that I can enter them.  
 I've attached link to a picture of what it looks like.
 
 https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png
 
 Thanks,
 Thomas Cleveland
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] iMosflm bug? - SOLVED

2013-06-26 Thread Harry Powell

Hi

I've just installed a Plain vanilla copy of Ubuntu 13.0.4 (aka  
rastafarian reefer or somesuch) with iMosflm 1.0.7 and CCP4 6.3.0  
and found that Roger's suggestions were all that was needed (but I  
did log out and in again to use them) -


sudo apt-get install ttf-mscorefonts-installer  # installs  
microsoft fonts
sudo apt-get install xfs xfstt xfonts-75dpi xfonts-100dpi  #  
installs xfonts and xfont server



Curiously, although Thomas found that the mscorefonts were  
installed by default, they weren't on my system.


For those of you with time to spare, the Unity desktop that comes  
with Ubuntu is interesting and may reward further investigation...


On 26 Jun 2013, at Wed26 Jun 06:21, Thomas Cleveland wrote:


Hi everyone,

Thanks again for the help.  As several people suggested, it seems  
to have been a fonts package that was needed.  I'm not sure if  
there is a single particular package that would have solved the  
problem, but I installed the following combination:


t1-xfree86-nonfree
ttf-xfree86-nonfree
ttf-xfree86-nonfree-syriac
xfonts-75dpi
xfonts-100dpi
xfs
xfstt
(ttf-mscorefonts-installer was already installed by default)

Everything is working fine now.  Thanks again.

-Thomas

On Tue, Jun 25, 2013 at 10:23 AM, Thomas Cleveland  
thomas.clevel...@gmail.com wrote:

Hi everyone,

Thanks for all your responses.  I will try working on the fonts  
when I get back to my computer and report back when I find a  
working solution.  I'm using a fresh installation of Ubuntu 13.04  
amd64, so hopefully it will be relevant to other users of newer  
Ubuntu releases.


Harry, I could drag the lower right corner to make the window  
*smaller*, but it would not let me make it any bigger.


Reginald, I'll take a look at that.

Thanks,
Thomas


On Mon, Jun 24, 2013 at 10:46 PM, Thomas Cleveland  
thomas.clevel...@gmail.com wrote:
Has anyone else encountered this?  When I go to processing  
options in iMosflm 1.0.7, many of the parameters on the right hand  
side of the window are cut off, and there is no way to scroll over  
so that I can enter them.  I've attached link to a picture of what  
it looks like.


https://www.dropbox.com/s/muwblcgohhxu94c/iMosflm-cut-off.png

Thanks,
Thomas Cleveland




Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] Where to cut the data in this medium resolution dataset

2013-07-23 Thread Harry Powell
Hi

I'd agree with Kay here - since the edge of the detector is at ~2.8Å. It is 
almost always worthwhile integrating to a higher resolution than you can see 
spots on the images - for what I would call normal datasets, I would always 
integrate to ~0.2Å higher (as a first estimate), then after examining scaling 
statistics (e.g. correlation coefficients!) decide if you can actually 
integrate even higher. For modern extra fine phi slicing, it's usually 
worthwhile integrating to an even  higher resolution before making any 
decisions about the true resolution, especially if you have non-negligible 
background on the images.

There are a couple of  issues with integrating to *much* higher resolution than 
you actually have - one is due to the crystal  detector refinements becoming 
less stable if you include too many reflections with insignificant !/sig(I) - 
i.e. refining against noise, and the other is in optimising the profiles  
measurement boxes (again, using noise to determine these will not lead to 
optimal values).

BTW, unless you have a *really* good reason for scaling with SCALA, I would 
seriously consider updating your CCP4 installation and using Aimless instead. 
Phil Evans is no longer developing SCALA, and doesn't seem to have updated the 
SCALA release notes since 2010, so I suspect that any newer versions (most 
recent is 3.3.21) only contain minor bug fixes (but I could be wrong).

On 23 Jul 2013, at 08:11, Kay Diederichs wrote:

 Hi Stefan,
 
 you write
 The diffraction pattern looks great, the 3.4A reflections are visible by eye 
 and the edge of the detector is about 2.8A.
 and for the 3.4A data  Mean((I)/sd(I))   in the highest shell is  2.3 .
 
 I'm tempted to ask: what prevents you from using higher resolution data to, 
 say, 3.2 or 3.0 A - what do you gain by throwing reflections away? Using 
 higher resolution _will_ reduce overfitting, and should improve the model.
 
 In the presence of NCS, Rfree will be biased towards Rwork. In your case of 
 high-order NCS, you might consider choosing the free reflections in thin 
 shells in reciprocal space.
 
 HTH,
 
 Kay
 
 
 The diffraction pattern looks great, the 3.4A reflections are visible by eye 
 and the edge of the detector is about 2.8A. The crystals were 10x20x50 um in 
 size and spacegroup is P6522.
 
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] Error running Pointless in CCP4-6.3 OSX (10.8)

2013-08-12 Thread Harry Powell
Hi

I noticed last week that, although the CCP4 updater for OSX requires 64-bit 
(see CCP4 discussions passim), all the executables are 32-bit (or at least in 
my current copy, updated a few weeks ago). So there is an inconsistency - no 
doubt this will be sorted out shortly.

If you want a 64-bit build of Pointless for OSX then see Phil Evans' ftp site - 

ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre

Use the most recent version - it may solve your problem.

On 12 Aug 2013, at 03:28, Bosch, Juergen wrote:

 Hi Sheena,
 
 simple quickfix to your problem:
 a) Run CAD and limit the output resolution on that mtz file so you don't run 
 into the memory allocation error of pointless.
 b) try phenix.xtriage also if it is not a CCP4 program
 
 Jürgen
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu
 
 
 
 
 On Aug 11, 2013, at 9:54 PM, Sheena McGowan (Med) wrote:
 
 Dear all
 
 We have been trying to run pointless on a large mtz file which seems to be 
 allocating more than 1.5Gb of memory resulting in the following error:
 
 The program run with command: /Applications/ccp4-6.3.0/bin/pointless 
 has failed with error message
 pointless(507) malloc: *** mmap(size=1577435136) failed (error code=12)
 *** error: can't allocate region
 *** set a breakpoint in malloc_error_break to debug
 
 We are using OSX 10.8.4 and believe that we need a 64bit version of 
 pointless.
 
 Looking at the pre release ftp site, we found the latest versions of 
 pointless compiled for OSX 10.8, however they do not run.
 
 dyld: Symbol not found: __ZNSt11range_errorD1Ev
   Referenced from: /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
   Expected in: /usr/lib/libstdc++.6.dylib
  in /Applications/ccp4-6.3.0/bin/pointless-1.8.7.osx10.8
 
 Any help would be greatly appreciated (and any know if there is a upcoming 
 release of a pre-compiled CCP4 OSX-64bit??)
 
 Regards
 Sheena
 
 
 
 SHEENA McGOWAN | ARC Future Fellow
 Department of Biochemistry and Molecular Biology
 MONASH UNIVERSITY 
 Rm 243, Building 77, Wellington Rd, Clayton
 Victoria, AUSTRALIA 3800
 T + 61 3 9902 9309 | F + 61 3 9902 9500
 E sheena.mcgo...@monash.edu | Skype s.mcgowan
 W http://www.med.monash.edu.au/biochem/staff/mcgowan.html
 
 Australian Society for Biochemistry and Molecular Biology (State 
 Representative) http://www.asbmb.org.au/
 
 39th Lorne Conference for Protein Structure and Function 
 http://www.lorneproteins.org
 February 9-13, 2014. Mantra Lorne, Lorne, AUSTRALIA
 
 
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] Data processing - twinned xtals

2013-08-16 Thread Harry Powell
Hi Mahesh

In addition to what Mark and Juergen have written, it looks to me like you have 
very high mosaicity in one direction - the first image shows no distinct lunes; 
I suspect that may have something to do with the failure to process - but what 
do you mean when you say you cannot process it? Was the failure at the 
indexing or integration stage? If the failure is at the indexing stage, it's 
possible that you may make some progress in indexing if you increase the 
I/sig(I) threshold in Mosflm processing.

Looking closely at some of the spots in the first image it does look like you 
have more than one lattice there, though I'm not sure I'd describe it as 
twinning.

On 16 Aug 2013, at 15:38, Mahesh Lingaraju wrote:

 Hi CCP4 folks 
 
 I have a data set which is looks twinned ( see the image-1  - I zoomed on to 
 the image so that one can spot the twinning. Furthermore, the spots are very 
 smeary from ~ 30 - 120 degrees of data collection, see image 2) I tried using 
 HKL2000 and mosflm to process this data but i cannot process it. I was 
 wondering if anyone has any ideas as to how to process this data or comments 
 on whether this data is even useful. Also, I would really appreciate if 
 someone could share their experiences on solving twinning issues during 
 crystal growth 
 
 Thanks in advance !
 
 Maheshimage 1.pngimage 2.png

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] Error with iMosflm 1.0.7 of CCP4 6.4.0 kit

2013-10-23 Thread Harry Powell

Hi David

Nothing to do with the iMosflm developers. CCP4 has made some changes  
that have caused this error to arise in 6.4.0 on Linux (this is not  
to say that the iMosflm code didn't have the bug, just that it  
doesn't appear with either our own version or with the same version  
distributed with ccp4 6.3.0).


The guys at ccp4 have produced a fix which will be released shortly,  
but they tell me this works;


For now a quick workaround is to add  2@1  after word exit in line  
847 in ccp4-6.4.0/share/ccp4i/imosflm/src/controller.tcl.


--- src/controller.tcl  2012-11-30 20:46:13 +
+++ src/controller.tcl  2013-10-19 08:52:29 +
@@ -844,7 +844,7 @@
# If an executable has been named...
if {$l_executable != } {
# test the executable, by running it
-   if {![catch {exec $l_executable  exit} l_result]} {
+   if {![catch {exec $l_executable  exit 2@1 }  
l_result]} {

if { [regexp -nocase windows $::tcl_platform(os)] } {
set summary_filename [file join $::env(MOSDIR)  
SUMMARY]

#set summary_filename [list $summary_filename]




Of course, my favourite fix is to run the version from our website  
which does not show this bug.


Best wishes


On 23 Oct 2013, at Wed23 Oct 17:39, David Schuller wrote:


iMosflm developers:

I have installed CCP4 6.4.0, which includes iMosflm 1.0.7 and  
ipmosflm 7.0.9.

This is on Scientific Linux 6.x, 64 bit distribution.

When I run iMosflm either from the command shell or from the ccp4i  
interface, I get an error just like this:

http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27243.html

iMosflm claims it cannot run without mosflm 7.0.9, followed by  
output indicating that mosflm 7.0.9 runs. (See attached screen  
capture of error message)
Note the linked description is for the previous versions of imosflm  
amd mosflm, so this error seems to be a repeat.


I downloaded the iMosflm and ipmosflm executables from the iMosflm  
web site, put ipmosflm in my executable directory, and this seems  
to fix the problem.


You should get the CCP4 folks to investigate this and propagate a fix.

Cheers,

--
== 
=

 All Things Serve the Beam
== 
=

   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu

imosf.err.jpg


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] strange unit cell

2013-10-25 Thread Harry Powell
Hi Sangheon

As others have said, there is nothing that stops a cell being monoclinic with 
those cell dimensions - indeed, there is nothing stopping it being triclinic, 
orthorhombic or tetragonal either (or even rhombohedral, for those of us who 
like to describe it with non-hexagonal axes). 

What *is* important is the symmetry of the reciprocal lattice; looking at 
projections of the reciprocal lattice along the major axes (i.e. a*, b* or c*) 
using a tool like hklview or viewhkl (both of which are in ccp4 6.4.0) should 
be sufficient to demonstrate whether you really have the higher symmetry.


On 25 Oct 2013, at 01:55, 유상헌 wrote:

 Hi everyone,
  
 Recently I’ve got a protein crystal and I did indexing and scaling with a 
 cubic space group (unit cell 104.115 104.115 104.115 90.0 90.0 90.0). But a 
 Rmerge value was too high (around 0.5-0.6). So, I tried lower symmetry space 
 groups and I successfully solved the structure with a space group P21 
 (Rwork/Rfree: 0.22/0.27). However, there was one strange fact. The unit cell 
 of the P21 was 104.209 104.225 104.254 90.000 89.967 90.000. I’m confused 
 with this fact that a, b, and c of the unit cell are almost same, and in 
 addition, the beta angle is too close to 90. I didn’t do refinement with a 
 twin option. So, is the space group correct? Is there anyone who know this 
 case?
  
 Thanks,
  
 Sangheon Yu
 Rm. 1053 Bldg. 200
 School of Agricultural Biotechnology
 College of Agriculture  Life Sciences
 Seoul National University
 Seoul 151-921, KOREA
  
  

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] A photograph of the Arndt-Wonacott rotation camera?

2013-10-30 Thread Harry Powell
There is, of course, a photo in The Rotation Method in crystallography, by 
Arndt and Wonacott, which currently fetches over $245 on Amazon...

On 30 Oct 2013, at 16:05, Gerard Bricogne wrote:

 Dear all,
 
 Apologies for such a retro and non-biological question, but would
 anyone have a photograph of an Arndt-Wonacott rotation camera that he/she
 would be willing to share? I collected data on the first two prototypes in
 the early seventies, then on one of the first commercial models, but I
 cannot find any images of this ground-breaking piece of equipement on the
 Web. I found images for the Enraf-Nonius precession camera and the CAD-4
 diffractometer, but not for the A-W rotation camera.
 
 This would be for use as visual material in presentations, and I would
 gratefully acknowledge the source of it. Thank you in advance!
 
 
 With fingers crossed ... .
 
  Gerard.
 
 -- 
 
 ===
 * *
 * Gerard Bricogne g...@globalphasing.com  *
 * *
 * Global Phasing Ltd. *
 * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
 * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
 * *
 ===

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] bluetooth monitor

2013-10-30 Thread Harry Powell
Hi

Or you could look at using something like an Apple TV connected to a wall 
mounted flat screen monitor to stream via wifi (which may be better suited to 
fast data rates than bluetooth). Roku or Chromecast might be cheaper 
alternatives to the Apple TV, but I know almost nothing about them.

Wireless presentations from iPad to Apple TV work pretty well, and I'm sure 
there must be more economical solutions out there.

On 30 Oct 2013, at 17:20, mesters wrote:

 Alternatively, several projectors can do that which could be an alternative? 
 Monitors have a too high resolution and that could be a problem.
 
 - J .-
 
 
  Am 29.10.13 18:05, schrieb Brett, Thomas:
 Hi all:
 I was wondering if anyone had economical suggestions on a bluetooth LED or 
 LCD monitor. I would like to have a wall mounted monitor that one could 
 easily connect laptops and imacs to for structure display, doing tutorials 
 on building into maps, etc. 
 thanks
 -tom
 
 
 Tom J. Brett, PhD
 Assistant Professor of Medicine
 Division of Pulmonary and Critical Care
 Washington University School of Medicine
 Campus Box 8052, 660 S. Euclid
 Saint Louis, MO 63110
 http://brettlab.dom.wustl.edu/
 
 
 -- 
 protest.jpgDr. Jeroen R. Mesters
 
 Gruppenleiter Strukturelle Neurobiologie und Kristallogenese
 Institut für Biochemie
 Universität zu Lübeck
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 Fax: +49-451-5004068
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Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

2014-01-20 Thread Harry Powell
Hi Wei

*Dead easy* in ccp4mg - display your object as ball and stick, clone it, then 
display the clone with reduced opacity (or increased transparency).


On 20 Jan 2014, at 04:40, Wei Shi wrote:

 Hi all,
 Please see attached Fig where they show the ligand both as sticks and spheres 
 at the same time. Does anyone happen to know how to display the ligand like 
 this? Thank you so much! 
 
 Best,
 Wei 
 
 
 Ligand.ppt

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] making high res image in pymol

2014-01-28 Thread Harry Powell
CCP4MG?

On 28 Jan 2014, at 15:27, A K wrote:

 Hi all,
 I am trying to generate a high resolution figure of a molecule together with 
 its symmetry mates (250 A readius) for a poster. If I try to ray it, the 
 pymol session crashes (perhaps too many molecules are open). Using png 
 xxx.png, dpi=300 or dpi=600 command doesn't make any difference; the image is 
 still kind of low resolution for A0 or A1. Any idea how I can generate this 
 in pymol? (I am using the free version of pymol)
 Thank you in advance,
 Alex

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











[ccp4bb] new release of Mosflm iMosflm version 7.1.0

2014-02-17 Thread Harry Powell

Hi folks

We are pleased to announce a new release of Mosflm  iMosflm; there  
are quite a few changes (a non-exhaustive list is at the end of this  
message). The default web-pages for both programs will now lead you  
directly to the new versions;


http://www.mrc-lmb.cam.ac.uk/harry/imosflm

and

http://www.mrc-lmb.cam.ac.uk/harry/mosflm
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-


Changes since 1.0.7 / 7.0.9

iMosflm has been re-numbered to 7.1.0 so that its index coincides  
with that for Mosflm.


There was no version of iMosflm between 1.0.7 and 7.1.0.

1. It is now possible to attempt to index and integrate images  
showing multiple lattices. This is an initial implementation and will  
only work in straightforward cases, for example the difference in  
orientation of the lattices must be greater than 1-2 degrees. Also at  
present it is only possible to use those reflections that are not  
overlapped when using the data in any downstream processing, and this  
will usually mean a significant drop in completeness. More details  
are given below.


2. It is now possible to distribute the integration task over  
multiple cores (parallel processing) while retaining the graphical  
output (only for OSX and Linux, not for Windows).


3.It is now possible to merge multiple MTZ files in QuickSymm/ 
QuickScale. In addition, it is possible to have some control over the  
scaling (exclude batches, reset resolution limits etc).


4. When completed, the results from the beam-search in the Indexing  
step are now sorted on the positional residual (discriminating  
against solutions with larger unit cells) to make it easier to  
identify the correct solution.


5. A traffic light system of warnings has been introduced, to make  
it easier to identify when there is a serious problem with processing.


6. Improved spot finding for very small spot sizes (eg in situ  
crystals with the Pilatus detector).


7. Small changes to autoindexing.

8. Resolution ranges to exclude from processing can now be defined  
explicitly, to avoid the severe loss in completeness that results  
from excluding all possible resolution shells for ice diffraction. In  
addition, anisotropic resolution limits may be specified.


9. It is now possible to define the detector omega angle for non- 
standard installations.


10. A site file can be used to specify experimental parameters that  
are known to be incorrect in the image header. This saves having to  
correct these parameters in every session of iMosflm. The site file  
has format  . Allowed keywords:
WAVELENGTH DISPERSION POLARISATION [PINHOLE | MIRRORS | MONO |  
SYNCHROTRON ] DIVERGENCE BEAM DISTANCE DISTORTION TILT DISTORTION  
TWIST GAIN DETECTOR REVERSEPHI DETECTOR OMEGA


11. A site file can be read or saved from the Session menu, or on  
startup using:

imosflm --site

A message will given in the launch window if any error in the keyword  
or value is detected. Other command line options are also available,  
listed by typing imosflm --help.


12. The CCP4 Uniqueify script is run automatically after TRUNCATE,  
providing an MTZ file with Rfree flags included.


13. QtRView replaces BAUBLES to present results from POINTLESS/ 
AIMLESS/TRUNCATE, so this no longer depends on a Web browser.


14. Multiple small bug fixes.

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)


Re: [ccp4bb] High Rwork/Rfree vs. Resolution

2014-02-23 Thread Harry Powell
Hi

Kay means, of course, the ACA meeting in Albuquerque, not the IUCr in Montreal!

Authors of the major processing packages will be competing for your attention...

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

 On 23 Feb 2014, at 07:55, Kay Diederichs kay.diederi...@uni-konstanz.de 
 wrote:
 
 Projects and problems like this are clearly a justification for asking to 
 deposit not only the results from data processing, but also the raw data 
 frames. These would allow developers to improve the models underlying their 
 algorithms, and to find those corner cases where the algorithms break. That 
 would help everyone.
 
 Maybe you could make this dataset (and sequence) available for the 
 forthcoming IUCr conference, as an example for a difficult dataset? (send 
 email to Ed Collins or me) You would profit from the fact that experienced 
 crystallographers do their best to make the most of your data.
 
 best,
 
 Kay
 
 On Fri, 21 Feb 2014 20:13:33 -0600, Chris Fage cdf...@gmail.com wrote:
 
 Thanks for the assistance, everyone.
 
 For those who suggested XDS: I forgot to mention that I have tried Mosfim,
 which is also better than spot fitting than HKL2000. How does XDS compare
 to Mosflm in this regard?
 
 I am not refining the high R-factor structure with NCS options. Also, my
 unit cell dimensions are 41.74 A, 69.27 A, and 83.56 A, so there isn't one
 particularly long axis.
 
 I'm guessing the low completeness of the 1.65 angstrom dataset has to do
 with obstacles the processing software encountered on a sizable wedge of
 frames (there were swaths of in red in HKL2000). I'm not sure why this
 dataset in particular was less complete than the others.
 
 Thanks,
 Chris
 
 
 On Fri, Feb 21, 2014 at 6:41 PM, Chris Fage cdf...@gmail.com wrote:
 
 Dear CCP4BB Users,
 
 I recently collected a number of datasets from plate-shaped crystals
 that diffracted to 1.9-2.0 angstroms and yielded very nice electron
 density maps. There is no major density unaccounted for by the model;
 however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
 ~0.30, respectively. Probably due to the more 2-dimensional nature of
 my crystals, there is a range of phi angles in which the reflections
 are smeared, and I am wondering if the problem lies therein.
 
 I would be grateful if anyone could provide advice for improving my
 refinement statistics, as I was under the impression that the
 R-factors should be ~5% lower for the given resolution.
 
 A few more pieces of information:
 -Space group = P21, with 2 monomers per asymmetric unit;
 -Chi square = 1.0-1.5;
 -Rmerge = 0.10-0.15;
 -Data were processed in HKL2000 and refined in Refmac5 and/or
 phenix.refine;
 -PHENIX Xtriage does not detect twinning, but hints at possible weak
 translational pseudosymmetry;
 -I was previously able to grow one atypically thick crystal which
 diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22.
 Unfortunately, the completeness of the dataset was only ~90%.
 
 Regards,
 Chris
 


Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

2014-03-03 Thread Harry Powell
Hi

If trying to build on Macs (OSX 10.5 - 10.9) I strongly recommend installing 
either the High Performance Computing gcc/gfortran or investing in the Intel 
Compilers. 

http://hpc.sourceforge.net/ 

http://software.intel.com/en-us/intel-compilers (if you have )

Performance-wise, there's not much to choose between them these days.

Clang just doesn't cut the mustard, and rolling your own compilers from the 
gcc archive can be fraught with difficulty and lead to incorrectly functioning 
compilers.

On 3 Mar 2014, at 11:08, wu donghui wrote:

 
 
 -- Forwarded message --
 From: wu donghui wdh0...@gmail.com
 Date: Mon, Mar 3, 2014 at 7:07 PM
 Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 
 10.8.5
 To: Marcin Wojdyr marcin.woj...@diamond.ac.uk
 
 
 Dear Marcin,
 
 Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line. 
 
 As is shown, it can identify gcc for gcc-4.2.1
 
  checking for gcc... gcc-4.2.1
  checking whether the C compiler works… no
 
 But indicating that the C compiler does not work.
 
 I will try Fortran compiler shortly and let you know.
 
 Best,
 
 Donghui
 
 
 
 On Mon, Mar 3, 2014 at 5:43 PM, Marcin Wojdyr marcin.woj...@diamond.ac.uk 
 wrote:
 On Mon, Mar 03, 2014 at 01:16:37PM +0800, wu donghui wrote:
 
  gcc version in my Mac OS X 10.8.5 is as below.
 
  Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
  --with-gxx-include-dir=/usr/include/c++/4.2.1
  Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
 
 That's Apple compiler. It supports C and C++ but not Fortran,
 so you also need a Fortran compiler such as gfortran.
 
  checking for gcc... gcc-4.2.1
  checking whether the C compiler works... no
 
 Did you set CC=gcc-4.2.1?
 
 Marcin
 
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 Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
 
 
 
 
 
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] Fwd: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 10.8.5

2014-03-03 Thread Harry Powell
Hi

I think you must be doing something wrong if you can't run Mosflm from the ccp4 
binary install - it runs for me. How are you trying to run it?

If you need the compilers to build Mosflm then I *very* strongly recommend 
using the compilers I mentioned in my earlier e-mail - they are what the 
developers of Mosflm (i.e. Andrew Leslie and me) use to build the distribution 
versions.

If you don't have them installed, and you need to build the Mosflm executable, 
then you should certainly install them. On OSX, installing the HPC compilers is 
a doddle.

However, my even stronger recommendation is to use the executables that we 
build here in Cambridge - they have been built and tested rigorously, and I 
don't think you will gain anything from building yourself (apart from maybe a 
headache...).

On 3 Mar 2014, at 14:51, wu donghui wrote:

 
 
 -- Forwarded message --
 From: wu donghui wdh0...@gmail.com
 Date: Mon, Mar 3, 2014 at 10:44 PM
 Subject: Re: [ccp4bb] CCP4-6.4.0 source code building failed in Mac OS X 
 10.8.5
 To: Marcin Wojdyr woj...@gmail.com
 
 
 Dear Marcin,
 
 The reason that I want to build from source is that running ipmosflm can not 
 be done from binary code, while binary code only supports imosflm running.
 
 Thanks.
 
 Best,
 
 Donghui
 
 
 On Mon, Mar 3, 2014 at 8:09 PM, Marcin Wojdyr woj...@gmail.com wrote:
  Yes, I set CC=gcc-4.2.1 in cj.rc file or type in command line.
 
  As is shown, it can identify gcc for gcc-4.2.1
 
  checking for gcc... gcc-4.2.1
  checking whether the C compiler works… no
 
 To me it looks that you set compiler to non-existent gcc-4.2.1, so it
 doesn't work.
 
 Do you have a reason to build CCP4 from source? There are binaries
 available for OSX.
 
 Best regards
 Marcin
 
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











[ccp4bb] iMosflm update available - version 7.1.1

2014-03-25 Thread Harry Powell
Dear all

We are pleased to announce an update to iMosflm available at 

http://www.mrc-lmb.cam.ac.uk/harry/imosflm

which addresses two main issues - 

(1) The QuickSymm and QuickScale options did not work correctly under some 
circumstances, e.g. on MS-Windows and also when running the iMosflm parallel 
task. They now work more reliably.

(2) A problem where a pop-up appeared with the message

can't read ::cursor::question_arrow: no such variable

when running on OSX using CCP4's TclTk has been fixed.

The current version of Mosflm (or ipmosflm...) is still 7.1.0 and this is 
compatible with iMosflm 7.1.1.

This version will be included in the next CCP4 update, due any day now.

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] jiffy for analyzing spot.xds?

2014-04-15 Thread Harry Powell
Hi Francis

At the risk of offending Wolfgang and Kay, why not try using other software to 
index  visualize spots found on the images? Mosflm is the one that comes to my 
mind straight away, but there are others that could probably do the job...

It would certainly be possible to write a jiffy that would read a SPOT.XDS and 
write it in Mosflm .spt format, which could then be read directly into iMosflm.

On 15 Apr 2014, at 02:24, Francis Reyes wrote:

 Hi all, 
 
 I'm trying to diagnose a tricky indexing issue and I suspect the spot picking 
 is poor. Any jiffy's for analyzing the spot.xds file (prior to running 
 IDXREF) ? (like an overlay onto the actual image)?
 
 Thanks,
 
 F
 
 
 
 -
 Francis E. Reyes PhD
 215 UCB
 University of Colorado at Boulder
 
 --

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] ipmosflm not connecting to XQuartz on Mac.

2014-04-16 Thread Harry Powell
Hi Francis

It works okay for me on OSX Mavericks when I use the “official” Mosflm build 
rather than the CCP4 one (choose the “X11” option when downloading).

I don’t think the CCP4 build of Mosflm includes the X11 GUI (since we’ve been 
trying for many years to wean people off it…). 

I’m assuming when you say you get a hang that it reads the commands but the X11 
GUI doesn’t appear (but I could be wrong).

It’s probably worth saying here that if people have features that they really 
do miss from the old GUI that they would like to see in iMosflm, then please 
let us know - if there’s enough demand we will do our best to oblige 
(particularly if it’s a straightforward addition to the code…).

--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 

On 15 Apr 2014, at 21:54, Francis Reyes francis.re...@colorado.edu wrote:

 Hi all,
 
 Anyone having issues getting ipmosflm to connect to XQuartz? I'm getting a 
 hang when running go just when I expect the old GUI to load. 
 
 Thanks,
 
 F
 
 
 
 -
 Francis E. Reyes PhD
 215 UCB
 University of Colorado at Boulder
 
 --


Re: [ccp4bb] PyMol and Schrodinger

2014-04-23 Thread Harry Powell

Hi

Since this is the CCP4 BB, I'd give ccp4mg a try...

On 23 Apr 2014, at Wed23 Apr 16:43, Cygler, Miroslaw wrote:


Hi,
I have inquired at Schrodinger about the licensing for PyMol. I was  
surprised by their answer. The access to PyMol is only through a  
yearly licence. They do not offer the option of purchasing the  
software and using the obtained version without time limitation.  
This policy is very different from many other software packages,  
which one can use without continuing licensing fees and additional  
fees are only when an upgrade is needed. At least I believe that  
Office, EndNote, Photoshop and others are distributed this way.
I also remember very vividly the Warren’s reason for developing  
PyMol, and that was the free access to the source code. He later  
implemented fees for downloading binary code specific for one’s  
operating system but there were no time restrictions on its use.
As far as I recollect, Schrodinger took over PyMol distribution and  
development promising to continue in the same spirit.  Please  
correct me if I am wrong.
I find the constant yearly licensing policy disturbing and will be  
looking for alternatives. I would like to hear if you have had the  
same experience and what you think about the Schrodinger policy.

Best wishes,

 Mirek





Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







[ccp4bb] HKL2MAP .sca files...

2014-04-28 Thread Harry Powell
Hi folks

When  I run hkl2map for SAD data using unmerged .sca files produced by Aimless, 
I am invariably bugged by the fact that merged .sca files (from Aimless) have 
the unit cell in the first few lines, but the unmerged files don't - so I have 
to either type in the cell dimensions or (usually) read in the merged file to 
get the cell dimensions then read in the unmerged file to get the data that 
SHELXC really wants.

So I'm wondering - what's the reasoning behind including the cell dimensions in 
the merged file and omitting them in the unmerged file? Would it break anything 
if the cell dimensions were included in the unmerged file?

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] error in starting imosflm

2014-04-28 Thread Harry Powell
Hi

When you get this error, and everything has been closed, what do you get if 
you type (in the same terminal window that you tried to start iMosflm) - 

$MOSFLM_EXEC

?

It's plain from the message that 

ipmosflm is not compatible'

that iMosflm is trying to run with an incompatible MOSFLM_EXEC (maybe from the 
old ccp4 6.3 distribution, but there could be other reasons).

On 28 Apr 2014, at 13:05, sreetama das wrote:

 Dear All,
Whenever I open up imosflm GUI from the terminal, I get the 
 following error:
 
 iMosflm version 7.1.1, 24th March 2014
 ipmosflm is not compatible.
 Please configure iMosflm with the correct executable.
 
 clicking the Configure button at the bottom of the error message panel closes 
 everything.
 the following is shown on the  terminal:
 
 MOSFLM_EXEC set to ipmosflm
 testing MOSFLM_WISH (/home/*/Software/CCP4/ccp4-6.3.0/bin/wish)
 Tcl platform is unix i686 Linux  3.8.0-32-generic
 TclTk version from info patchlevel is 8.4.19
 Tk windowing system is x11
 
 
 I had run imosflm successfully just 2 hours before this instance. After that, 
 I had enabled the older version of CCP4-6.3 (by sourcing it from the .bashrc 
 file)  for sometime to look at the options in molrep (in CCP4-6.3), and then 
 re-enabled the newer CCP4-6.4.
 Enabling ccp4-6.3 from the .bashrc file  typing imosflm opens up the older 
 7.0.1 version.
 
 The option settingsenvironment variables is not working in the newer 
 imosflm version now, changing the value in the GUI of the older version of 
 imosflm doesn't help either.
 I applied the latest CCP4 updates; that doesn't set things right.
  
 Please let me know how to re-configure iMosflm to run with ccp4-6.4.
 
 thanks  regards,
 sreetama

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] error in starting imosflm

2014-04-28 Thread Harry Powell
Hi Sreetama

That's the problem - sourcing the old ccp4 6.3 distro has set up MOSFLM_EXEC to 
point to an old copy of ipmosflm that will not run with the latest iMosflm.

   Mosflm version 7.0.9  for Image plate and CCD data 14th May 2012

which cannot be used with iMosflm 7.1.0.

So it looks like there might be an issue with the ccp4 6.4 setup not 
over-writing the environment variable MOSFLM_EXEC as it should. The immediate 
way round this would be to not source ccp4 6.3 in any terminal that you want to 
run iMosflm from.

Can you send me  c...@stfc.ac.uk (*not* to the ccp4bb, please) the output of 

echo $PATH
which $MOSFLM_EXEC
 
(1) before you source ccp4-6.3
(2) after you source ccp4-6.3
(3) after you source ccp4-6.4

So that we can get a clear idea of what is happening to your PATH when you do 
each of these three things.

On 28 Apr 2014, at 14:38, sreetama das wrote:

 Dear Sir,
   If I sorce ccp4-6.3, and then change in the bashrc file  
 source ccp4-6.4, (and source the modified .bashrc file in either case) but 
 don't close the previous terminal, then opening imosflm gives the 
 aforementioned error. After closing the imosflm GUI, if I type at the 
 terminal, I get the following:
 
 sreetama@sreetama-laptop:~/data $ $MOSFLM_EXEC
 BFONT COLOR=#FF!--SUMMARY_BEGIN--
 html !-- CCP4 HTML LOGFILE --
 hr
 !--SUMMARY_END--/FONT/B
 
 
   Mosflm version 7.0.9  for Image plate and CCD data 14th May 
 2012  ***
  Andrew Leslie and Harry Powell, MRC Laboratory of Molecular Biology,
  Hills Road, Cambridge CB2 0QH, UK
  E-mails: and...@mrc-lmb.cam.ac.uk, ha...@mrc-lmb.cam.ac.uk
  References:
  Mosflm: A.G.W. Leslie and H.R. Powell (2007), Evolving Methods for 
  Macromolecular Crystallography, 245, 41-51 ISBN 978-1-4020-6314-5
  New auto-indexing based on DPS: I. Steller R. Bolotovsky and M.G. Rossmann
  (1997) J. Appl. Cryst. 30, 1036-1040
  New iMosflm GUI:  T.G.G. Battye, L. Kontogiannis, O. Johnson, H.R. Powell 
  and A.G.W. Leslie.(2011) Acta Cryst. D67, 271-281)
 
  How much of this information is useful in diagnosing user problems?
   Mosflm run on Monday, April 28 2014 at 19:01 by sreetama
   Compiler command: gfortran
   Compiler version: GNU Fortran (GCC) 4.4.7 Copyright (C) 2010 Free 
 Software Foundation, Inc. GNU Fortran comes with NO WARRANTY, to the extent 
 permitted by law. You may redistribute copies of GNU Fortran under the terms 
 of the GNU General Public License. For more informatio
   Executable type:  ELF 32-bit LSB executable, Intel 80386, version 1 
 (SYSV), dynamically linked (uses shared libs), not stripped
   This executable was built by ccb on Thursday, June 28 2012 at 09:33
 
  MOSFLM = 
 
 Also the terminal refuses to close if I type exit. Forcibly closing the 
 terminal , and typing imosflm in a new terminal solves the problem.
 regards,
 sreetama
 On Monday, 28 April 2014 6:52 PM, Harry Powell ha...@mrc-lmb.cam.ac.uk 
 wrote:
 Hi
 
 When you get this error, and everything has been closed, what do you get if 
 you type (in the same terminal window that you tried to start iMosflm) - 
 
 $MOSFLM_EXEC
 
 ?
 
 It's plain from the message that 
 
 ipmosflm is not compatible'
 
 that iMosflm is trying to run with an incompatible MOSFLM_EXEC (maybe from 
 the old ccp4 6.3 distribution, but there could be other reasons).
 
 On 28 Apr 2014, at 13:05, sreetama das wrote:
 
  Dear All,
 Whenever I open up imosflm GUI from the terminal, I get the 
  following error:
  
  iMosflm version 7.1.1, 24th March 2014
  ipmosflm is not compatible.
  Please configure iMosflm with the correct executable.
  
  clicking the Configure button at the bottom of the error message panel 
  closes everything.
  the following is shown on the  terminal:
  
  MOSFLM_EXEC set to ipmosflm
  testing MOSFLM_WISH (/home/*/Software/CCP4/ccp4-6.3.0/bin/wish)
  Tcl platform is unix i686 Linux  3.8.0-32-generic
  TclTk version from info patchlevel is 8.4.19
  Tk windowing system is x11
  
  
  I had run imosflm successfully just 2 hours before this instance. After 
  that, I had enabled the older version of CCP4-6.3 (by sourcing it from the 
  .bashrc file)  for sometime to look at the options in molrep (in CCP4-6.3), 
  and then re-enabled the newer CCP4-6.4.
  Enabling ccp4-6.3 from the .bashrc file  typing imosflm opens up the older 
  7.0.1 version.
  
  The option settingsenvironment variables is not working in the newer 
  imosflm version now, changing the value in the GUI of the older version of 
  imosflm doesn't help either.
  I applied the latest CCP4 updates; that doesn't set things right.
   
  Please let me know how to re-configure iMosflm to run with ccp4-6.4.
  
  thanks  regards,
  sreetama
 
 
 Harry
 --
 ** note change

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

2014-04-30 Thread Harry Powell

Hi

Marcus Mueller (from Dectris, who develop and manufacture the  
Pilatus) did some work on this a couple of years ago and determined  
that an oscillation angle ~ 0.5x the mosaicity of the crystal (using  
the XDS value of mosaicity, which is not the same as Mosflm's); the  
abstract says -


The results show that fine ’-slicing can substantially improve  
scaling statistics and anomalous signal provided that the rotation  
angle is comparable to half the crystal mosaicity.



Acta Cryst. (2012). D68, 42-56[ doi:10.1107/S0907444911049833 ]
Optimal fine 
-slicing for single-photon-counting pixel detectors

M. Mueller, M. Wang and C. Schulze-Briese



My reading of this is that there is still a place for strategy  
calculations.




On 30 Apr 2014, at Wed30 Apr 15:06, Sanishvili, Ruslan wrote:


Hi Jacob,

I'll take a first crack as I am sure many will follow.
It is true that with CCD detectors one has to be careful how small  
an oscillation range to use for a frame before read noise starts to  
eat into the data quality.
Pilatus offers two major new features - is fast and is photon  
counting as opposed to integrating detector.
The speed allows to collect data without a shutter and it is very  
important as it can dramatically improve data quality. Now there  
are fast CCD detectors as well on the market.
Being a photon counter, Pilatus has no read noise which, as you  
have pointed out, allows you to collect as thin a frame as you  
want. However, it is if you consider the detector only. In reality,  
if you go very thin and very fast, you may not have enough flux to  
record the data. Also, even once we get rid of the shutter, there  
are still other sources of instabilities and they do affect the  
fast data collection adversely. One could try going (very) thin  
sliced and somewhat slow but there is another gotcha there. Most  
rotation stages used for rotating the sample crystal, do not like  
going extremely slow which would be the case with thin frames and  
long exposure times. In this case the speed may not remain as  
constant as we would like during data collection.
I think there was a publication from Diamond Synchrotron discussing  
strategies of data collection with Pilatus.
We've done a little bit of systematic studies as well and while  
things may well be sample- and facility-dependent, ~0.2 degree  
frames with ~0.2 sec exposure time seemed to make good compromise  
between above-mentioned issues. Here I would like to emphasize  
again - there certainly will be samples which will benefit from  
somewhat different parameters.

Hope it helps,
Cheers,
N.

Ruslan Sanishvili (Nukri)
Macromolecular Crystallographer
GM/CA@APS
X-ray Science Division, ANL
9700 S. Cass Ave.
Lemont, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov



From: CCP4 bulletin board [CCP4BB@jiscmail.ac.uk] on behalf of  
Keller, Jacob [kell...@janelia.hhmi.org]

Sent: Wednesday, April 30, 2014 7:49 AM
To: CCP4BB@jiscmail.ac.uk
Subject: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

Dear Pilatus/Radiation Damage Cognoscenti,

I read a few years ago, before the advent of Pilatus detectors,  
that the best strategy was a sort of compromise between number of  
images and detector readout noise overhead. I have heard that  
Pilatus detectors, however, have essentially no readout noise, so I  
am wondering whether strategies have changed in light of this,  
i.e., is the best practice now to collect as many images as  
possible at lowest exposure possible?


JPK

***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] report mosaicity

2014-05-16 Thread Harry Powell
Hi

I'm sure that a real HKL or Denzo/Scalepack expert will correct me, but my 
recollection is that you don't use any of the values from Denzo, but the value 
from Scalepack (see 
http://www.hkl-xray.com/sites/default/files/HKL2000manual/chapter3/step14-1.htm,
 for example).


On 16 May 2014, at 00:26, hongshi WANG wrote:

 Hello everyone,
 
 I am gonna report the mosaicity of my data set as required by the journal. I 
 processed the data using HKL2000. So I checked the denzo log file. I found 
 many different mosaicity values. The first one is default input (0.3), the 
 rest are corresponding to specific images. I think the mosaicity value 
 required should be an overall value or averaged value. Could you please let 
 me know how I can get it.  Or some other software can determine it. 
 I really appreciate your help and response!
 
 Hongshi

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] data processing with XDS

2014-05-19 Thread Harry Powell
Hi Almudena

Have you tried Mosflm (since this is the CCP4 BB...)? 

On 19 May 2014, at 17:18, Almudena Ponce Salvatierra wrote:

 Dear all, 
 
 I am looking for some suggestions here. I have lately collected some datasets 
 but the spots are very very weak... it is very difficult to process them. At 
 times it looks like XDS is stalled or at times it just says that it can not 
 interpret the lattice parameters... also while running integrate I have such 
 a message after each range of images:
 
 !!! WARNING !!! REFINEMENT DID NOT CONVERGE
  LAST CORRECTION SHIFT WAS   9.1E-03 (should be   1.0E-03)
 
 I guess this is not good at all. And I wonder what to do? Is there any info 
 that I can get out from these data at all? or rather not? 
 
 I wonder if the problem is to find the spots, I have tried with HKL2000 and 
 it can't even find enough of them for indexing. 
 
 Any ideas are welcome. 
 
 Best wishes, 
 
 Almudena.
 
 -- 
 Almudena Ponce-Salvatierra
 Macromolecular crystallography and Nucleic acid chemistry
 Max Planck Institute for Biophysical Chemistry
 Am Fassberg 11 37077 Göttingen
 Germany
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Harry Powell
Hi Felix

Couldn't agree more, particularly when non-native anglophones have to contend 
with limiting themselves to ASCII  characters in their filenames anyway (e.g. 
Spanish users have to carefully rename the OSX unnamed folder (carpeta sin 
título) to something without an accent...)

On 3 Jun 2014, at 12:58, Felix Frolow wrote:

 Possibility to have file names with the spaces is a curse put on the 
 community by Microsoft, and it will be a big mistake to introduce this to 
 CCP4 (my opinion).
 I guess there are much more important things new CCP4 GUI should deal with. 
 If CCP4 GUI will start to go this way,
 file names with spaces will become file names with spaces and multilingual, 
 in some these languages writing is going in the different direction.
 In my introduction to UNIX, I teach in the beginning of practical protein 
 crystallography my first demand from student is to forget about spaces in the 
 fie names and the life will be much easier.
 No fix is needed for that, concentrate on more important problems :-)
 Dr Felix Frolow   
 Professor of Structural Biology and Biotechnology, Department of Molecular 
 Microbiology and Biotechnology
 Tel Aviv University 69978, Israel
 
 Acta Crystallographica F, co-editor
 
 e-mail: mbfro...@post.tau.ac.il
 Tel:  ++972-3640-8723
 Fax: ++972-3640-9407
 Cellular: 0547 459 608
 
 On Jun 3, 2014, at 14:47 , Eugene Krissinel eugene.krissi...@stfc.ac.uk 
 wrote:
 
 I take this chance to to confirm once more, as publicly as possible, that 
 file paths with spaces are discouraged in today's CCP4. This inconvenience 
 originates from ancient times in computing when good half of CCP4 was 
 written and when spaces were disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives (albeit 
 infrequent) bug reports, where surprising behaviour is due to using file 
 paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because of technical 
 choices made quite a number of years ago. But good news are that this 
 limitation will be removed in new CCP4 Gui under development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
 This also occurred to me once where the file path had a space,(/Google 
 Drive/), when I moved the file somewhere else it worked. I was using 
 baverage from the CCP4i GUI.
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 09:20, Tim Gruene wrote:
 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit 
 to check the temperature factor, it always tell me No tables were fund 
 in this file. Could you tell me how to fix this problem? Or is there 
 another software instead of baverage I could use to check the temperature 
 factor?
 
 Thanks!
 
 Bing
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 
 
 -- 
 Scanned by iCritical.
 
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] baverage: no tables were found in this file

2014-06-03 Thread Harry Powell
I'm wondering if GUI2 will cope with accents as well as spaces (e.g. in the 
Spanish carpeta sin título which is the default new folder on Macs)?

Discipline. That's what we need...

On 3 Jun 2014, at 13:03, Mark J van Raaij wrote:

 completely agree with avoiding spaces in paths and file names, but Google 
 Drive is very handy for sharing files, so every once in a while I forget to 
 move a file someone shares with me before running Unix programs on it and get 
 strange errors. Depending on how awake one is at the time finding out the 
 source can be time-consuming...Google should really remove the space!
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 13:47, Eugene Krissinel wrote:
 
 I take this chance to to confirm once more, as publicly as possible, that 
 file paths with spaces are discouraged in today's CCP4. This inconvenience 
 originates from ancient times in computing when good half of CCP4 was 
 written and when spaces were disallowed on file system nodes.
 
 Please take a notice of this fact as CCP4 core still receives (albeit 
 infrequent) bug reports, where surprising behaviour is due to using file 
 paths with white spaces.
 
 Fixing this has proved to be a hard problem, purely because of technical 
 choices made quite a number of years ago. But good news are that this 
 limitation will be removed in new CCP4 Gui under development.
 
 Eugene
 
 On 3 Jun 2014, at 08:23, Mark J van Raaij wrote:
 
 This also occurred to me once where the file path had a space,(/Google 
 Drive/), when I moved the file somewhere else it worked. I was using 
 baverage from the CCP4i GUI.
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 
 
 
 
 
 On 3 Jun 2014, at 09:20, Tim Gruene wrote:
 
 Dear Bing,
 
 can you post the exact command you were using, please? Also please check
 with a different PDB file. In case you are using baverage from the
 command line, can you make sure you are actually using the program from
 ccp4 by typing 'which baverage' at the command prompt?
 
 Regards.
 Tim
 
 On 06/02/2014 10:16 PM, Wang, Bing wrote:
 
 Hi CCP4,
 
 Recently when I input my pdb file and run the baverage in the ccp4 suit 
 to check the temperature factor, it always tell me No tables were fund 
 in this file. Could you tell me how to fix this problem? Or is there 
 another software instead of baverage I could use to check the temperature 
 factor?
 
 Thanks!
 
 Bing
 
 
 -- 
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen
 
 GPG Key ID = A46BEE1A
 
 
 
 -- 
 Scanned by iCritical.
 

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] Proper detwinning?

2014-07-12 Thread Harry Powell
hi Chris

Can you send the date-stamped log file (called something like 
mosflm_20140712_140235.lp, I.e. with the year, month, date, etc when you ran 
the program) to me directly (i.e. not to the BB, since it's likely to be of 
little interest to all the other subscribers...) so I can have a look at the 
results of indexing, and the processing that led up to the MASKIT error?

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing)

 On 12 Jul 2014, at 00:33, Chris Fage cdf...@gmail.com wrote:
 
 Nat and Misha,
 
 Thank you for the suggestions.
 
 Xtriage does indeed detect twinning in P1, reporting similar values
 for |L|, L^2, and twin fraction as in P212121.
 
 The unit cell dimensions for the 2.0-A structure (P1) are:
 72.050  105.987  201.142  89.97  89.98  89.94 P 1
 
 The unit cell dimensions for the 2.8-A structure (P212121) are:
 75.456  115.154  202.022  90.00  90.00  90.00 P 21 21 21
 
 I have been processing in HKL2000, which only recognizes one set of
 unit cell parameters for each Bravais lattice (does anyone know how to
 change this?). Specifically, for a primitive monoclinic unit cell it 
 estimates:
 104.53  71.82  200.99  89.86  91.80  91.16
 This is the unit cell which refined to Rwork/Rfree ~ 27%/34%.
 
 Indexing in mosflm gives three options for primitive monoclinic:
 105.6  71.7 200.9  90.0  90.1  90.0
 71.7 105.6  201.0  90.0  89.9  90.0
 71.7 200.9  105.6  90.0  90.3  90.0
 Attempting to integrate in any of these space groups leads to a fatal
 error in subroutine MASKIT. I can also use the index multiple
 lattices feature to get a
 whole slew of potential space group; however, integrating reflections
 leads to the same fatal error.
 
 Finally, Zanuda tells me that P212121 is the best space group,
 according to R-factors. However, I do not believe P212121 is the
 correct assignment.
 
 Best,
 Chris
 
 
 On 7/10/14, Isupov, Michail m.isu...@exeter.ac.uk wrote:
 I would recommend to run ZANUDA in the default mode from ccp4i or on CCP4
 web server.
 ZANUDA has resolved several similar cases for me.
 
 Misha
 
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Chris Fage
 [cdf...@gmail.com]
 Sent: 10 July 2014 01:14
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Proper detwinning?
 
 Hi Everyone,
 
 Despite modelling completely into great electron density, Rwork/Rfree
 stalled at ~38%/44% during refinement of my 2.0-angstrom structure
 (P212121, 4 monomers per asymmetric unit). Xtriage suggested twinning,
 with |L| = 0.419, L^2 = 0.245, and twin fraction = 0.415-0.447.
 However, there are no twin laws in this space group. I reprocessed the
 dataset in P21 (8 monomers/AU), which did not alter Rwork/Rfree, and
 in P1 (16 monomers/AU), which dropped Rwork/Rfree to ~27%/32%. Xtriage
 reported the pseudo-merohedral twin laws below.
 
 P21:
 h, -k, -l
 
 P1:
 h, -k, -l;
 -h, k, -l;
 -h, -k, l
 
 Performing intensity-based twin refinement in Refmac5 dropped
 Rwork/Rfree to ~27%/34% (P21) and ~18%/22% (P1). Would it be
 appropriate to continue with twin refinement in space group P1? How do
 I know I'm taking the right approach?
 
 Interestingly, I solved the structure of the same protein in P212121
 at 2.8 angstroms from a different crystal. Rwork/Rfree bottomed out at
 ~21%/26%. One unit cell dimension is 9 angstroms greater in the
 twinned dataset than in the untwinned.
 
 Thank you for any suggestions!
 
 Regards,
 Chris
 


Re: [ccp4bb] Who is using 64-bit Linux?

2012-04-03 Thread Harry Powell

Hi Roger

CCP4 and Mosflm work fine in my testing - I do builds for Linux and  
Macs, both 32 and 64 bits. I wouldn't expect to see a difference in  
performance (and don't see anything significant in practice).


One thing - I think you will need to install 32-bit compatibility  
libraries for some of the code that is dynamically linked and has  
been built as 32-bit, e.g. I think ActiveTcl distros might need them  
(for iMosflm).


On 3 Apr 2012, at 20:57, Roger Rowlett wrote:

The time has come for me to upgrade my Linux OS to something more  
recent for me and my student workstations. A 32-bit distro is  
certainly conservative and compatible with CCP4 and Coot, but it  
seems like that solution hobbles my hardware and puts some  
limitations on available memory, even with PAE enabled. So who is  
using a 64-bit distro these days, and are there lingering issues of  
compatibility and dependency hell with commonly used XRD software,  
like CCP4, Coot, iMOSFLM etc.?


Ubuntu 12.04 LTS (beta) actually works OK with one simple  
workaround for the global menu for CCP4 and Coot, and wine  
compatibility is fine for running CrysalisPro in the same  
environment, so it's really comes down to whether or not the extra  
performance of a 64-bit OS is worth the pain of compatibility  
issues for XRD software. Any thoughts?


Cheers,

___
Roger S. Rowlett
Gordon  Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] Who is using 64-bit Linux?

2012-04-05 Thread Harry Powell

Hi David

I'm curious - do you mean running on a 32-bit Centos box or running  
the 32-bit Mosflm executable on a 64-bit Centos box?


We did have one report of problems with the 32-bit exe on a 64-bit  
box, which (seemingly) randomly gave one of two different results  
(either the same failure or success) - but that was fixed in the beta  
we released in July last year, and didn't occur with the 64-bit exe  
at all.


We really are grateful to people who tell us about the bugs they find  
rather than try to struggle on in silence!




Funny enough I can't get iMosflm running reliably on 32 bit CentOS  
5 or CentOS 6 and I can on 64 bits versions.


We have all running (CCP4, Coot, iMosflm, XDS, phenix, best, etc,  
etc) running in 64 bit and intent to move all user computers to  
uniform 64 bit environment on the next shutdown as it is more  
difficult to support both 32 and 64 bit enviroment.


David
--
David Aragao, PhD | Research Fellow - MX | Australian Synchrotron
p: (03) 8540 4121 | f: (03) 8540 4200 | m: 0467 775 203
david.ara...@synchrotron.org.au | www.synchrotron.org.au
800 Blackburn Road, Clayton, Victoria 3168, Australia


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] Refmac executables - win vs linux in RHEL VM

2012-04-08 Thread Harry Powell

Hi

I suspect that this is more to do with the amount of memory required,  
size of arrays etc; refinement will (in general) be more demanding in  
terms of these than an integration program like Mosflm. The last time  
I compared the Mosflm performance (which was a few years ago),  
running the same batch job on OSX 10.4 (Tiger), and on Windows XP and  
Linux Feisty Fawn (so you can tell how long ago this was) - both the  
latter running under virtual machines on the same 32-bit Intel Mac  
that the OSX job ran on) there was essentially no difference in  
performance (though I have a vague memory of Ubuntu being a little  
faster, maybe ~3%).


Some caveats -

* I used a gfortran build for OSX and Linux, g77 build for Windows
* I didn't spend too much time on this
* I wasn't running a GUI - all three as foregrounded jobs, nothing  
else running on the machine (I tried to make sure only the OS and  
essential services were running). So this wasn't a batch job in the  
traditional sense...
* gfortran builds these days are considerably faster (and compare  
well to ifort builds)


On 7 Apr 2012, at 17:50, Roger Rowlett wrote:

I don't know the state of current software, because I haven't tried  
recently, but when I set up my student crystallography workstations  
a few years back I noticed many packages (e.g. EPMR, Phaser) that  
had potentially long run times (where it is really noticeable)  
would run on the identical hardware about 2-3 times faster in Linux  
than in Windows XP. Memory swapping wasn't the issue. I was  
astounded there could be that much overhead in Windows. A Linux VM  
on a windows machine being faster than native Win7 is pretty weird,  
though.


Cheers,



On 4/7/2012 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.) wrote:


Something the developers might be interested in:

The  Refmac_5.6.0117 32-bit windows binaries run native on a  
win64  3-4x

slower than
those from  the linux distribution run
**in a RHEL6.2-64 VMware virtual machine  hosted the same windows7/64
system.**
VM/RHEL:
Refmac_5.6.0117:  End of Refmac_5.6.0117
Times: User:1015.3s System:  135.0s Elapsed:19:17
Win native
Refmac_5.6.0117:  End of Refmac_5.6.0117
Times: User:   0.0s System:0.0s Elapsed:67:49

Most peculiaralthough I think but I do not know whether the linux
binaries are 64 bit
I don't think that address space is the issue here if they are.

Maybe the paranoia-checkers in windows slow everything down
although I did not see any resources overwhelmed...

Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the
production of this email.
-


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] .CBF raw images in iMOSFLM- error

2012-04-12 Thread Harry Powell
Dear all

The problem was indeed the distance being written in mm rather than m, so some 
of our internal maths gave surprising results. This will be fixed in the next 
versions of iMosflm and Mosflm - barring finding any killer bugs I hope this 
will be released next week.
 
On 11 Apr 2012, at 16:43, Harry wrote:

 Hi Yuri
 
 If you can put some of the images on our ftp site (instructions sent 
 separately) we'll have a look. There was a problem a while ago when some 
 Pilatus  detectors changed from writing the distance in metres to writing it 
 in millimetres, but no-one told us until iMosflm started having problems.
 
 On 11 Apr 2012, at 16:08, Yuri Pompeu wrote:
 
 Hello everyone,
 
 I am trying to process ###.cbf raw images (BNL X25) using the iMOSFLM 
 utility and I get the following error message:
 Distance has refined to an unreasonable value
 This causes the program to freeze and  not open the rest of the frames.
 Also it is not picking up the X and Y beam positions.
 It looks to me like its just simply not reading the image file HEADER 
 properly.
 Anyone has encountered this before and has any ideas on how to get 
 around/fix this?
 Thanks a lot!
 Yuri
 
 
 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
 Cambridge, CB2 0QH
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





[ccp4bb] iMosflm version 1.0.6 Mosflm version 7.0.8

2012-04-16 Thread Harry Powell
Dear all

We are pleased to announce the public release of new versions of iMosflm and 
Mosflm. We have addressed many bugs and performance issues, and also tidied 
things up in some of the tasks.

If you are using a previous version we strongly recommend that you upgrade.

In brief - 

Improved processing for Pilatus images (both 6M and 2M) 
Faster processing for large datasets in iMosflm
More reliability in indexing, refinement  integration
Better feedback
Easier multi-crystal strategy

Available from our website - 

http://www.mrc-lmb.cam.ac.uk/harry/mosflm

==

In more detail  (see 
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/Release_notes for more) - 

Mosflm
==
Non-Bragg spots (eg zingers and hot pixels) and ice spots are now 
automatically removed when forming the standard profiles.

Improvements in mosaicity estimation and refinement.

Improvements in standard deviation estimates.

Improved spot finding parameters for in-house diffraction images 
and for the very small spots that can be obtained from room 
temperature (in situ screening) crystals.

More robust integration of images with very small spot separation.

iMosflm
==
The colour of the predicted reflections can be changed to improve 
visibility on weak diffraction images.

Improved selection of the correct indexing solution in cases of 
pseudosymmetry.

Scaling and merging now performed with AIMLESS rather than SCALA.
Release Notes for iMosflm version 1.0.6

New features


The speed of the interface has been much improved when processing a
large number of images in the Integration pane. The largest speed-up
came from not refreshing the profile displays afresh with every new
image integrated.

A greatly improved multi-crystal strategy option is available that
makes it much simpler to calculate a data collection strategy when
multiple crystals or multiple segments from one crystal are required 
(see below, and also see the new iMosflm tutorial for details).

Bad spots identified during processing and whose numbers are plotted
during integration can now be displayed in the Image display window.

New mosaicity estimation will produce successive plots up to 8 degrees
if required.  

Space group validation has been improved wherever a symbol can also be
typed in editable, pull-down lists (Indexing and Strategy panes).

The multi-sector, pull-down sectors list used in the Integration pane
has been adopted in the Indexing and Cell refinement panes.

Initial detector and crystal parameters are saved before refinement
and checked that they have not refined to unreasonable values. Users
may accept the warnings ( reset the parameters) or ignore them.

New items added to the Advanced integration tab of Processing options
includes provision for outliers affected by ice rings.

The maximum number of images in an integration block has been
increased from 20 to 200.  

The FindHKL function has been placed within the Image display
window's toolbar.

Smaller rotation increments have been added to the Rotation: setting
in the Auto-complete menu in the Strategy pane.

The editable 'pie' widget displayed at the bottom of the Strategy pane
for any sector can now be adjusted in single degree steps (previously
only 5 degree changes were possible).  

Individual images can now be deleted from the Images pane by selecting
them (left-click) and then right-clicking on the selected image. This
was previously only available for complete sectors.

Scala has been replaced by Aimless as the default scaling program used
by the QuickScale command button. Scala can be chosen from the
Processing options-Advanced integration tab under the Pointless 
Aimless/Scala switches.

Files containing lists of spots can be read into iMosflm and displayed
on the appropriate image. Files can be read from the main Session menu
item 'Read spots file...' and from the 'Read spots file...' button
(with an open file icon) next to the 'Index' button in the
Autoindexing pane.


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH


[ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

2012-05-11 Thread Harry Powell
Hi folks

Any of you who are considering attending ECM27 in Bergen may be interested in 
some of the sessions that have been arranged at this Software Fayre.

The full list of Microsymposia at ECM27 should be available in the next couple 
of days

 From: Martin Lutz m.l...@uu.nl
 Date: 10 May 2012 13:48:11 GMT+01:00
 To: undisclosed-recipients:;
 Subject: Crystallographic Software Fayre (ECM27, Bergen)
 
 Dear all,
 
 thanks to the local organizers, there will be a Crystallographic Software 
 Fayre
 at the ECM27 meeting in Bergen (Norway). Authors of of academic and/or 
 open-source software can present their new developments. The presentations 
 should have a tutorial character with one or more practical examples.
 
 The available time slots can be seen on the website:
 http://www.cryst.chem.uu.nl/lutz/software_fayre.html
 (This website will be updated regularly)
 
 If you are interested, please send an e-mail with your name and a preliminary
 title of the presentation to Martin Lutz, m.l...@uu.nl. The time slots will 
 be filled according to the first-come first-served principle.
 
 For information about the ECM27 congress (August 6-11, 2012), see:
 http://ecm27.ecanews.org
 
 With kind regards,
 Martin
 
 (Please forward this e-mail to anyone, who might be interested.)
 
 --
 Martin Lutz
 Crystal and Structural Chemistry
 Bijvoet Center for Biomolecular Research
 Faculty of Science
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 Tel. [+31] 030-2533902
 Fax [+31] 030-2533940

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





Re: [ccp4bb] how to ignore spot overlap in imosflm?

2012-05-14 Thread Harry Powell

Hi

This is all good advice, but there is more that you could do if  
you're desperate to use these images.


Having made sure that your spots on the images are not actually  
overlapping (i.e. by looking closely at the images), but just flagged  
as overlapping in iMosflm, you may be able (i.e. no guarantees) to  
persuade Mosflm to use them by -


(i) go to Processing Options-Advanced Integration and increase the  
values for the Profiles-Tolerance. There's a tool-tip that becomes  
visible if you hover the mouse cursor over the entry boxes which  
gives more advice on values.


(ii) if you're *really* desperate, and you have noticed that the  
overall box width and box height has increased to values much bigger  
than your spots (e.g. your spots are really only ~5-10 pixels across,  
but the box size has increased to ~30) you could try setting the  
overall box size to ~the separation distance in pixels and UNchecking  
the Optimise overall box size check box - this will fix the overall  
dimensions but allow the spot size within it to optimise. This might  
get you out of a hole...


As Zhije says, the proper solution is to collect the data without  
overlaps, though. Either of the above steps will reduce the  
measurement quality, though (i) is better than (ii).


A rule of thumb is to set the crystal to detector distance (in mm) to  
at least [maximum cell edge(Å)/wavelength(Å)] (pedants might want to  
multiply the RHS of that by 1mm. There are better methods than rules  
of thumb, though, e.g. the strategy options that are now widely  
available.


On 14 May 2012, at 04:48, Zhijie Li wrote:


Hi Xinghua,

The total intensity of each reflection needs to be accurately  
quantitated in order to calculate the structure factors. Not only  
the dots need to be well separated in the 3D reciprocal space, but  
also a small area around the dots are often needed to calculate the  
background for subtraction. That is why when two dots are getting  
too close, the programs will reject both dots. The first thing you  
need to do is to inspect the images reported with large number of  
overlaps to see if the dots are really overlapping or just close to  
each other. If the dots are barely touching or just too close to  
each other, you can manipulate the SEPERATION parameter to force  
the program to take the closely spaced spots. But keep in mind that  
you may get less accurate integration by doing so. If many spots  
are really touching each other, normally we won't force the  
programs to use them. Then the proper remedy is to move the  
detector farther and collect the dataset again (also, try to  
optimize your freezing to get the mosaicity as low as possible).


For how to play with the mosflm parameters, please read here:  
http://www.mrc-lmb.cam.ac.uk/harry/cgi-bin/keyword2.cgi?SEPARATION.  
What you need is probably CLOSE.


The hazard of high percentage of overlaps:
If the overlaps are only scattered in a whole dataset, it is OK,  
even if they make up 5-10% or even 20% of the whole dataset. It  
will only give you a lower completeness, which is not too  
detrimental to the structure solution. However, if large,  
continuous regions in the dataset are missing, that will cause you  
to have poorly defined regions in the calculated map, often seen as  
featureless stripes or layers in the map. Unfortunately, when you  
have closely spaced reflections, the latter is often the case. The  
proper solution is to collect the data at a greater detector  
distance to resolve the spots (after taking the test images, both  
imosflm and HKL2000 can simulate the collection run to help you to  
decide what distance you need). In cases that you have a long unit  
cell (200A), the first thing you need to do is to align the long  
edge of the Unix cell with the rotational axis of the pin. In the  
difficult cases, you probably even need to shoot multiple crystals  
and combine the datasets to get enough completeness.


Zhijie


From: Xinghua Qin
Sent: Sunday, May 13, 2012 10:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] how to ignore spot overlap in imosflm?

Dear CCP4ers,

We collected a diffraction dataset with high percentage of spot  
overlaps, It would be so kind to tell me how to ignore spot overlap  
in imosflm and explain the hazard of high percentage of spot overlaps.

Thanks in advance.

Best wishes

Xinghua Qin
--
Xinghua Qin
State Key Laboratory of Plant Physiology and biochemistry
College of Biological Sciences
China Agricultural University
No.2, Yuan Ming Yuan West Road
Haidian District, Beijing, China 100193
Tel: +86-10-62732672
E-mail: xinghua...@126.com




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






[ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

2012-05-22 Thread Harry Powell
Hi folks

The list of microsymposia at ECM27 is now available, but the list of speakers 
has not yet been finalised. Bear in mind that earlybird registration closes 
on 31st May, when the cost jumps by 750 NOK (~€100) for full participants, 
550NOK (~€72) for students.

The meeting website is 

http://ecm27.ecanews.org/

On 11 May 2012, at 10:36, Harry Powell wrote:

 Hi folks
 
 Any of you who are considering attending ECM27 in Bergen may be interested in 
 some of the sessions that have been arranged at this Software Fayre.
 
 The full list of Microsymposia at ECM27 should be available in the next 
 couple of days
 
 From: Martin Lutz m.l...@uu.nl
 Date: 10 May 2012 13:48:11 GMT+01:00
 To: undisclosed-recipients:;
 Subject: Crystallographic Software Fayre (ECM27, Bergen)
 
 Dear all,
 
 thanks to the local organizers, there will be a Crystallographic Software 
 Fayre
 at the ECM27 meeting in Bergen (Norway). Authors of of academic and/or 
 open-source software can present their new developments. The presentations 
 should have a tutorial character with one or more practical examples.
 
 The available time slots can be seen on the website:
 http://www.cryst.chem.uu.nl/lutz/software_fayre.html
 (This website will be updated regularly)
 
 If you are interested, please send an e-mail with your name and a preliminary
 title of the presentation to Martin Lutz, m.l...@uu.nl. The time slots will 
 be filled according to the first-come first-served principle.
 
 For information about the ECM27 congress (August 6-11, 2012), see:
 http://ecm27.ecanews.org
 
 With kind regards,
 Martin
 
 (Please forward this e-mail to anyone, who might be interested.)
 
 --
 Martin Lutz
 Crystal and Structural Chemistry
 Bijvoet Center for Biomolecular Research
 Faculty of Science
 Utrecht University
 Padualaan 8
 3584 CH Utrecht
 The Netherlands
 Tel. [+31] 030-2533902
 Fax [+31] 030-2533940
 
 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
 Cambridge, CB2 0QH
 
 
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





Re: [ccp4bb] Fwd: Crystallographic Software Fayre (ECM27, Bergen)

2012-06-05 Thread Harry Powell

Dear all

The deadlines below have been extended to 15th June. Note that, since  
the deadline for abstracts is still open, there should still be the  
opportunity of having your work chosen to be an oral presentation  
(three of the five talks in MS are chosen from the abstracts).


The lists of speakers have not yet been finalised (how can they be  
when the abstract submission process is still open?), but a taster of  
some of the talk titles and speakers in a few of the MS is listed at -


http://sig9.ecanews.org/sig9_activities.html

Students of history may be interested to learn that Bergen was  
apparently founded by the son of Harald Hardrada, the Norwegian king  
who was killed at the battle of Stamford Bridge in 1066, just over a  
fortnight before a seminal moment in English history.


On 22 May 2012, at 15:08, Harry Powell wrote:


Hi folks

The list of microsymposia at ECM27 is now available, but the list  
of speakers has not yet been finalised. Bear in mind that  
earlybird registration closes on 31st May, when the cost jumps by  
750 NOK (~€100) for full participants, 550NOK (~€72) for students.


The meeting website is

http://ecm27.ecanews.org/

On 11 May 2012, at 10:36, Harry Powell wrote:


Hi folks

Any of you who are considering attending ECM27 in Bergen may be  
interested in some of the sessions that have been arranged at this  
Software Fayre.


The full list of Microsymposia at ECM27 should be available in the  
next couple of days



From: Martin Lutz m.l...@uu.nl
Date: 10 May 2012 13:48:11 GMT+01:00
To: undisclosed-recipients:;
Subject: Crystallographic Software Fayre (ECM27, Bergen)

Dear all,

thanks to the local organizers, there will be a Crystallographic  
Software Fayre
at the ECM27 meeting in Bergen (Norway). Authors of of academic  
and/or open-source software can present their new developments.  
The presentations should have a tutorial character with one or  
more practical examples.


The available time slots can be seen on the website:
http://www.cryst.chem.uu.nl/lutz/software_fayre.html
(This website will be updated regularly)

If you are interested, please send an e-mail with your name and a  
preliminary
title of the presentation to Martin Lutz, m.l...@uu.nl. The time  
slots will be filled according to the first-come first-served  
principle.


For information about the ECM27 congress (August 6-11, 2012), see:
http://ecm27.ecanews.org

With kind regards,
Martin

(Please forward this e-mail to anyone, who might be interested.)

--
Martin Lutz
Crystal and Structural Chemistry
Bijvoet Center for Biomolecular Research
Faculty of Science
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
Tel. [+31] 030-2533902
Fax [+31] 030-2533940


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] error popup with imosflm 1.0.6 despite valid executable MOSFLM_EXEC for mosflm 7.0.8

2012-06-15 Thread Harry Powell
Hi folks

This problem arises because I inadvertently included the versions of 
MOSFLM_EXEC that require X11 libraries in the iMosflm distribution (for Linux 
only - Macs and Windows were okay) - iMosflm doesn't need these. 

I've put fixed binaries on the Mosflm download site for Linux - 


http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/pre-built/mosflm_linux_32_noX11.zip

and 


http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver708/pre-built/mosflm_linux_64_noX11.zip


If you haven't had this problem you don't need to download the new copies.


On 15 Jun 2012, at 16:10, hari jayaram wrote:

 Hi,
 I just installed imosflm 1.0.6 and the associated mosflm 7.0.8. I can
 run the mosflm executable by itself . Yet when imosflm starts it gives
 me an error popup
 
 iMosflm cannot run /home/hari/imosflm_download/1.06/imosflm/bin/mosflm.
 
 And then gives me the output from the running of the mosflm executable
 
 BFONT COLOR=#FF000:/...etc
 
 
 I have chmod-ed +x the MOSFLM_EXEC mosflm and it runs quite well on the shell.
 
 I also have an older imosflm and mosflm that work..any ideas why I get
 the error popup .
 
 I have a feeling its something that bleeding through my .bashrc file
 because it complains that some Postgres library is not there in the
 path further down after it gives the header from the mosflm executable
 output. This postgres error msg may be coming from something else
 being sourced.
 
 Help in troubleshooting will be greatly appreciated
 
 
 I am attaching a screenshot.
 
 Thanks for your help
 Hari
 imosflm-1.0.6-wrror-popup.png

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





Re: [ccp4bb] High Rfree values and using Bruker detector w/ iMosflm

2012-06-25 Thread Harry Powell
Hi Annette

Mosflm can only read Bruker images correctly after they have been converted 
with frm2frm (available from Bruker) - this program unwarps them and writes 
them in a format that Mosflm can understand. 

On 25 Jun 2012, at 17:25, Annette Medina Morales wrote:

 Also, I have recently tried using iMosflm to refine the data but using the 
 .sfrm images from the Bruker detector is problematic since I get an 
 Application error that reads invalid command name and an Image read error 
 that reads Error reading image header.  Message from Mosflm is error reading 
 record 33: check image is correct size.  Does anyone have any advice on how 
 to correct this since I understand that iMosflm is supposed to be able to 
 read Bruker .sfrm images? Thanks! Annette

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





[ccp4bb] Release of iMosflm 1.0.7 and Mosflm 7.0.9

2012-07-05 Thread Harry Powell
Dear all 

We wish to announce the release of the latest versions of iMosflm and Mosflm, 
downloadable via our web-pages at 

http://www.mrc-lmb.cam.ac.uk/harry/mosflm/

These address a number of bugs and inconveniences that have been brought to our 
notice following the release of iMosflm 1.0.6 and Mosflm 7.0.8, especially:

• Fixed the solution picking code in autoindexing (broken in 1.0.6)

• Improved rendering of Pilatus images in Image Display

• Ensure the user's choice to use Scala in preference to Aimless for 
scaling persists between sessions

• The addition of the image_template in the XML for the bad spots 
response now means iMosflm 1.0.7 requires iMosflm 7.0.9

• Ensure the 'Add images' menu can be resized to show a longer list of 
files  directories by moving the 'Selected images' only checkbox down to final 
row.

• Add traps to prevent 'Index' button being clicked if image number(s) 
are present but no spot finding has been done.

• Ensure the MTZ filename is updated when toggling between sectors.

• Add ROFF and TOFF to the refined parameter checking.

• Fixed typographical error in the path to baubles when running 
Pointless.

• Do not require the scaling programs to be in CBIN as CCP4_BIN is in 
the PATH.

• Save the Strategy file as soon as the yellow, cross-hatched sector is 
plotted after the Auto-complete calculation.




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH


[ccp4bb] Master in Crystallography and Crystallisation?

2012-07-31 Thread Harry Powell
Hi folks

First off, apologies to all who are not members of the BCA, since this is a 
question for the BCA members amongst you - I asked BCA to send out an advert 
for this course, and their admin people say they have done so - but I haven't 
received it, so I was wondering if anyone had got it? 

If you are a member and either have or have not received it, could you let me 
know asap? PLEASE don't reply to the BB, reply to me directly!

BTW, the URL for the course is 

http://lafactoria.lec.csic.es/mcc/

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH


Re: [ccp4bb] Process multiple data sets

2012-08-01 Thread Harry Powell

Hi

I'd process (i.e. index, refine, integrate) each data set  
individually, check that (at least) they all have the same crystal  
system, then combine the datasets using Pointless. Then scale with  
Aimless.


Of course, I'd use Mosflm/Pointless/Aimless rather than HKL, but  
that's another question (pace, ZO, WM, MM!)


On 1 Aug 2012, at 14:08, Uma Ratu wrote:

The data sets were collected from the same crystal by scan  
collecting 40 frames from each section. The space group of this  
crystal is P2.


My guess that I may have to index and integrate each set  
indivadually, and then scale them together.


Thanks

Uma

On Wed, Aug 1, 2012 at 9:01 AM, Machius, Mischa Christian  
mischa_mach...@med.unc.edu wrote:

Not much info to go by...

Anyway, if the program 'goes crazy' you either have very different  
exposure levels, radiation damage leading to non-isomorphism, or  
you have a trigonal space group (P3xxx or P6xxx) and forgot to make  
sure all batches are indexed the same way.


If you have translated your crystal between batches, HKL2000 won't  
of course be able to process all batches in one go. If you haven't  
touched the crystals at all, and alln-in-one processing doesn't  
work, the parameters at the end of one batch may not be accurate to  
start off a new batch, which is mostly due to inaccurate  
goniostats. In that case, you will need to process the batches  
individually and them combine them during scaling.


Hope that helps.

MM


On Aug 1, 2012, at 8:50 AM, Uma Ratu wrote:

 Dear All:

 I collected 5 data sets from one crystal and would like to  
process them together.


 Here is how I did:

 In HKL2000, load the all data sets. Index each set. When I try  
Intergrate, the program automatically go through the whole data  
sets there, and do not go through.


 I then process data sets by loading one at each time. Index,  
intergrate and scale all go through very smoothly. But when I put  
them together, the program just goes crazy.


 Thank you for advice

 Uma




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] Process multiple data sets

2012-08-01 Thread Harry Powell

Hi

I don't think Phil or I are saying that HKL is not a good tool to use  
in this case - but


(*) I develop Mosflm, so I have a certain bias.

(*) As far as Pointless and Aimless are concerned, to get the best  
out of them you need to have some geometrical information that the  
authors of HKL have not included in the reflection output files.  
Mosflm (and XDS  Saint...) do give this information. So if you want  
to use Pointless and Aimless at any point, it may be better to use a  
different integration package than HKL (bearing in mind Phil's point  
about checking your symmetry with Pointless)...


On 1 Aug 2012, at 16:16, Uma Ratu wrote:


Please correct me if I am wrong:

The HKL is not good to combine multiple data sets, even they are  
come from the same crystal?


With HKL, I also tried this way:

Index, integrate each data set individually, they all have the same  
space group.

Then scale them together.

Still, the graph from scale of the whole set look very wired  
compared with those of individuals.


Uma

On Wed, Aug 1, 2012 at 9:55 AM, Phil Evans p...@mrc-lmb.cam.ac.uk  
wrote:
Note that neither Aimless nor Scala will do a particularly good job  
at scaling data from Denzo or Scalepack, since the output files  
from Scalepack are missing essential geometrical information. They  
work well with data from Mosflm or XDS (or Saint) (although AFAIK  
the XDS  Saint scaling programs work perfectly well)


However, Pointless may still be useful to check that you have  
indexed them consistently


Phil

On 1 Aug 2012, at 14:36, Harry Powell wrote:

 Hi

 I'd process (i.e. index, refine, integrate) each data set  
individually, check that (at least) they all have the same crystal  
system, then combine the datasets using Pointless. Then scale with  
Aimless.


 Of course, I'd use Mosflm/Pointless/Aimless rather than HKL, but  
that's another question (pace, ZO, WM, MM!)


 On 1 Aug 2012, at 14:08, Uma Ratu wrote:

 The data sets were collected from the same crystal by scan  
collecting 40 frames from each section. The space group of this  
crystal is P2.


 My guess that I may have to index and integrate each set  
indivadually, and then scale them together.


 Thanks

 Uma

 On Wed, Aug 1, 2012 at 9:01 AM, Machius, Mischa Christian  
mischa_mach...@med.unc.edu wrote:

 Not much info to go by...

 Anyway, if the program 'goes crazy' you either have very  
different exposure levels, radiation damage leading to non- 
isomorphism, or you have a trigonal space group (P3xxx or P6xxx)  
and forgot to make sure all batches are indexed the same way.


 If you have translated your crystal between batches, HKL2000  
won't of course be able to process all batches in one go. If you  
haven't touched the crystals at all, and alln-in-one processing  
doesn't work, the parameters at the end of one batch may not be  
accurate to start off a new batch, which is mostly due to  
inaccurate goniostats. In that case, you will need to process the  
batches individually and them combine them during scaling.


 Hope that helps.

 MM


 On Aug 1, 2012, at 8:50 AM, Uma Ratu wrote:

  Dear All:
 
  I collected 5 data sets from one crystal and would like to  
process them together.

 
  Here is how I did:
 
  In HKL2000, load the all data sets. Index each set. When I  
try Intergrate, the program automatically go through the whole  
data sets there, and do not go through.

 
  I then process data sets by loading one at each time. Index,  
intergrate and scale all go through very smoothly. But when I put  
them together, the program just goes crazy.

 
  Thank you for advice
 
  Uma



 Harry
 --
 Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH







Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






Re: [ccp4bb] d*trek

2012-08-24 Thread Harry Powell
Hi

It should do. Jim will know for sure.

On 23 Aug 2012, at 23:08, jlliu liu wrote:

 My real questions is:
  
 Does d*trek recognize the img file format collected at ALS or APS and process 
 the data?
  
 Thanks!
  
 
  
 On Thu, Aug 23, 2012 at 6:00 PM, jlliu liu jlliu20022...@gmail.com wrote:
 Do anybody know if d*trek can process data collected from APS?  Thanks a lot 
 in advance. 
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH





Re: [ccp4bb] imosflm, bad predictions - solved!

2012-10-19 Thread Harry Powell
Hi

This was indeed the issue - on this beamline (I think it's 19-ID-D at APS, but 
I'm waiting on confirmation of this) the phi axis rotates the opposite way to 
usual, so Mosflm needs to be told.

(As an aside, in the most recent release we automatically check the serial 
number of the detector to see if it's in a list where we know this is done - 
but our internal list is not comprehensive [and some detectors don't record 
this information in a useful way...]. We'll add the detector from Jan's  
dataset to our list)

The best way to check if this is the problem is to - 

(1) index in the normal way using two images. If 

(a) the predictions don't look right
and
(b) the sigma(x,y) (the column to the right of the cell dimensions) is 
more than you would normally expect (say, for a good looking crystal if it's 
more than ~0.1mm) 

(c) the cell is not close to what you expect

then this may be the issue.

(2) Index from the first image chosen by Mosflm and see if the predictions 
match and sigma(x,y) is much smaller than in (1b)

(3) Index from the second image chosen by Mosflm and check predictions (for 
this image) and sigma (x,y)

If (2) and (3) look good but (1) is bad, there's a good chance the phi is 
rotating the opposite way to that which Mosflm expects. In this case, check the 
setting box in the Settings  - Experiment Settings - Experiment window and 
try (1) again - remembering that if you do this you need to repeat the spot 
search.

The orientation of the displayed image has no bearing on the beam centre used 
by Mosflm as read from the image header. Some beamlines record the beam centre 
in the Denzo frame, some in the Mosflm frame, some in both (and possibly some 
do in some other frame - there's a wide choice!). 

In iMosflm, the image is displayed with respect to the internal Mosflm frame - 
so it's consistent with how we treat the images computationally. Other programs 
(probably?) display the image as thee detector software displays it.

On 18 Oct 2012, at 22:12, Ben wrote:

 I had a very similar problem with data collected on a particular beamline.  
 The issue was that I had to reverse the spindle direction in imosflm 
 settings.  Also, when I load data from this beamline into imosflm the program 
 rotates the images by 90 degrees for some reason (this does not happen in 
 HKL2000).  Because of this rotation, the beam center that I used in HKL2000 
 was different than the beam center position for imosflm.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 








Re: [ccp4bb] relations between groups and subgroups?

2012-11-13 Thread Harry Powell
Hi

The relations are in International Tables Vol A; in the 2006 edition you find 
them in section 9.2 by P.M. de Wolff, pp 750 - 755; the transformations for the 
44 characteristic lattices (or lattice characters...) are in Table 9.2.5.1.

In Mosflm, the autoindexing penalties are based on the differences between the 
result of the transformations applied to the real triclinic basis and what you 
would get if the result was perfect.

On 13 Nov 2012, at 09:55, vincent Chaptal wrote:

 Dear all,
 
 I am not sure I understand point groups and relations between groups and 
 subgroups anymore, and would appreciate some guidance.
 
 I was under the impression that all point groups were related to an original 
 P1 cell, and that by applying specific lattice symmetries, one could get 
 higher point groups. Thus, if one knows the symmetry operators, one could 
 jump from one point group to another. Inspection of the reflections can then 
 determine the real point group and space group.
 At least that's what I thought Mosflm was doing? Am I correct?
 P1 +(symm-opp)C2 + (symm-opp2)P3
 same P1 +(symm-opp3) P2 + (symm-opp4)P222 
 If that's the case, could someone point to me where to find these symmetry 
 opperators (International tables?), because it's not obvious to me.
 
 Or are these relations between groups and subgroups only true for certain 
 crystals where the cell parameters are specific, and allows a symmetry 
 operator to generate a higher symmetry point group?
 
 Thank you for your help.
 vincent

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 








Re: [ccp4bb] Yesterday (was) Today yesterday...

2012-12-21 Thread Harry Powell
Hi all

Since this is a discussion by protein crystallographers about a possible 
standard, I will expect a consensus (or several conflicting consensuses*) to be 
reached sometime after I have retired...

I'll look forward to the discussions spilling out into the CCP4 Study Weekend. 

* Since consensus was originally a fourth (not second) declension Latin noun, 
the nominative and accusative plurals are also consensus (but with a long 
u). Consensi is just wrong...

Have a nice break!

On 21 Dec 2012, at 14:45, Bosch, Juergen wrote:

 Hi David,
 
 on a computer I agree 20121221 is the way to go (but even then you could 
 still do ls -lta), but on Eppendorf tubes that is precious real estate for 
 other important numbers or letters hence the 12d21 :-)
 
 And thanks for catching my double J this was just a test if somebody would 
 actually read what I wrote :-)
 And the corrected values were indeed right, aka following the simple rule I 
 mentioned.
 
 Jürgen
 
 On Dec 21, 2012, at 9:15 AM, David Schuller wrote:
 
 On neither case does an alphanumeric sort coincide with a chronological 
 sort. The obvious solution is to petition to have the months renamed 
 alphabetically.
 
 On 12/21/12 03:23, Tom Murray-Rust wrote:
 Hi Juergen,
 
 Your scheme as printed has two J's - so January and July are 
 indistinguishable! I would suggest the letters should instead be 
 JFMAYULGSOND. 
 
 On 21 Dec 2012, at 01:52, Bosch, Juergen jubo...@jhsph.edu wrote:
 
 May I introduce you to another fool proof way:
 12d12 ...
 J, F,M,A,Y,J,U,G,S,O,N,D for the months, simply first letter, but if taken 
 move to the second letter etc.
 
 
 -- 
 ===
 All Things Serve the Beam
 ===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu
 
 
 
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 








[ccp4bb] Coot's hidden talents!

2013-01-11 Thread Harry Powell
Hi

Just noticed this - 

http://www.bbc.co.uk/news/uk-20978904

do we know the artist? He has just moved to Cambridge...

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 








Re: [ccp4bb] need some suggestions for crystallization

2013-02-04 Thread Harry Powell

Hi David

try going back to the one that started it all,* myoglobin, a recipe  
is at


http://www.rigaku.com/products/protein/recipes

(* feel free to argue about this)

On 4 Feb 2013, at Mon4 Feb 16:03, David Roberts wrote:

So, I know I say this every time I post on this board, but here it  
goes again.


I'm at an undergrad only school, and every 2 years I teach a class  
in protein crystallography.  This year I'm being super ambitious,  
and I'm going to take a class of 16 to the synchrotron for data  
collection.  It's just an 8 hour thing, to show them the entire  
process.  I'm hoping that we can collect 5-6 good data sets while  
there.


I would like them to grow their own crystals, and go collect data.  
Then we'd come back and actually do a molecular replacement (pretty  
easy/standard really).  Just to get a feel for how it works.


The protein I do research on is not one that I would push on this,  
as the crystals are hard to grow, they are very soft, and the data  
just isn't the best (resolution issues).  I do have a few that will  
work on my proteins, but I was thinking of having others in the  
class grow up classic proteins for data collection.  Obviously  
lysozyme is one, but I was wondering what other standard  
bulletproof conditions are out there.


Can you all suggest some protein crystallization conditions (along  
with cryo conditions) for some commercially available proteins?   
I'm looking to get 6-8 different ones (and we'll just take them and  
see how it goes).  I wouldn't mind knowing unit cell parameters as  
well (just a citation works, I can have them figure it out).  I  
have about 7 weeks to get everything grown and frozen and ready to go.


Any help would be greatly appreciated.  It always amazes me how  
helpful this group is.  Thank you very much.


Dave


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] need some suggestions for crystallization

2013-02-04 Thread Harry Powell

I don't know. Is there?

On 4 Feb 2013, at Mon4 Feb 16:15, Jayashankar wrote:


Dear Powell,

Isn't it there a way to data mine the PDB or the other repository  
source for the time/duration/days of the crystals obtained.


Dr. Jayashankar Selvadurai
Hannover
Germany



On Mon, Feb 4, 2013 at 5:10 PM, Harry Powell harry@mrc- 
lmb.cam.ac.uk wrote:

Hi David

try going back to the one that started it all,* myoglobin, a recipe  
is at


http://www.rigaku.com/products/protein/recipes

(* feel free to argue about this)

On 4 Feb 2013, at Mon4 Feb 16:03, David Roberts wrote:

So, I know I say this every time I post on this board, but here it  
goes again.


I'm at an undergrad only school, and every 2 years I teach a class  
in protein crystallography.  This year I'm being super ambitious,  
and I'm going to take a class of 16 to the synchrotron for data  
collection.  It's just an 8 hour thing, to show them the entire  
process.  I'm hoping that we can collect 5-6 good data sets while  
there.


I would like them to grow their own crystals, and go collect data.  
Then we'd come back and actually do a molecular replacement  
(pretty easy/standard really).  Just to get a feel for how it works.


The protein I do research on is not one that I would push on this,  
as the crystals are hard to grow, they are very soft, and the data  
just isn't the best (resolution issues).  I do have a few that  
will work on my proteins, but I was thinking of having others in  
the class grow up classic proteins for data collection.  Obviously  
lysozyme is one, but I was wondering what other standard  
bulletproof conditions are out there.


Can you all suggest some protein crystallization conditions (along  
with cryo conditions) for some commercially available proteins?   
I'm looking to get 6-8 different ones (and we'll just take them  
and see how it goes).  I wouldn't mind knowing unit cell  
parameters as well (just a citation works, I can have them figure  
it out).  I have about 7 weeks to get everything grown and frozen  
and ready to go.


Any help would be greatly appreciated.  It always amazes me how  
helpful this group is.  Thank you very much.


Dave


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)








Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] Pilatus 300K CBF to Oxford Diffraction format convert

2013-02-06 Thread Harry Powell

Hi Tim

I've looked at these images and they differ from the normal 6M images  
(miniCBF) in that they are a stab at writing fullCBF, i.e. with  
imgCIF style data content - unfortunately, there are a few syntax  
errors which need fixing before programs that use the header  
information (like Crysalis Pro, inter alia;-)) can do much useful  
with them.


XDS (and any other programs that ignore header information) should be  
able to process these provided the correct beamline values are supplied.


On 6 Feb 2013, at Wed6 Feb 11:19, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jose,

it is odd the software should read 6M but not 0.3M Pilatus files - the
format is probably the same, only the dimensions would differ - at
least that's my guess.
While you are waiting you might start processing your data with XDS,
which is well suited also for small molecules crystals. If your cell
is small, I recommend turning of refinement during the integration
step (REFINE(INTEGRATE)=!) and only refine all parameters during the
CORRECT step.
You need to make sure the spots are correctly predicted on the
FRAME.cbf, i.e. the cell from indexing is close enough to the  
correct one.


Best wishes,
Tim

On 02/06/2013 11:35 AM, Jose Trincao wrote:

Dear all, sorry for the semi-off-topic but I'm trying to help
convert some diffraction images and this seemed like a good place
to ask. We are trying to process some images collected on a Pilatus
300K with the Crysalis Pro software (small molecule) but it seems
to only be able to read Pilatus 6M frames. Is there an easy way to
convert the 300K dbf files to something readable by Crysalis?
(Oxford Diffraction, marCCD, Rigaku or Bruker AXS-SAXI). Thanks!

Jose


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Harry
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Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] Measure Cell option in imosflm

2013-02-25 Thread Harry Powell
Hi Richard

I'm afraid it doesn't exist at the moment. It could be added if there's 
sufficient demand for it.

On 25 Feb 2013, at 12:57, Bayliss, Richard (Dr.) wrote:

 Does anyone know how to access the 'Measure Cell' function in iMosflm? This 
 function in ipmosflm allowed you to click on a pair of spots, then input the 
 number of diffraction orders, to output a rough measure of the cell length. 
 
 Any help appreciated!
 Thanks
 Richard
 
 =
 Dr Richard Bayliss, Reader in Structural Biology
 Department of Biochemistry
 Henry Wellcome Building
 University of Leicester
 Lancaster Road, Leicester
 LE1 9HN
 
 Tel: 0116 2297100
 Web: 
 http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/research
 
 Elite Without Being Elitist
 Times Higher Awards Winner 2007, 2008, 2009, 2010, 2011
 Follow us on Twitter http://twitter.com/uniofleicester
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 









Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

2013-03-06 Thread Harry Powell

Hi Fred

If you look very carefully at your Fortran code you will probably   
find a small error/inconsistency that g77 allowed but gfortran picked  
up on or compiled as written rather than as intended. My move from  
g77 to gfortran when building Mosflm (which is moderately large) was  
pretty painless, but I did find that when I got errors of this type  
the fault was when the code did not adhere to standards.


Generally speaking, gfortran adheres to the current Fortran standards  
more strictly than g77. Recent versions give Mosflm executables that  
are within a few percent of the performance that I get with the Intel  
Fortran ifort compilers (actually, sometimes faster, sometimes  
slower)- I've checked this on both Mac and Linux.


I use gfortran for development, ifort for checking things are still  
okay, and also run an old Linux box with g77 for further checking in  
case I've missed something earlier. My Windows executable of Mosflm  
still uses g77 (the mingw cross-compiler run on OSX).


However, there are persistent reports out there of people who find  
their code runs much faster when compiled with ifort - so I guess  
this is very much code dependent.


I can have a look at your code if it would help.

HTH

On 6 Mar 2013, at Wed6 Mar 09:48, vellieux wrote:


Hello,

For those who still know the Fortran language and its Fortran 77  
variant, I used to have a g77 compiler here (Linux box), and now on  
the new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for  
compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign- 
double -funroll-loops -ffast-math -fno-second-underscore $1.f ,  
followed by the libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77  
- I removed the flag -fno-globals which doesn't seem to exist any  
more in gfortran) the Fortran code that I see appears to have all  
parentheses in the correct places.


Any idea of what must be done with existing Fortran 77 code in  
order to get it to compile and run with gfortran ? Otherwise any  
idea which compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] first use of synchrotron radiation in PX

2013-03-13 Thread Harry Powell
Hi 

Not sure if this is strictly speaking the first protein *solved* on a 
synchrotron, but I think this is the first report of shooting protein crystals 
at a synchrotron in the widely available literature - 

http://www.pnas.org/content/73/1/128.full.pdf+html

Phillips J C, Wlodawer A, Yevitz M M and Hodgson K 0 1976 Proc. Nat. 
Acad. Sci. USA 73 128-32

Applications of synchrotron radiation to protein crystallography: 
Preliminary results


On 13 Mar 2013, at 14:38, Alan Cheung wrote:

 Hi all - i'm sure this many will know this : when and what was the first 
 protein structure solved on a synchrotron?
 
 Thanks in advance
 Alan
 
 
 -- 
 Alan Cheung
 Gene Center
 Ludwig-Maximilians-University
 Feodor-Lynen-Str. 25
 81377 Munich
 Germany
 Phone:  +49-89-2180-76845
 Fax:  +49-89-2180-76999
 E-mail: che...@lmb.uni-muenchen.de

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] How to calculate data collection strategy manually?

2013-03-26 Thread Harry Powell
Hi Saleem

I can strongly recommend reading and digesting this paper (open access from the 
IUCr website, so you don't need a subscription) - 

Dauter, Z., Acta Cryst. (1999). D55, 1703-1717   -  Data-collection 
strategies

http://journals.iucr.org/d/issues/1999/10/00/ba0020/ba0020.pdf

Once you've read it, the issues that you should take into account when devising 
your strategy shuld be apparent.

Of course, all the best integration programs also have strategy options built 
into them as well if you decide not to do it manually after all

On 26 Mar 2013, at 12:25, saleem raza wrote:

 How to calculate data collection strategy manually. I was wondering if any 
 one can answer this, if we have to calculate data collection strategy 
 manually? regards Saleem

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 


Re: [ccp4bb] process data from two crystals in-house data

2013-03-28 Thread Harry Powell

Hi

I'd just integrate them individually with Mosflm, then merge the two  
MTZ files into one with Pointless(*), then scale with Aimless.


(*)
pointless hklin first.mtz second.mtz hklout pointless.mtz
aimless hklin pointless.mtz hklout aimless.mtz

should do the trick - pointless even works with a wild card if you  
have many mtz files to merge (not sure how many many can be, but  
it's certainly a lot more than 10), e.g.


pointless hklin part_*.mtz hklout pointless.mtz

Dead easy with normal CCP4 programs, RTM for pointless for further  
details.


You can even do this in ccp4i *really easily*!

On 28 Mar 2013, at Thu28 Mar 10:08, S. Thiyagarajan wrote:


Dear all
I have two data sets, 75 frames each from crystals of the same  
protein - same cell parameters/space group (P4).
I could process them seperately each yielding  90% completeness  
but with  poor multiplicity (  2 )


If I merge the data sets using CAD, I loose the data reduction  
statistics of the combined data set.


I do not have HKL2000.

Which (free) tool can handle two different diffraction data sets,  
process them together to give a single final data statistics.


Thanks and regards
Thiyaga



S. Thiyagarajan
Centre of Excellence in Bioinformatics
School of Biotechnology
Madurai Kamaraj University
Madurai - 625021
Ph: +91-9159224881 (cell)


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] 2Theta data set solving problem

2013-04-09 Thread Harry Powell

Hi Navin

I'll assume you are using iMosflm from the CCP4 suite. Have you tried  
increasing the resolution in the Processing Options window, under  
the Processing tab?


The option to display resolution rings and change the resolution by  
dragging the ring does not work at present in iMosflm.


On 9 Apr 2013, at Tue9 Apr 12:41, navin narayanan wrote:


Hello everybody,

We have a diffraction data set from home source with 2theta at  
20deg. But we are not able to solve the data set using CCP4 suite.  
The software is picking up only the lower resolution data but not  
the higher resolution data points. Also we are not able to merge  
data two sets, one with 2theta at 0deg and the other with 2theta at  
20deg. Is there anyway to solve the data. Any help will be truly  
appreciated. Thank you in advance.




Navin V Narayanan


Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick  
Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH
Chairman of European Crystallographic Association SIG9  
(Crystallographic Computing)







Re: [ccp4bb] CCP4 Update victim of own success

2013-04-12 Thread Harry Powell
Hi

I'd second NX; you can install a free server for one or two (I think - I only 
use one at a time ;-)) concurrent connections and a local client, then it's 
almost like being there.

On 11 Apr 2013, at 22:54, Dyda wrote:

 Or nx, which works very well, although the server has to be installed at
 the remote end and client on the local.
 
 www.nomachine.com
 
 Fred
 ***
 Fred Dyda, Ph.D.   Phone:301-402-4496
 Laboratory of Molecular BiologyFax: 301-496-0201
 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov  
 Bldg. 5. Room 303 
 Bethesda, MD 20892-0560  URGENT message e-mail: 2022476...@mms.att.net
 Google maps coords: 39.000597, -77.102102
 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred
 ***

Harry
--
** note change of address **
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, 
Cambridge Biomedical Campus, Cambridge CB2 0QH
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 











Re: [ccp4bb] CCP4 GUI

2007-05-11 Thread Harry Powell
Hi

 Maybe any parameter setting unchanged from the values in the
 $CCP4/ccp4i/tasks/*.def file should be internally flagged as being at
 the 'default value' - resulting in them _not_ being written to the
 com-file? This way any potential change in defaults inside the actual
 program would have immediate effect, even if the CCP4i hasn't been
 updated yet.

This is a _really_ good idea for another reason. There are programs which
determine processing parameter values dyamically, based on what they have
actually been presented with - UNLESS those values have been input by the
user, who is assumed to know better. If an interface (e.g. ccp4i) sets
the value to a default, the program really has no way of knowing that it
was the interface and not a user who knows their data which has input the
value.

Just my two ha'porth...

Harry
-- 
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] anomalous signal

2007-06-01 Thread Harry Powell

Hi

In the same way the Toyota MRD-2 doesn't sell in France?

MRD would indeed be a poor name. For French scientists it might be difficult 
to get funding for an MRD experiment

Regards
Yves


--

Prof. Yves Muller   Phone: +49-(0)-9131-8523082, 8523081
Lehrstuhl fuer BiotechnikFAX:   +49-(0)-9131-8523080
www.biologie.uni-erlangen.de/biotechnik Institut fuer Biologie
Friedrich-Alexander-Universität, Erlangen-Nuernberg
Im IZMP, Henkestrasse 91, D-91052 Erlangen 





Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


[ccp4bb] number of MTZ files input to scaleit

2007-06-26 Thread Harry Powell

Hi folks

silly question, I know, and I'm sure this must have been answered before, 
but I want to put 10+ datasets into the same file and get scaling 
statistics between them.


I find that SCALEIT is happy to do the scaling once all the datasetsa re 
together (according to the man page it's okay with 20) but CAD will only 
let me put 9 datasets in an MTZ file. Do I have to run CAD twice (or 
more...) to get all my datasets together? Or is there some other way that 
I've missed?


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] Release of Mosflm version 7.0.1 iMosflm 0.5.3

2007-08-20 Thread Harry Powell

Hi folks

a sharp-eyed user has noticed a bug in the Windows version of iMosflm 
0.5.3; this does not affect any other version.


If you have already downloaded the Windows version, you should replace the 
file imosflm.tcl in the top-level imosflm folder with this file -


http://www.mrc-lmb.cam.ac.uk/harry/imosflm/downloads/imosflm.tcl

NOTE that this is _not_ the file of the same name in the src folder.

I've fixed this in the imosflm.zip file so any further downloads will not 
display this bug.


Sorry about this!

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] mosflm and APS BM17

2007-08-22 Thread Harry Powell

Hi

I'd guess from the input file that the beam centre may be defined in a 
different reference frame to that which Mosflm expects in the image 
header; other possibilities are that the distance, wavelength, or 
something else (!) is wrong. Indexing is critically dependent on having 
the beam centre, distance and wavelength all being pretty close to the 
true values, though some indexing routines allow more latitude than 
others.


My understanding (IMWBW) is that other programs (such as XDS or HKL2000) 
don't use the information in the image headers, and expect the parameters 
to be supplied by the user. With Mosflm, we try to make the user's life 
easier by trusting this information, especially from images collected at 
synchrotron beamlines; sometimes this trust is not warranted, and the user 
has to intervene!



processing data collected on APS beamline BM17 on a MAR165 detector
causes unexpected troubles. Even though the crystals are
well-diffracting and the spots are sharp and well-resolved, indexing
only works with a certain selection of frames, the refinement the goes
totally hairwire. Probalby just a parameter or so set wrong. My input
file in the attachment. The last three lines do not make much of a
difference. Any ideas?
Thanks!

Cheers
Jan


mosflm.in:
detector marccd
directory ../Images
template Image_0###.img
image 001
nullpix 1
separation 0.95 0.95 close
!LIMITS XMIN 0 XMAX 165 YMIN 0 YMAX 165 xscan 2048 yscan 2048
!SIZE 2048 2048
!PIXEL 0.07934




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] diffraction images images/jpeg2000

2007-08-24 Thread Harry Powell

Hi

Lossy compression should be okay, provided that the errors introduced are 
smaller than those expected for counting statistics (assuming that the 
pixels are more-or-less independent) - i.e. less than the square-root of 
the individual pixel intensities (though I don't see why this can't be 
extended to the integrated reflection intensities). So it's more important 
to accurately retain your weak pixel values than your strong ones - an 
error of ±10 for a pixel in a background count where the background should 
be 40 is significant, but an error of ±10 for a saturated pixel on most 
detectors (say, about 64K for a CCD) wouldn't affect anything.



On the question of lossy compression, I think we'd have to ask some data
reduction guru's how much the noise would affect the data reduction. I
suspect that the main problem is that the noise added would be
correlated across the image and would therefore affect the background
statistics in a non-trivial way. Although the intensity measurements may
not be badly affected the error estimates on them could be...


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] diffraction images images/jpeg2000

2007-08-24 Thread Harry Powell


Wow.

I don't know about the rest of you, but I got told three times.

Gerard is, of course, right about pixel non-independence (think point 
spread function, among other things), and I wouldn't care to argue 
statistics with him, but as far as I know (and I could well be wrong) most 
of the integration programs out there _do_ use counting statistics (i.e. 
Poisson statistics) at least as a first approximation for the random error 
in measurement; this may be modified by some detector inefficiency 
factor (See Borek, Minor  Otwinowski, Acta Cryst (2003) D59 2031 - 
2038), but it's still there and being used by everyone, nonetheless.


Having said that, regarding the storage of images, my personal feeling is 
that there's no real point in using a lossy compression when there are 
good lossless systems out there. I also think that almost no-one would 
ever bother to reprocess deposited images anyway; my guess is that 
unusual structures would be detected by other means, and that examining 
the original images would rarely shed light on the problem.



I think we need to stop and think right here. The errors in pixel
values of images are neither Poisson (i.e. forget about taking square roots)
nor independent. Our ideas about image statistics are already disastrously
poor enough: the last thing we need is to make matters even worse by using
compression methods based on those erroneous statistical arguments!


With best wishes,

 Gerard.

--
On Fri, Aug 24, 2007 at 01:20:29PM +0100, Harry Powell wrote:

Hi

Lossy compression should be okay, provided that the errors introduced are
smaller than those expected for counting statistics (assuming that the
pixels are more-or-less independent) - i.e. less than the square-root of
the individual pixel intensities (though I don't see why this can't be
extended to the integrated reflection intensities). So it's more important
to accurately retain your weak pixel values than your strong ones - an
error of ±10 for a pixel in a background count where the background should
be 40 is significant, but an error of ±10 for a saturated pixel on most
detectors (say, about 64K for a CCD) wouldn't affect anything.


On the question of lossy compression, I think we'd have to ask some data
reduction guru's how much the noise would affect the data reduction. I
suspect that the main problem is that the noise added would be
correlated across the image and would therefore affect the background
statistics in a non-trivial way. Although the intensity measurements may
not be badly affected the error estimates on them could be...


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH



--

===
* *
* Gerard Bricogne [EMAIL PROTECTED]  *
* *
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* Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
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Harry
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Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


[ccp4bb] Mosflm v 7.0.1 Mac Intel pre-built executable.

2007-08-24 Thread Harry Powell

Hi folks

If you've recently downloaded a pre-built copy of Mosflm version 7.0.1 for 
Intel Mac (including the universal binary) and been surprised by the need 
for libgfortran.1.dylib, read on. Otherwise, feel free to ignore this!


It seems my attempts to produce a statically linked OS X executable with 
gfortran weren't as successful as I thought! Although the executable was 
(in a logical sense) statically linked, the linker put information in the 
header suggesting that it required the dynamic library. This is wrong and 
may be viewed as a linker bug.


However, I've now sorted out the problem and produced executables which do 
link the libgfortran statically, and these replace the earlier copies.


If you've managed to run Mosflm version 7.0.1 on an Intel Mac there is no 
need at all to download this executable, so you can ignore this. However, 
if you've been stymied in your attempt to run it by being told that 
/sw/lib//gcc4/lib/libgfortran.1.dylib doesn't exist, it is probably 
worthwhile downloading this new executable.


have a nice weekend!

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] ipmosflm

2007-09-02 Thread Harry Powell

Hi Eric

You need to make sure g77 is properly installed on your system. For any FC 
system, if you install g77 from an RPM (e.g. see your FC install 
DVD/CD/website) you should get this file in the right place.


If you don't want the whole compiler there, you should be able to get 
round this on an FC system by just installing the libg2c.so file 
explicitly, perhaps from an RPM.


It may be that the correct file is on your system, but either called 
something else (similar, e.g. libg2c.so.0) and not linked correctly to 
libg2c.so, or it isn't in your LD_LIBRARY_PATH; on my systems it's in the 
directory /usr/lib (on others it's found in /usr/local/lib).


I've put a copy on the Mosflm v 7.0.1 pre-built site (I haven't 
put a link on the page for it, but you can get it by following this -


http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver701/pre-built/suse-libg2c.so

Personally, I really hate shared objects and have tried (oh, how I've 
tried!) to eliminate them from Mosflm distributions, but they seem to 
sneak in when I'm not looking...



Hi,
I try to install the latest version of ipmosflm and the small display
version on my laptop (fedora 7). I got the following error message when I
try to run it:
$./mosflm_linux_suse_SD
mosflm_linux_suse_SD: error while loading shared libraries: libg2c.so.0:
cannot open shared object file: No such file or directory

It might not related to the program. However, please advise. Thx.

Eric



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] pointless (1.2.0) and enantiomorphic SG's

2007-11-09 Thread Harry Powell
Of course, you may need to re-index even if you have the right space 
group...



Offering a selection of space groups compatible with a point group 
will not require reindexing.
Some point groups of course permit reindexing, but one hope you have 
chosen a consistent set as you combine data sets into an MTZ file - 
pointless and the GUI both offer ways to check this.


Phasing cannot be carried out till you have chosen a spacegroup, and 
any existing phase associated data should probably be weeded out as 
part of a Assign Spacegroup function.



Eleanor



 Kevin Cowtan wrote:
This is great! But before we all get carried away, a quick reality 
check is in order. This isn't an area I've thought about, but my 
limited understanding raises the following issues


Given that an MTZ file contains a cell, an indexing of the data, and 
possibly phases involving a choice of origin, the use of an MTZ file 
immediately implies that some decision has been made about the 
spacegroup.


Selecting a different spacegroup from a list of possibilities may 
involve reindexing, and/or changing origin/enantiomorph dependent 
properties such as phases and HLs.


It would be possible for an MTZ file to say something like this:
 'This file is generated assuming spacegroup X. Spacegroups X1, X2, 
X3, X4, X5 are also possible.'.


It should also be possible to compute on the fly whether a particular 
column type needs to be modified for a different spacegroup.


How will we present this in user interfaces? As a starting point, 
until a spacegroup has been settled upon, the user will need the 
option of picking the spacegroup after having selected the MTZ. This 
means potentially a reindexing step added to every single task - 
messy. As an intermediate, being able to change the 'currently 
selected' spacegroup as a separate task would be an improvement.



Phil Evans wrote:

I agree

On 9 Nov 2007, at 13:50, Eleanor Dodson wrote:

As I often say!!! The mtz format should carry point group and 
alternate SGs - then be upgraded when youknow the correct SG..


Eleanor

Phil Evans wrote:
It just picks the first in the list, to store in the output MTZ 
file, which can only handle one (92  96)

Phil


On 8 Nov 2007, at 22:26, Bryan W. Lepore wrote:

when pointless (1.2.0) finds enantiomorphic SG's, what is the 
criterion for 'Selecting' one over the other?


e.g. i ran pointless on some tetragonal data, and the 
enantiomorphs SG92/SG96 are selected as strong candidates


   Spacegroup TotProb SysAbsProb Reindex 
Conditions
   P 41 21 2 ( 92)0.956  0.956 00l: 
l=4n, h00: h=2n (zones 1,2)
   P 43 21 2 ( 96)0.956  0.956 00l: 
l=4n, h00: h=2n (zones 1,2)


... then pointless reports :

Selecting space group P 41 21 2 as solutions are enantiomorphic
Best Solution space group P 41 21 2

... is that b/c pointless can only report one, and SG92 came up 
first?


-bryan













[ccp4bb]

2007-11-13 Thread harry powell

Hi

I don't know about reviews, but there were a couple of papers a few  
years ago that might have clues in their references -


Margiolaki et al, Acta Cryst D61, 423-432 (2005)
Basso et al Acta Cryst D61, 1612-1625 (2005)

On 13 Nov 2007, at 19:59, Marius Schmidt wrote:


Somebody out there who could direct me to
a nice review of protein powder diffractometry
including the application of Rietveld refinement
to such data.

Any hint appreciated
many thanks in advance

Marius


Dr.habil. Marius Schmidt
Asst. Professor
University of Wisconsin-Milwaukee
Department of Physics Room 454
1900 E. Kenwood Blvd.
Milwaukee, WI 53211

phone: +1-414-229-4338
email: [EMAIL PROTECTED]
http://users.physik.tu-muenchen.de/marius/


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] To bathe or not to bathe.

2007-11-24 Thread harry powell
.

These days scaling algorithms are good, the detectors are  
excellent, and
very often it pays to employ a beam smaller than the x-tal.  This,  
the

non-uniformity of many synchrotron beams, and the systematic damage
to crystals that we observe now with synchrotron sources cause  
serious

systematic errors.  We're forced to depend on good scaling and good
detectors to get accurate measurements.  Making the measurements  
in many

different crystal orientations (redundancy) helps to smooth out these
systematic errors.

Nonetheless, it will always pay you to watch for EACH of these  
sources of

error and to minimize them as best you can.

Bob

= 


 Robert M. Sweet E-Dress: [EMAIL PROTECTED]
 Group Leader, PXRR: Macromolecular   ^ (that's L
   Crystallography Research Resource at NSLS 
not 1)

   http://px.nsls.bnl.gov/
 Biology Dept
 Brookhaven Nat'l Lab.   Phones:
 Upton, NY  11973631 344 3401  (Office)
 U.S.A.  631 344 2741  (Facsimile)
= 





Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







[ccp4bb] ccp4i integration task

2007-11-27 Thread Harry Powell

Hi folks

Can you reply directly to me rather than ccp4bb?

I was wondering how many people out there actually use the 
integration task in ccp4i? We're trying to work out how much support 
it needs, and how it needs to be developed, so comments on usage, 
problems, etc. would all be gratefully received!


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH




Re: [ccp4bb] ccp4i integration task

2007-11-27 Thread Harry Powell
Many thanks to everyone who took the time to reply! It will all be very 
helpful.


On 27 Nov 2007, at 11:59, Harry Powell wrote:


Hi folks

Can you reply directly to me rather than ccp4bb?

I was wondering how many people out there actually use the 
integration task in ccp4i? We're trying to work out how much support 
it needs, and how it needs to be developed, so comments on usage, 
problems, etc. would all be gratefully received!


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH





Re: [ccp4bb] scale data with multiple MTZ files

2008-01-11 Thread harry powell

Hi

There's a way to avoid having to do this - use the ADD sub-keyword  
when processing in Mosflm, so that the batch number for each image  
data is given an offset; see


http://www.mrc-lmb.cam.ac.uk/harry/cgi-bin/keyword2.cgi?PROCESS

Both the traditional X11 gui and the new iMosflm allow you to add an  
offset easily, allowing the subsequent CCP4 programs to work with  
multiple MTZ files produced by Mosflm.



On 11 Jan 2008, at 09:49, Phil Evans wrote:


There is an (possibly) easier way now in pre-release

1) Download  install (manually) from the CCP4 pre-release site the  
program pointless and the ccp4i task interface


2) Use the Find or Match Laue Group option (under Data  
Reduction) to open the interface window to the program Pointless
This will allow input of multiple MTZ files (or indeed files from  
XDS  Scalepack), check them for consistent indexing if  
appropriate, and enforce unique batch numbers (a long-standing  
irritation).


By default it will try to determine the Laue group  space group,  
but it can also match space group  indexing with a reference file,  
or just sort the files together (replacing sortmtz).


3) Put the output (HKLOUT) file into Scala (Scale and Merge  
intensities task)


Note that Pointless ( Scala) are still (!) under development, and  
the versions in the next CCP4 release (or indeed pre-release) will  
be updates of these versions. Latest versions of Pointless  Scala  
are also available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/


Phil


On 11 Jan 2008, at 05:40, Roger Rowlett wrote:


Huiying Li wrote:
I tried to scale, using SCALA through CCP4i GUI, three blocks of  
data collected with one crystal (3 mtz files output from MOSFLM).  
The GUI has only one MTZ input slot. Which program can be used to  
combine the 3 unmerged mtz files together? CAD refused to handle  
these raw mtz files.


Thanks in advance for any help.

Huiying


Using the CCP4 GUI, employ the following steps:

1. Open a Sort/Modify/Combine job and renumber your data sets  
(reset batch numbers option). A simple method is to add 1000 to  
the batch numbers for one data set and 2000 to the batch numbers  
for the second data set (assuming you have less than 999 frames of  
data output from MOSFLM.)


2. Open another Sort/Modify/Combine job and combine the renumbered  
MTZ files into one merged file. Click on Add File to add  
additional renumbered batches from step 1. Each batch of  
reflections will now have unique batch numbers.


3. Open a Scale and Merge Intensities task window. Select as your  
input the sorted and combined file output from step 2. In the  
Define Datasets section, choose Combine All Input Datasets into a  
Single Output Dataset. You can convert the scaled intensities to  
structure factors by checking the appropriate box. The combined  
datasets will not have monotonically varying R(merge) values  
across batches (1-1000, 1001-2000, 2001-3000) becuase of  
discontinuities in the data. However the merged datasets should  
have good overall statistics if appropriate for merging.


Cheers,


--
- 
---

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] x ray data sets for teaching

2008-01-11 Thread harry powell

Hi Jeremiah

We (the Mosflm developers) use a mercury derivative HypF dataset  
collected on a Mar IP - there are things wrong with the crystal and  
the data collection, but it processes nicely (you can identify the  
problems easily), and you can solve the structure from the data; it's  
available at http://www.ccp4.ac.uk/autostruct/testdata/ - look for  
HypF, about half-way down the page.


There are tutorials that go through the data with both the  
traditional X11 GUI and the new TclTk-based iMosflm on the Mosflm  
website.



On 11 Jan 2008, at 14:58, Jeremiah Wagner wrote:


Hello Everyone,

I am going to be teaching a class this spring and protein
structure and function.  I would like to have my students
see some diffraction data and integrate images with mosflm.
Are there any free or available data sets (possibly
lysozyme) out there that can be used?

Thanks,

Jeremiah Wagner

---
Jeremiah Wagner
Visiting Assistant Professor of Biology
Beloit College
700 College Street phone: 608-363-2743
Beloit, WI  53511 FAX:  608-363-2052



---
Jeremiah Wagner
Visiting Assistant Professor of Biology
Beloit College
700 College Street phone: 608-363-2743
Beloit, WI  53511 FAX:  608-363-2052


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] Calculating volume of Ligands

2008-01-16 Thread harry powell

Hi

A simple trick that small molecule crystallographers have been using  
for decades is based on the average volume of non-hydrogen atoms  
being about 18 Å^3 (this is close to being more-or-less correct for  
C, N and O, and the presence of one or two S or P atoms usually makes  
little difference) - they simply multiply the number of non-H atoms  
in the ligand by 18 and - hey presto!


If you've only got a few atoms in your ligand, this is dead easy and  
you don't need a program to do it. If you're in a hurry, use 20Å^3  
instead for a slight overestimate...


On 15 Jan 2008, at 21:39, Rajan Pillai wrote:


Hi All,

Can anyone tell me any program that calculates voume of a ligand?  
Moreover, is there also any program that can calculate the volume  
of a ligand from its coordinates?


Thanks,

Rajan.


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


[ccp4bb] New versions of Mosflm and iMosflm

2008-01-28 Thread Harry Powell

Hi folks

We are pleased to announce updated versions of Mosflm (version 7.0.2) 
and iMosflm (0.6.0).


If you upgrade iMosflm, you should certainly upgrade Mosflm at the same 
time; there are many changes which depend on both parts being in sync.


The main change is that we have a new developer for iMosflm; Luke 
Kontogiannis ([EMAIL PROTECTED]) has been with us since October 
and has been very busy implementing improvements to iMosflm, so that it 
is now more robust and even easier to use.


Most of the changes to Mosflm itself are involved with bug fixing and 
improved communications with iMosflm, so you shouldn't notice a lot of 
difference.


Changes to Mosflm since 7.0.1

 * New detectors - Mar555 Flat Panel. Pilatus miniCBF images 
added.
 * Better support for Bruker 100 Format images (converted with 
frm2frm).

 * Change IP address for communication with iMosflm to the loopback
   address (127.0.0.1 or localhost).
 * Rectangular non-square detectors added for output to iMosflm 
display.
 * Bug involving R-Axis detectors writing d*Trek style headers 
fixed.
 * Many small bugs fixed - many thanks to all those who gave us 
feedback, especially

   Clemens Vonrhein  Jim Pflugrath.

Changes to iMosflm since 0.5.3

 * Resizeable image display by dragging the window edges
 * Ability to delete sectors in the image selection panel by 
right-clicking

   on selected sector
 * iMosflm correctly deals with datasets where the first image has 
an index
   of zero. The batch number is offset to 1000 and the processing 
and writing

   out of the mtz file proceed normally
 * The spotfinding summary pane in the indexing panel now shows the 
number

   of spots with an intensity greater than the I/sigI threshold
 * Ability to stop the log file view autoscrolling with 
Control-UpArrow key

   combination. Resume autoscrolling with Control-DownArrow
 * Search the log file by bringing up the search panel with 
Control-F key
   combination. Control-F searches forward and Control-G searches 
backwards


Harry  Luke
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH




Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

2008-02-04 Thread Harry Powell

Okay, I was wrong. On two points...

What I'd forgotten is that LCD displays produce polarized light (and so 
do TFT displays, for that matter), so you don't need a sheet of 
Polaroid to polarize the light from the vertical display.


The half-silvered mirror is there (of course, I hear the cries) to make 
sure you have enough light reflected from the horizontal monitor to 
be about the same as the light transmitted from the vertical one.



On 4 Feb 2008, at 12:09, Harry Powell wrote:


Hi

Just looking at the diagrams, I don't think the glass is half-silvered 
- it looks like a large sheet of Polaroid™. It only needs to polarize 
the transmitted light from the vertically oriented monitor, since the 
reflected light from the interface between two materials (at least one 
of which has a refractive index) will be polarized in any case (that's 
why your Polaroid™ sunglasses let you see below the waves...). My 
physics is too rusty to remember, but I think the vertical monitor in 
this case needs to be polarized vertically, since the reflected 
polarized light will be horizontal.


No idea where you can buy large sheets of Polaroid™  though.

IMWBW, though...

On 4 Feb 2008, at 11:30, P Hubbard wrote:


 Hi Andrew,

Just like the commercial systems, the glass is the only special piece 
of kit (which can be bought separately). The LCD monitors are just 
set up to display either left or right channel. If you ask me, I 
think these companies are just a rip off!


Paul

 Date: Mon, 4 Feb 2008 11:24:32 +
 From: [EMAIL PROTECTED]
 Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
 To: CCP4BB@JISCMAIL.AC.UK

 P Hubbard wrote:

  Just an FYI you can build those yourself at a fraction of the 
price!
  You just need the special piece of glass, two identical LCD 
monitors,

  and an edited X config file.

 The clever bit of the Omnia system (and the similar one from Planar,
 which being from the US might be cheaper there...?) is the DVI
 reflector card that flips the image to be displayed on the screen 
seen

 in the half-silvered mirror.

 Are you implying that an appropriately written Xorg.conf can get the
 graphics card to do this instead? The prospect is very appealing!

 Regards,

 Andrew

 --
 Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
 Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
 phone: +44 (0)1223 252830 fax: +44 (0)1223 252835
 web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Helping your favorite cause is as easy as instant messaging. You IM, 
we give. Learn more.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, 
Hills Road, Cambridge, CB2 2QH





Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH





Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional

2008-02-04 Thread Harry Powell

Hi

Just looking at the diagrams, I don't think the glass is half-silvered 
- it looks like a large sheet of Polaroid™. It only needs to polarize 
the transmitted light from the vertically oriented monitor, since the 
reflected light from the interface between two materials (at least one 
of which has a refractive index) will be polarized in any case (that's 
why your Polaroid™ sunglasses let you see below the waves...). My 
physics is too rusty to remember, but I think the vertical monitor in 
this case needs to be polarized vertically, since the reflected 
polarized light will be horizontal.


No idea where you can buy large sheets of Polaroid™  though.

IMWBW, though...

On 4 Feb 2008, at 11:30, P Hubbard wrote:


 Hi Andrew,

Just like the commercial systems, the glass is the only special piece 
of kit (which can be bought separately). The LCD monitors are just set 
up to display either left or right channel. If you ask me, I think 
these companies are just a rip off!


Paul

 Date: Mon, 4 Feb 2008 11:24:32 +
 From: [EMAIL PROTECTED]
 Subject: Re: [ccp4bb] 3D Glasses - Vuzix HMD by eDimensional
 To: CCP4BB@JISCMAIL.AC.UK

 P Hubbard wrote:

  Just an FYI you can build those yourself at a fraction of the 
price!
  You just need the special piece of glass, two identical LCD 
monitors,

  and an edited X config file.

 The clever bit of the Omnia system (and the similar one from Planar,
 which being from the US might be cheaper there...?) is the DVI
 reflector card that flips the image to be displayed on the screen 
seen

 in the half-silvered mirror.

 Are you implying that an appropriately written Xorg.conf can get the
 graphics card to do this instead? The prospect is very appealing!

 Regards,

 Andrew

 --
 Dr. Andrew Raine, Head of IT, MRC Dunn Human Nutrition Unit,
 Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, UK
 phone: +44 (0)1223 252830 fax: +44 (0)1223 252835
 web: www.mrc-dunn.cam.ac.uk email: [EMAIL PROTECTED]

Helping your favorite cause is as easy as instant messaging. You IM, 
we give. Learn more.

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH





[ccp4bb] new versions of Mosflm (7.0.3) and iMosflm (0.6.1)

2008-03-03 Thread Harry Powell

Hi folks

We are pleased to announce the release of Mosflm version 7.0.3 and 
iMosflm 0.6.1.


These are bug-fix releases for versions 7.0.2 and 0.6.0, which affect 
the following detectors and circumstances only. If your detector is not 
listed, it isn't affected, so you shouldn't need to update your copies 
of Mosflm and/or iMosflm - but you may want to anyway.


Many thanks to those people who brought these issues to our attention.

Fixes to Mosflm:
 * Image display for R-Axis detectors was reversed in iMosflm
   (the new interface), not in the old interface.
 * The presence of extremely large pixel values (262128) for Mar
   IP scanners caused Mosflm to shut down.
 * Direct beam co-ordinates read from Mar CCD image headers not
   sited at ESRF had X and Y swapped.
 * Direct beam co-ordinates were not used from Ed Westbrook NOIR
   images by iMosflm (although they were used by Mosflm).
 * Reversephi check box in iMosflm did not function as intended.

Fix to iMosflm:
 * Bruker .sfrm suffix included in list in image browser.


Special thanks to Jan for reminding me that I should include the 
download sites when announcing new releases!


Downloads are available through the normal web-pages and ftp sites -

Everything Mosflm - http://www.mrc-lmb.cam.ac.uk/harry/mosflm

specific places -

Mosflm v.7.0.3 - http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver703

iMosflm v. 0.6.1 - http://www.mrc-lmb.cam.ac.uk/harry/imosflm/


Harry  Luke
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH




[ccp4bb] Missing fonts...

2008-03-05 Thread Harry Powell

Hi folks

I've had a couple of reports recently of people trying to run ipmosflm 
on Fedora Core 8 machines, and they get the following error -


** xdl_view error in routine xdl_open_view **
** Unable to load *adobe-courier-medium-r*--8* font **

I'm assuming that the install for FC8 is not including all the Courier 
fonts; since I don't have an FC8 machine handy, could anyone here offer 
advice about the best way to install these?


 Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills 
Road, Cambridge, CB2 2QH





Re: [ccp4bb] problems about installation of mosflm701

2008-03-27 Thread harry powell

Hi

First off, you really shouldn't be installing mosflm version 7.0.1 -  
version 7.0.3 is the current one, and contains numerous bug fixes.  
The developers are likely to meet any problem queries relating to  
7.0.1 with update to the current version first, then try again; if  
the problem persists, we will look at it...


Your immediate problem is that you are trying to run a csh script as  
a bash script, without editing the file properly; e.g., you can't  
just change setenv (csh) to export (bash) - the syntax is not the  
same - you'd need to change it thus -


setenv CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'

would become something like

export CCP4_LIB_FILES='-lccp4f -lccp4c -lxdl_view'

You would also need to change the top line of the file so that it was  
something like #!/bin/bash -f, though I would be more inclined to  
use a proper traditional Bourne shell for this and use #!/bin/sh -f  
and use sets and exports throughout.


If you really want to run the script, I would use tcsh or csh, rather  
than trying to modify it so that it is a bash script.


BTW, the Intel compiler setup in that file is way out of date - you'd  
need to change that as well to point to current copies of the compilers.


I would be very strongly inclined to install the mosflm_linux_suse  
pre-built executable - it should certainly work on FC5, and saves you  
the trouble of trying to build it. The speedup by using an executable  
compiled with the Intel compiler is probably not that great - recent  
g77s and gfortrans give excellent and stable optimization!


On 27 Mar 2008, at 04:57, Lu Yongzhi wrote:



- Original Message -
From: Lu Yongzhi
To: ccp4 bb
Sent: Wednesday, March 26, 2008 7:41 PM
Subject: problems about installation of mosflm701

Hi,

My OS is fedoral core 5. I have installed ccp4-6.0.2 which include  
the mosflm 6, but I want to install mosflm7.0.1. I downloaded the  
program, but I can't install it properly. I source the file  
'intel', the echo is (I have changed the 'setenv' to 'export'):



bash: export: `-lccp4f -lccp4c -lxdl_view': not a valid identifier
MOSROOT has been set to

bash: export: `/index': not a valid identifier
bash: export: `/src/dps/util': not a valid identifier
bash: export: `/jpg': not a valid identifier
bash: intel: line 65: syntax error: unexpected end of file

could anyone can help me.

the lines in the 'intel' file are:

#!/bin/csh -fv
#
# setup shell script for the development copies of Mosflm for  
different

# platforms.
#
# Common stuff first
#
export CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'
set mosroot = ${cwd:h}
export MOSROOT $mosroot
echo MOSROOT has been set to $MOSROOT
set moshome = ${cwd}
export MOSHOME $moshome
echo $MOSHOME
export AR_FLAGS vru
export DPS ${MOSHOME}
export IND ${MOSHOME}/index
export UTIL${MOSHOME}/src/dps/util
export JPG ${MOSHOME}/jpg
# intel compiler specifics - change this to your local installation
if ( -e /opt/intel/compiler70/ia32/bin/ifcvars.csh )then
source /opt/intel/compiler70/ia32/bin/ifcvars.csh
else
echo You must either edit the file called \intel\ to source  
the correct
echo ifcvars.csh file or install both the Intel C++ and FORTRAN  
compilers

exit
endif
if ( -e /opt/intel/compiler70/ia32/ifc_fudge.o )then
export FUDGE /opt/intel/compiler70/ia32/ifc_fudge.o
export NOFUDGE 
else
export FUDGE 
export NOFUDGE -i_dynamic
endif
export DEBUG 
export F77   ifc ${DEBUG}
export FCOMP   ${F77}
export FC  ${F77}
export CC icc ${DEBUG}
export FLINK   ${F77} ${DEBUG}
export FFLAGS  -O -align -w90 -cm
export CFLAGS   -O0 -O -DPROTOTYPE -DIFC  -c -w
# if no fudge.o vide infra export LFLAGS-Vaxlib -i_dynamic
export LFLAGS-Vaxlib $NOFUDGE
#
# (2) Mosflm directory
#
export MOSFLAGS  -O3 -align -w90 -cm
# export MOSFLAGS  -O3 -align -w90 -cm -prof_gen this line for  
profiling only
# export MOSFLAGS  -O3 -align -w90 -cm -prof_use  change $F77  
etc to include -ipo flag


export MCFLAGS   -O0
export MOSLIBS -L${CCP4_LIB} ${CCP4_LIB_FILES} -lncurses -L/ 
usr/X11R6/lib -lXt -lSM -lICE -lX11 -ldl -lpthread -lm ${FUDGE}

#
# (3) CBF directories
#
export CBFCFLAGS   -O -DPROTOTYPE -DIFC
# DPS
export VERBOSE v
export UTILFLAGS   -O -DPROTOTYPE -DIFC  -c -w
export EXTRAFLAGS  -I${UTIL} 
export STDCFLAGS   

exit



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] is it Ok to freeze

2008-06-19 Thread harry powell

Hi

If you mean organic small molecules, then the opinion for the last 15  
years at least is probably yes, unless you know you'll have a phase  
change.


Most small molecule crystals don't have the same problems with  
needing cryoprotectants as macromolecules, due in large part to not  
having a large proportion of water in the lattice, so the process is  
somewhat more straightforward. Also, most small molecule crystals can  
be handled quite happily in the absence of mother liquor, and you  
don't have to worry about them drying out while transferring to the  
fibre (rather than loop) which would normally be used for mounting  
them. Of course, there are numerous exceptions to the most I'm  
referring to here.


In most cases you'll get a substantially better structure at cryo  
temperatures (of course, what better means may be open to debate).



On 19 Jun 2008, at 09:47, Jayashankar wrote:


Dear Scientists and Friends,

I am not sure, whether  organic crystals  need to be in cryo stream  
necessarily during data  collection from  an  in house

xray machine .

How most of the organic crystals have been solved mostly?


--
S.Jayashankar
(A bit confused new generation researcher).
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] is it Ok to freeze

2008-06-19 Thread harry powell

Hi Colin

yes, both of those. Plus freezing out multiple conformations so you  
can model them properly - bear in mind that a small molecule  
structure at a resolution worse than 1Å would be challenging to get  
past the normal criteria of referees, so you should be able to see  
them at least some of the time (depending on how distinct the  
multiple conformations are).


It may be easier to distinguish the atom type (C,N,O?) if you have a  
lower temperature dataset - at least 50% of the small molecule  
structures I did when I was working in that field were _not_ of the  
compound the chemist thought they had, so working out the atom type  
was rather important. However, I'm not sure this is a strong reason  
for doing cryo work on its own - any half decent modern automated  
small molecule structure solution program could do it with most room  
temperature datasets.


Also, if you have an air-sensitive crystal (chemists say this as a  
shorthand when they mean more specific things like the chemical is  
oxygen or moisture-sensitive) you can slow the reactions down enough  
so that your crystal doesn't decompose because of those. But that's  
more of a problem with organometallics than organics, except with  
some of the more exotic organic species...


And if your crystal loses solvent (e.g. I used to use CH2Cl2  
(methylene chloride to the old hacks here) as a solvent, and that  
will just evaporate at room temp, leaving you with a powder rather  
than a beautiful single crystal.


Although you can get round air-sensitivity and solvent loss by  
mounting in a capillary, there are good reasons to avoid that and  
cryo-cool with a naked (or semi-naked, dressed only in a gossamer- 
like film of perfluoropolyether oil) crystal if you can, as those of  
us who have done both regularly know.


I'm sure there are other reasons why it would be substantially  
better, but I also know that there is considerable effort going into  
high-temperature devices, which will be used to help collect  
substantially better datasets for the crystals that their  
developers are interested in.


does this help?

On 19 Jun 2008, at 10:25, Nave, C (Colin) wrote:


Harry
Can you clarify why you get a substantially better structure at  
cryo temperatures
e.g higher intensity at high resolution due to reduction in B  
factors, reduction in radiation damage, anything else?


Colin

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf  
Of harry powell

Sent: 19 June 2008 10:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] is it Ok to freeze

Hi

If you mean organic small molecules, then the opinion for the last  
15 years at least is probably yes, unless you know you'll have a  
phase change.


Most small molecule crystals don't have the same problems with  
needing cryoprotectants as macromolecules, due in large part to not  
having a large proportion of water in the lattice, so the process  
is somewhat more straightforward. Also, most small molecule  
crystals can be handled quite happily in the absence of mother  
liquor, and you don't have to worry about them drying out while  
transferring to the fibre (rather than loop) which would normally  
be used for mounting them. Of course, there are numerous exceptions  
to the most I'm referring to here.


In most cases you'll get a substantially better structure at cryo  
temperatures (of course, what better means may be open to debate).



On 19 Jun 2008, at 09:47, Jayashankar wrote:

Dear Scientists and Friends,

I am not sure, whether  organic crystals  need to be in cryo  
stream necessarily during data  collection from  an  in house

xray machine .

How most of the organic crystals have been solved mostly?


--
S.Jayashankar
(A bit confused new generation researcher).
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH






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Re: [ccp4bb] is it Ok to freeze

2008-06-19 Thread harry powell

Hi

I just noticed I scrambled that first paragraph. I didn't intend to  
imply you should be able to see your referees (or their criteria) at  
least some of the time. It should have read something more like-



yes, both of those. Plus freezing out multiple conformations so  
that you can model them properly; you should be able to see them at  
least some of the time (depending on how distinct the multiple  
conformations are).  Bear in mind that a small molecule structure  
at a resolution worse than 1Å would be challenging to get past the  
normal criteria of referees.




On 19 Jun 2008, at 11:05, harry powell wrote:


Hi Colin

yes, both of those. Plus freezing out multiple conformations so  
you can model them properly - bear in mind that a small molecule  
structure at a resolution worse than 1Å would be challenging to get  
past the normal criteria of referees, so you should be able to see  
them at least some of the time (depending on how distinct the  
multiple conformations are).




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] is it Ok to freeze

2008-06-19 Thread harry powell

Hi

Without wishing to start an argument, I've been checking with some of  
my colleagues who are chemical crystallographers - the reply I get is  
that, for routine structural analysis, pretty well all datasets are  
collected at 100K unless the crystals fall apart at low T, or if the  
cryostream is broken.


I should point out that the first production Cryostream that I came  
across (serial number 2, which I think may have been the first one  
sold!) was in the Cambridge Department of Chemistry in about 1985.  
They didn't become common until the mid-1990's in PX labs, when they  
were already well-established as a bit of pretty well essential kit  
for small molecule work.


So although what Remy says is true, the practice is to cryocool most  
of the time.


On 19 Jun 2008, at 12:08, Remy Loris wrote:

Typically crystals of small organic compounds do not require  
freezing as there are no solvent channels. They do in general not  
suffer from radiation damage at room temperature the way protein  
crystals do. Occasionally they are mounted in a capillary instead  
of simply glueing them to a goniometer if they are air sensitive.  
In principle freezing should not damage the crystals, but one still  
may have to be carefull if the crystals are large. I think you risk  
increasing mosiacity, and any manipulation that is not needed will  
on average only reduce the quality of the specimen rather than  
improve it


Remy Loris
Vrije Univesiteit Brussel

Jayashankar wrote:

Dear Scientists and Friends,
I am not sure, whether  organic crystals  need to be in cryo  
stream necessarily during data  collection from  an  in house

xray machine .
How most of the organic crystals have been solved mostly?
--
S.Jayashankar
(A bit confused new generation researcher).
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] program for distribution of distances

2008-06-24 Thread harry powell

Hi

SHELX should be able to do this if you convert your co-ordinates into  
the appropriate format...


On 24 Jun 2008, at 12:30, Eleanor Dodson wrote:


It sounds like something the CCDC software might do?

Eleanor

DISTANG will do it for pdb input



Kristof Van Hecke wrote:

Dear all,

I apologize for the off-topic question.

I'm looking for some software that is able to read in (small  
molecule) structure files (e.g. .pdb, .cif,..)
and subsequently outputs a listing of bond lengths AND  
'environment' distances for each atom within a certain radius.


Additionally, the listing should allow to construct a distribution  
diagram for each atom-atom distance.



I already played a bit with Vista en Mercury (CCDC), but to my  
knowledge it's not possible to include such 'environment'  
distances...



Thanks a lot

Kristof


--
Kristof Van Hecke, PhD
Biomoleculaire Architectuur
Celestijnenlaan 200 F
B-3001 Heverlee (Leuven)
Tel: +32(0)16327477
--





Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm




Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] Question re: ice rings in diffraction data

2008-07-15 Thread harry powell

Hi

You can exclude the ice rings easily in Mosflm - from the command line -

(a) Autoindexing -

AUTOINDEX EXCLUDE ICE (but see user guide for more on this)

(b) Processing -

RESOLUTION EXCLUDE ICE

Or if you try iMosflm, just check the button that says exclude ice  
rings (Indexing pane) or Do not integrate near ice  
rings (Processing pane).


These are good for hexagonal ice (what you probably have), but if  
you've got cubic (or other) ice, you need to exclude the rings by  
their explicit resolution.


On 15 Jul 2008, at 15:14, Mona Rahman wrote:


Hello all,

I have a query re: processing data.  I have some lovely diffraction  
data that has been marred by ice rings (so...not as lovely as it  
could be).  I was told it may be possible to mask the regions of  
the ice rings (obviously sacrificing completeness) during  
processing.  I have been using HKL2000 to process data.  Is this  
feature available with this program?  Otherwise, we also have  
Mosfilm.  Any advice would be greatly appreciated.


Thank you.

Sincerely in anticipation
Mona Rahman

---
Mona N. Rahman, Ph.D.
Dept. of Biochemistry/Pharmacology  Toxicology
Botterell Hall, Rooms 623 and 634 (lab)
Queen's University, Kingston, ON, K7L 3N6
Phone:  613-533-2993, 613-533-6293 (lab)
E-mail:  [EMAIL PROTECTED]



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] Crystallographic computing platform recommendations?

2008-11-18 Thread harry powell

Hi

I would tend to go with a system type that you're familiar and happy  
with, rather than buying into someone else's idea of the best system.  
So if you are used to running any particular type (Windows, OSX,  
Linux), I'd spend a little time setting it up on what you've  
currently got and see if you can do what you want, and where you want  
it to perform better. Of course, you get a much wider range of  
available hardware if you go for Linux or Windows (unless you really  
want to build a Hackintosh).


Most (or at least enough to be able to process data  solve  
structures) of the software out there has been ported to the popular  
platforms, and it's likely that in the short term at least, that  
you'd be more productive in not having to learn a new environment,  
with all its idiosyncrasies...






Dear list,
I haven't seen the crystallographic computing platform thread come
up for a while, and I've got a chance to upgrade my desktop to a
workstation, so I thought I'd ask the CCP4BB for advice on:

1. Mac vs. Linux (which flavor?) vs. Windows
2. Graphics cards
3. Displays
4. Processors - multiple processors, multiple cores? Speed?

About half of what I do involves ~1.0 A X-ray structures - data
processing, rebuilding in Coot, refinement, and so forth - so my
current desktop (Optiplex GX745, Radeon X1300) machine drags on
graphics sometimes. I don't seem to need stereo these days, for what
it's worth.

Anybody have suggestions or specs they'd like to share? Thanks in
anticipation of your advice.

Regards,
Anna Gardberg






Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 2QH


Re: [ccp4bb] iMosflm in 6.1 under OS X

2008-12-17 Thread Harry Powell

Hi

I should say, while this subject has been brought up, that Luke and I  
are working hard to remove many of these dependencies, so iMosflm  
should work with a more plain vanilla version of TclTk (but you will  
still need iTcl and iTk.


On 17 Dec 2008, at 16:34, William G. Scott wrote:


More specifically, issue

fink selfupdate-cvs  (or fink selfupdate-rsync)
fink install  itcl itk iwidgets tdom tkimg tktreectrl




On Dec 17, 2008, at 7:56 AM, Andrzej Lyskowski wrote:


Hi,

I've just upgraded my fink distro and was wondering what else has  
to be done concerning configuration in order to make the iMosflm  
run on Mac OS.

So far I'm getting the following error:

Error in startup script: unknown namespace in import pattern  
itcl::*

  while executing
namespace import itcl::*
  (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/src/imosflm.tcl  
line 91)

  invoked from within
source $env(IMOSFLM)
  (file /sw/share/xtal/ccp4-6.1.0/ccp4i/imosflm/imosflm.tcl line  
111)


Regards, Andrzej


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


[ccp4bb] Mosflm cover was: CCP4 cover over the Yuletide and Study Weekend periods

2008-12-23 Thread Harry Powell

Hi folks

Just to let you all know - there will be no Mosflm cover during this  
period either.


However, Luke, Andrew and I will all be at the CCP4 Study Weekend in  
Nottingham; we will be ready, willing and able to deal with any  
enquiries you may wish to bring.



On 23 Dec 2008, at 13:01, Ballard, CC (Charles) wrote:


Dear All

I am afraid that there will be no cover from the CCP4 droids at  
Daresbury from 24 December until 2 January, with limited cover until  
6 January.


Here's wishing you all a Happy New Year

Charles

CCP4 core team



Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH






[ccp4bb] information for study weekend attendees...

2008-12-23 Thread harry powell

Hi folks

I found some tourist advice for visitors to Nottingham in the New  
Year...


http://news.bbc.co.uk/1/hi/england/nottinghamshire/7798194.stm


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] Mac pro

2009-01-06 Thread Harry Powell

Hi

I use Parallels on my Mac at home for both Windows XP and Ubuntu - it  
works fine for me when running the more number-crunching parts of CCP4  
- haven't really looked at graphics programs like Coot  MG.


At work I'm running VMWare (Workstation 6.0.0) on a Linux box for  
Vista, and that, too, is fine.


If anyone from Redmond is reading this, both my Windows licenses are  
legit.


On 6 Jan 2009, at 17:55, Nathaniel Echols wrote:

There are also options for virtualization of Windoze and Linux via  
the software Parallels although I have yet to test this out.


Parallels is okay; I only use it for testing GUI code on Linux.  It  
doesn't support multiple processors, which probably isn't necessary  
for most people.  The graphics support was somewhat flaky in the  
past, but it now emulates 3D acceleration well enough to run Coot or  
PyMOL.  I've heard anecdotal evidence that VMWare Fusion is better,  
but I've only used the Linux version.


Unrelated advice: try iWork before spending a massive amount of  
money on MS Office.  It's only about $40-$50 with the academic  
discount, and much less bloated.  It'll still read and export Office  
documents, although I don't know how robust this is.


-Nat


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems

2009-01-07 Thread Harry Powell

Hi folks

We have had a good look at this at Mosflm HQ now on Linux.

The CCP4 TclTk++ distribution seems to work okay, and there's no need  
to install the ActiveTcl version to run iMosflm.


It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation 
) things work okay.


Bear in mind that there are now *two* include files you need to source  
when setting up ccp4 - both ccp4.setup (as before) and ccp4- 
others.setup (new).


I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html 
), since it's built without the (unnecessary) libtermcap dependency -  
if you download the noX11 version you can avoid some rare bugs that  
only show up with iMosflm.


Also, take care to heed Ronan's point about having the ccp4i project  
set up *before* running iMosflm from ccp4i, so that the directories  
are properly assigned.


On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote:


Dear Paula,

The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras 
 should work fine - if you unpack this somewhere, export CCP4I_TCLTK  
appropriately and add the lib directory to the LD_LIBRARY_PATH it  
should solve your problem. If you would like more detail please  
don't hesitate to get in touch. This works fine on all the 32 and 64  
linux systems I have tested.


Best wishes,

Graeme


-Original Message-
From: CCP4 bulletin board on behalf of Salgado, Paula
Sent: Tue 1/6/2009 11:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems

Hi everyone

I've been trying to run the new imosflm version from ccp4i 6.1.0 gui  
on ubuntu 8.0.4, but keep having problems. After struggling with it  
to search for the correct MOSDIR directory path, it then complained  
it was missing several packages from wish8.4. I did manage to find  
some of them, but after searching the web I still can't find:


treectrl 2.1
img::png 1.3
img::gif 1.3
img::jpeg 1.3

can anyone tell me where I can download them or what other solutions  
to get imosflm to run properly?


Thanks a lot
Paula


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Re: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems

2009-01-07 Thread Harry Powell

Hi

Sorry - just noticed that ccp4-others.setup doesn't seem to be in  
the source distribution, just in the binary distro. My assumption is  
that if you build from source (or install the Mac OS X binary  
installation) , it's not necessary.


On 7 Jan 2009, at 11:54, Phil Evans wrote:

What is this ccp4-others.setup? I don't have it in my working 6.1.0  
installation (built from source)


Phil


On 7 Jan 2009, at 11:50, Harry Powell wrote:


Hi folks

We have had a good look at this at Mosflm HQ now on Linux.

The CCP4 TclTk++ distribution seems to work okay, and there's no  
need to install the ActiveTcl version to run iMosflm.


It seems that if you use the CCP4 instructions on the wiki (http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4_installation 
) things work okay.


Bear in mind that there are now *two* include files you need to  
source when setting up ccp4 - both ccp4.setup (as before) and ccp4- 
others.setup (new).


I strongly recommend downloading ipmosflm from the Mosflm website (http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ver704/pre-built/index.html 
), since it's built without the (unnecessary) libtermcap dependency  
- if you download the noX11 version you can avoid some rare bugs  
that only show up with iMosflm.


Also, take care to heed Ronan's point about having the ccp4i  
project set up *before* running iMosflm from ccp4i, so that the  
directories are properly assigned.


On 7 Jan 2009, at 08:32, Winter, G (Graeme) wrote:


Dear Paula,

The tcltk++ binary either from the downloads pages or ftp://ftp.ccp4.ac.uk/ccp4/current/extras 
 should work fine - if you unpack this somewhere, export  
CCP4I_TCLTK appropriately and add the lib directory to the  
LD_LIBRARY_PATH it should solve your problem. If you would like  
more detail please don't hesitate to get in touch. This works fine  
on all the 32 and 64 linux systems I have tested.


Best wishes,

Graeme


-Original Message-
From: CCP4 bulletin board on behalf of Salgado, Paula
Sent: Tue 1/6/2009 11:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] imosflm in ccp4 6.1.0 in linux problems

Hi everyone

I've been trying to run the new imosflm version from ccp4i 6.1.0  
gui on ubuntu 8.0.4, but keep having problems. After struggling  
with it to search for the correct MOSDIR directory path, it then  
complained it was missing several packages from wish8.4. I did  
manage to find some of them, but after searching the web I still  
can't find:


treectrl 2.1
img::png 1.3
img::gif 1.3
img::jpeg 1.3

can anyone tell me where I can download them or what other  
solutions to get imosflm to run properly?


Thanks a lot
Paula


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Re: [ccp4bb] Issue on MOSFLM 7.0.4 with image collected on NOIR detector

2009-02-12 Thread harry powell

hi folks

I've had a look at Quentin's images, and have found out that some of  
the information that we are using in Mosflm to determine the pixel  
size and the beam centre is missing.


For the record, if anyone else wants to process NOIR images with  
Mosflm and notices this problem, you should (for the present) tell  
Mosflm that the pixel size is 0.07767mm (same in both X  Y) and also  
convert the beam centre from the image header from pixels to mm -  
while noting that the beam co-ordinates in the header are swapped in  
X  Y compared to the Mosflm definition.


Sorry for any inconvenience - we'll get this fixed for the next release!

On 12 Feb 2009, at 21:08, Quentin Vicens wrote:


Dear All,

I used MOSFLM 7.0.4 to open some images originally collected on a  
NOIR-1 detector at the HHMI beamline at ALS.


Problem #1: the resolution is not displayed accurately, even tough  
the reader seems to be read correctly (instead of being 1.28 in the  
attached example, it should be around 8 angstroems).


Problem #2: autoindexing fails, which I now think may be related to  
problem #1.


Thanks if you have any input!
Quentin



--
Quentin Vicens, Ph.D.

University of Colorado
Department of Chemistry and Biochemistry
UCB 215
Boulder, CO 80309
USA

tel: + 1 (303) 735-6338
fax: + 1 (303) 492-6194
e-mail: quentin.vic...@colorado.edu
screen.tiff


Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 2QH







Re: [ccp4bb] images

2009-03-16 Thread Harry Powell

Hi

I'm afraid the adoption of imgCIF (or CBF, its useful binary  
equivalent) doesn't help a lot - I know of three different  
manufacturers of detectors who, between them, write out four different  
image formats, all of which apparently conform to the agreed IUCr  
imgCIF standard. Each manufacturer has its own good and valid reasons  
for doing this. It's actually less work for me as a developer of  
integration software to write new code to incorporate a new format  
than to make sure I can read all the different imgCIFs properly.



On 16 Mar 2009, at 09:32, Eleanor Dodson wrote:

The deposition of images would be possible providing some consistent  
imagecif format was agreed.
This would of course be of great use to developers for certain  
pathological cases, but not I suspect much value to the user  
community - I down load structure factors all the time for test  
purposes but I probably would not bother to go through the data  
processing, and unless there were extensive notes associated with  
each set of images I suspect it would be hard to reproduce sensible  
results.


The research council policy in the UK is that original data is meant  
to be archived for publicly funded projects. Maybe someone should  
test the reality of this by asking the PI for the data sets?

 Eleanor


Garib Murshudov wrote:

Dear Gerard and all MX crystallographers

As I see there are two problems.
1) Minor problem: Sanity, semantic and other checks for currently  
available data. It should not be difficult to do. Things like I/ 
sigma, some statistical analysis expected vs observed statistical  
behaviour should sort out many of these problems (Eleanor mentioned  
some and they can be used). I do not think that depositors should  
be blamed for mistakes. They are doing their best to produce and  
deposit. There should be a proper mechanism to reduce the number of  
mistakes.

You should agree that situation is now much better than few years.

2) A fundamental problem: What are observed data? I agree with you  
(Gerard) that images are only true observations. All others  
(intensities, amplitudes etc) have undergone some processing using  
some assumptions and they cannot be considered as true  
observations. The dataprocessing is irreversible process. I hope  
your effort will be supported by community. I personally get  
excited with the idea that images may be available. There are  
exciting possibilities. For example modular crystals, OD, twin in  
general, space group uncertaintly cannot be truly modeled without  
images (it does not mean refinement against images). Radiation  
damage is another example where after processing and merging  
information is lost and cannot be recovered fully. You can extend  
the list where images would be very helpful.


I do not know any reason (apart from technical one - size of files)  
why images should not be deposited and archived. I think this  
problem is very important.


regards
Garib


On 12 Mar 2009, at 14:03, Gerard Bricogne wrote:


Dear Eleanor,

   That is a useful suggestion, but in the case of 3ftt it would  
not have
helped: the amplitudes would have looked as healthy as can be  
(they were
calculated!), and it was the associated Sigmas that had absurd  
values, being
in fact phases in degrees. A sanity check on some (recalculated) I/ 
sig(I)

statistics could have detected that something was fishy.

   Looking forward to the archiving of the REAL data ... i.e. the  
images.
Using any other form of data is like having to eat out of  
someone else's

dirty plate!


   With best wishes,

Gerard.

--
On Thu, Mar 12, 2009 at 09:22:26AM +, Eleanor Dodson wrote:
It would be possible for the deposition sites to run a few simple  
tests to
at least find cases where intensities are labelled as amplitudes  
or vice
versa - the truncate plots of moments and cumulative intensities  
at least

would show something was wrong.

Eleanor




--

   ===
   * *
   * Gerard Bricogne g...@globalphasing.com  *
   * *
   * Global Phasing Ltd. *
   * Sheraton House, Castle Park Tel: +44-(0)1223-353033 *
   * Cambridge CB3 0AX, UK   Fax: +44-(0)1223-366889 *
   * *
   ===






Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Re: [ccp4bb] images

2009-03-18 Thread harry powell

Hi

I've heard of a tool from the Golden State which could (potentially)  
be used for forging diffraction images... I believe it's called  
mlfsom.


On 18 Mar 2009, at 17:50, Felix Frolow wrote:


One convincing argument I have:
We will be able to catch fraud ultimately. Fraud is a devastation  
for structural biology.
...Unless they will be smart enough to forge diffraction data  
images, not a big deal.


The second one - in the case of a controversy of the deposited  
results (possible thing) we can try to re-interpret the space group  
and Bravais lattice


And one more, when we have time we can show that we know better to  
process and to refine ;-)


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

Acta Crystallographica D, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:   ++972 3640 8723
Fax:  ++972 3640 9407
Cellular:   ++972 547 459 608

On Mar 18, 2009, at 6:41 PM, Garib Murshudov wrote:


Dear all

Before going into and trying to find a technical solution to the  
problem it would be good if decide if we need images. As far as I  
know if we face with a problem to solve and we know that it is  
necessary to solve then we find technical solution to the problem  
(either from other fields or we find our own solution with some  
elements of reinvention of new MX wheels).


Do we need images to store? What kind of information we can  
extract from images that we cannot from amplitudes, intensities  
(even unmerged)? Does anybody have a convincing argument for  
favour of images?



regards
Garib



On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote:

Actually the radiologists who manage CT and PET scans of brains  
do have

a solution, called DICOM, see http://medical.nema.org/.  If we work
together as a community we should be able to do as well as the
rocket scientists and the brain surgeons' radiologists, perhaps even
better. -- Herbert

=
Herbert J. Bernstein, Professor of Computer Science
 Dowling College, Kramer Science Center, KSC 121
  Idle Hour Blvd, Oakdale, NY, 11769

   +1-631-244-3035
   y...@dowling.edu
=

On Wed, 18 Mar 2009, Jacob Keller wrote:

Apparently it DOES take a rocket scientist to solve this  
problem. Maybe the brain surgeons also have a solution?


JPK

***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
***

- Original Message - From: Klaas Decanniere  
klaas.decanni...@vub.ac.be

To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, March 18, 2009 5:36 AM
Subject: Re: [ccp4bb] images



Herbert J. Bernstein wrote:
Other sciences have struggled with this and seem to have found  
an answer.

Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html
kind regards,
Klaas


This is a good time to start a major crystallogrpahic image
archiving effort.  Money may well be available now that will  
not be

avialable six month from now, and we have good, if not perfect,
solutions available for many, if not all, of the technical issues
involved.  Is it really wise to let this opportunity pass us by?
The deposition of images would be possible providing some  
consistent

imagecif format was agreed.
This would of course be of great use to developers for certain
pathological cases, but not I suspect much value to the user
community - I down load structure factors all the time for test
purposes but I probably would not bother to go through the data
processing, and unless there were extensive notes associated  
with
each set of images I suspect it would be hard to reproduce  
sensible

results.






Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 0QH


Re: [ccp4bb] imosflm STARTDIR

2009-03-19 Thread Harry Powell

Hi folks

The real problem here is that the imosflm you run by default after  
installing the latest CCP4 is a shell script in $CBIN (i.e. where all  
the compiled programs are), which doesn't actually set things up  
properly. This has been addressed by the guys in Daresbury and the fix  
will appear in the next release (after which you should be able to  
ignore the rest of this message).


If, on the other hand, you run the imosflm in the directory $CCP4/ 
ccp4i/imosflm/src, everything should be hunky-dory - you can do this  
by setting your PATH environment variable so it finds this script  
first, e.g. in tcsh -


setenv PATH $CCP4/ccp4i/imosflm/src:$PATH

_after_ doing the normal source'ing ccp4.setup; then imosflm on the  
command line should work.


The other option would be to install imosflm from our web-pages and  
run that, but since this is currently the one that ccp4 distribute  
there's no obvious advantage to that, other than removing the ambiguity.


HTH

On 19 Mar 2009, at 10:03, Williams, MA (Mark) wrote:



imosflm also takes the command line switch --startdir so you could try
an alias of

alias imosflm='imosflm --startdir $PWD'

Mark


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
William G. Scott
Sent: 18 March 2009 17:17
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] imosflm STARTDIR

You could try something like this (bash/zsh/sh):

alias imosflm='MOSDIR=${PWD} imosflm'

The single quotes are required for it to do the right thing.


Bill





On Mar 18, 2009, at 6:49 AM, James Foadi wrote:


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



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Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,  
Hills Road, Cambridge, CB2 0QH


Re: [ccp4bb] mosflm in script mode

2010-05-28 Thread Harry Powell
Hi Jan

The IMAGE  command turns the old gui on - always has done, as far as I know.

With Strategy auto you shouldn't need to give an image number.

HTH

On 28 May 2010, at 14:35, Jan Abendroth wrote:

 Hi all,
 I have been trying to use mosflm in script mode, in a quick-n-dirty effort to 
 pipe some information from labelit.index into a simple data collection 
 strategy. While doing that, I run into the following issue. I have not been 
 able to find a way to read in image information without starting the old gui. 
 Is there a command in the current mosflm versions to run it in shell mode 
 only? Below the script that I have been using.
 Any ideas?
 
 Thanks
 Jan
 
 
 ---
 ipmosflm summary integrate02.sum eof
 DIRECTORY ../images
 TEMPLATE image_###.img
 IMAGE 1
 HKLOUT integration02.mtz
 GENFILE integration02.gen
 #detector-take defaults
 
 #UIS_PIXEL 0.102400
 #UIS_SIZE 3072
 
 NUSPOT OFF
 BEAM 155.400500 158.807700
 DISTANCE 299.775600
 TWOTHETA 0.0
 
 WAVE 0.977400
 #beam
 SYNCHROTRON POLARIZATION 0.9
 DIVERGENCE 0.100 0.020
 DISPERSION 0.0001
 
 
 MOSAICITY 0.60
 SYMMETRY p2
 RESOLUTION 3.5
 MATRIX integration02.mat
 
 PROFILE OVERLOAD PARTIALS
 RASTER 19 19 9 4 4
 SEPARATION 1.80 1.80 CLOSE
 REFINEMENT RESID 7.5
 REFINEMENT INCLUDE PARTIALS RESID 10.0 #High s/n
 
 
 scanner adsc
 strategy auto
 stats on
 go
 end
 exit
 eof
 
 
 --
 Jan Abendroth
 Emerald BioStructures
 Seattle / Bainbridge Island WA, USA
 home: Jan.Abendroth_at_gmail.com
 work: JAbendroth_at_embios.com
 http://www.emeraldbiostructures.com
 
 
 
 
 
 

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, 
Cambridge, CB2 0QH



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