[ccp4bb] Douglas Instruments Oryx crystallisation robots
We are thinking about getting the Oryx8 robot (Douglas Instruments) for crystallisation experiments. Is anyone out there with any kind of experience with these? Jan Dohnalek IMC Prague
Re: [ccp4bb] anomalous signal
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
Re: [ccp4bb] Second moments of Z but not twinning
Hi Graeme, How is your data binned? I don't claim to be any statistician, but I seem to remember being told by such an individual that you need a decent number of reflections to be able to calculate a accurate/reliable second moment - and if, in your low-res bins, you have relatively few reflections, your values of second moment of Z can start to vary wildly. HTH, Dave On 01/06/07, Winter, G (Graeme) [EMAIL PROTECTED] wrote: Hi Folks, I was wondering if there is a document somewhere explaining some of the more interesting things which can be interpreted from the plot of second moment of Z = I'/I' anywhere? I've looked around and I can't find much beyond the things pertaining to twinning, where it will have the magical values of 2.0 or 1.5. What about if it is say 2.0 around the low resolution regions but gets much bigger? Looking at the truncate source code there is a note to the effect that the second moments may be greater than two in when you have pseudotranslational symmetry. In this case, however, I would expect that the effect would be uniform across the resolution ranges… any thoughts? Any pointers would be greatly appreciated. Thanks, Graeme -- --- David Briggs, PhD. Father Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile --- Anyone who is capable of getting themselves made President should on no account be allowed to do the job. - Douglas Adams
Re: [ccp4bb] Douglas Instruments Oryx crystallisation robots
Dear Jan Dohnalek IMC Prague We bought an Oryx 8 last year, and have been pleased with it. It's robust and I can fix many things myself. The best thing though have been that every time I have problems, e.g. after version update I have had support immediately - so that the robot didn't have weeks of downtime. We do many different experimental setups - without proper statistics I still believe that about 90 % of the experiments we setup are setup of low drop volume screening using commercial available screens. We have recently implemented a method for Oryx 8 published in Acta Cryst D, An automated micro seed matrix-screening method for protein crystallization with tremendous success with great success. You welcome to contact me by phone, if you want to discuss the purchase further. Best regards Jens-Christian Navarro Poulsen Dept of Chemistry, University of Copenhagen Phone +45 3532 0287 -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Jan Dohnalek Sent: 1. juni 2007 11:39 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Douglas Instruments Oryx crystallisation robots We are thinking about getting the Oryx8 robot (Douglas Instruments) for crystallisation experiments. Is anyone out there with any kind of experience with these? Jan Dohnalek IMC Prague
[ccp4bb] New version of clipper (includes buccaneer, pirate, ...) available from CCP4 download pages
We are pleased to announce the release of the Clipper2 module as part of the CCP4 6.0.2 public release. The Clipper2 module includes Pirate v0.4.9, Buccaneer 0.7.1, and the Clipper 2.0 software library including the Clipper Utilities. This software is kindly provided by Kevin Cowtan. The Clipper2 module is available through the automated Downloads page, http://www.ccp4.ac.uk/download/downloadman.php and from the Daresbury ftp server. The module can be taken as a module of a fresh CCP4 6.0.2 installation, or it can be added to an existing 6.0.2 installation. In particular, the automated script install.sh will check for an existing CCP4 installation, and give you the option of installing Clipper2 there. On windows platform you are normally provided with an Update.exe file that should apply the update and known fixes. The separate release of the Clipper2 module is part of a general move towards a more modular system for the CCP4 suite. As a separate development, the Downloads page now includes an InstallShield (Windows-like) installer for Linux, containing the same packages as the download pages (in particular it contains clipper2 within its ccp4 package).
[ccp4bb] ccp4mg povray rendering
Hi all, I am generating images using ccp4mg (which is wonderful by the way), but I can not figure out how to generate a povray input file that will yield an image with a transparent background. Getting a transparent background using the screen snapshot works fine, but I would like to have a rendered image. I have tried adding the +UA tag (which I believe should render the alpha channel as transparent) as a povray command line option so that my input looks like such: povray +A +J0 +Q9 +UA +H2400 +W2400 input_file.pov Yet this still does not give me a transparent background. When generating povray input files, does ccp4mg output the background as the alpha channel or do I need to go about this a different way? Thanks, Ray -- Raymond W. Bourdeau University of Chicago - Tang Lab 929 E 57th St. W423J Chicago, IL 60637 tel: 773-702-4608 email: [EMAIL PROTECTED] email: [EMAIL PROTECTED]
[ccp4bb] shutter trouble on the MicroMax007HF
Apologies for the non-CCP4 question, but I think this would of interest to anyone thinking of purchasing the 007 from Rigaku. To praise the instrument, we have been able to evaluate crystals that were previously only assessable at the synchrotrons. The intensities are ten times that of the RU-H2R and the spots are beautiful. BUT, we had it installed in February 07 and since then we have not been able to use both ports simultaneously due to a problem with the shutter board (or shutters or both). I am curious to know whether we are the only ones with this problem where the generator sometimes goes off when both shutters are opened. Thanks, Deena Deena Abells Oren, PhD Laboratory of Molecular Biophysics Rockefeller University 1230 York Ave New York, NY 10021 phone: 212-327-7429
Re: [ccp4bb] ccp4mg povray rendering
For povray, background is implicit (it exists as black if unspecified). According to the docs when the alpha channel is turned on, all areas of the image where the background is partly or fully visible will be partly or fully transparent. I haven't used ccp4mg, but it might be making a sphere or a sky_sphere for the background instead of using the background designator, which could be causing problems. I suspect this is the case. Spheres are not transparent unless specified with an rgbt color_vector in the pigment specifier. Setting 1.0 as the 4th term in the rgbt vector will give full transparency. Also, some viewing programs do not display the alpha channel and they will look non-transparent, but this is less likely than the sphere or sky_sphere scenarios. If you post your pov files somewhere, I can give them a look. You will probably not want to attach them if you post to the ccp4bb as they can be quite big, but you can include them as attachments if you mail them directly to me ([EMAIL PROTECTED]). James On Friday 01 June 2007 10:54, Ray Bourdeau wrote: Hi all, I am generating images using ccp4mg (which is wonderful by the way), but I can not figure out how to generate a povray input file that will yield an image with a transparent background. Getting a transparent background using the screen snapshot works fine, but I would like to have a rendered image. I have tried adding the +UA tag (which I believe should render the alpha channel as transparent) as a povray command line option so that my input looks like such: povray +A +J0 +Q9 +UA +H2400 +W2400 input_file.pov Yet this still does not give me a transparent background. When generating povray input files, does ccp4mg output the background as the alpha channel or do I need to go about this a different way? Thanks, Ray -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com
Re: [ccp4bb] ccp4mg povray rendering
Thanks for the advice. You were right in that the background designator was
not the only thing defining the background. The fog designator was the
problem, as it apparently put a black fog behind my molecule. Once I
removed it, I got a nice transparent background (original header below).
#include colors.inc
camera {
orthographic location 0,0,-60
look_at 0,0,0up 0,35.2678904747,0right 36.5470367614,0,0}
background { color rgb 0,0,0 }
light_source { 0.0,0.0,-600.0color White}
fog { distance 100 colour rgb0,0,0 }
Thanks,
Ray
On 6/1/07, James Stroud [EMAIL PROTECTED] wrote:
For povray, background is implicit (it exists as black if unspecified).
According to the docs when the alpha channel is turned on, all areas of
the
image where the background is partly or fully visible will be partly or
fully
transparent. I haven't used ccp4mg, but it might be making a sphere or a
sky_sphere for the background instead of using the background
designator,
which could be causing problems. I suspect this is the case. Spheres are
not
transparent unless specified with an rgbt color_vector in the pigment
specifier. Setting 1.0 as the 4th term in the rgbt vector will give full
transparency. Also, some viewing programs do not display the alpha channel
and they will look non-transparent, but this is less likely than the
sphere
or sky_sphere scenarios.
If you post your pov files somewhere, I can give them a look. You will
probably not want to attach them if you post to the ccp4bb as they can be
quite big, but you can include them as attachments if you mail them
directly
to me ([EMAIL PROTECTED]).
James
On Friday 01 June 2007 10:54, Ray Bourdeau wrote:
Hi all,
I am generating images using ccp4mg (which is wonderful by the way), but
I
can not figure out how to generate a povray input file that will yield
an
image with a transparent background. Getting a transparent background
using the screen snapshot works fine, but I would like to have a
rendered
image. I have tried adding the +UA tag (which I believe should render
the
alpha channel as transparent) as a povray command line option so that my
input looks like such:
povray +A +J0 +Q9 +UA +H2400 +W2400 input_file.pov
Yet this still does not give me a transparent background. When
generating
povray input files, does ccp4mg output the background as the alpha
channel
or do I need to go about this a different way?
Thanks,
Ray
--
James Stroud
UCLA-DOE Institute for Genomics and Proteomics
Box 951570
Los Angeles, CA 90095
http://www.jamesstroud.com
--
Raymond W. Bourdeau
University of Chicago - Tang Lab
929 E 57th St. W423J
Chicago, IL 60637
tel: 773-702-4608
email: [EMAIL PROTECTED]
email: [EMAIL PROTECTED]
