Re: [ccp4bb] .phs file conversion
Dear all, Graeme Winter wrote: I find this very helpful for inspecting and using maps from shelxe. There is no need to convert the phs to mtz if you just want to inspect the map from Shelxe. You can read in the .phs file into Coot. Since the .phs file does not have unit cell dimensions, you also need to read in a pdb. Unfortunately the pdb file written by Shelxe does not contain the spacegroup, but fortunately the res file does, and Coot is able to read this file too. So if you read in the .phs and the .res file, Bob's your uncle. Cheers, Bram *Bram Schierbeek* Application Scientist Structural Biology Bruker AXS B.V. Oostsingel 209, P.O.Box 811 2600 AV Delft, the Netherlands Tel.: +31 (15) 2152508 Fax:+31 (15)2152599 bram.schierb...@bruker-axs.nl _www.bruker-axs.com_ www.bruker-axs.de
Re: [ccp4bb] .phs file conversion
Bram, If you use the beta-test autotracing SHELXE, the .pdb file containing the poly-Ala trace also contains the space group. You presumably meant that the space group is missing from the SHELXL and SHELXD .pdb files, but of course you can read the .res files into Coot. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Thu, 5 Mar 2009, Bram Schierbeek wrote: Dear all, Graeme Winter wrote: I find this very helpful for inspecting and using maps from shelxe. There is no need to convert the phs to mtz if you just want to inspect the map from Shelxe. You can read in the .phs file into Coot. Since the .phs file does not have unit cell dimensions, you also need to read in a pdb. Unfortunately the pdb file written by Shelxe does not contain the spacegroup, but fortunately the res file does, and Coot is able to read this file too. So if you read in the .phs and the .res file, Bob's your uncle. Cheers, Bram *Bram Schierbeek* Application Scientist Structural Biology Bruker AXS B.V. Oostsingel 209, P.O.Box 811 2600 AV Delft, the Netherlands Tel.: +31 (15) 2152508 Fax:+31 (15)2152599 bram.schierb...@bruker-axs.nl _www.bruker-axs.com_ www.bruker-axs.de
[ccp4bb] XDS Viewer
Hi, I very recently downloaded and installed the Mac OS X executable of the new XDS Viewer program to inspect diffraction images. I have moved the program to /Applications. It starts up fine, but when I try to load an image it complains: Cannot open file! For image formats other than .cbf you need to install the 2cbf script. Please make sure you have added it to the executable path. Now 2cbf is in /usr/local/bin, which is in my path. I use /bin/tcsh as shell. Is there some confusion between the shell used by XDS Viewer (if any) and my preferred shell? Looking in the XDS Viewer.app directory I can't find any obvious clues. Thanks Derek __ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden
Re: [ccp4bb] Eukaryotic Membrane Proteins
Hi there, The human protein FLAP from the MAPEG family was expressed in E. coli and also the K-channel, KirBac1.3 (although this is a chimera of mouse and B. xenovorans). The pubmed id codes for related papers are: 17703190 and 17600184 and the pdb codes for the structures are: 2QKS and 2Q7M. Hope this helps. Regards, Karen On 5 Mar 2009, at 13:04, Raji Edayathumangalam wrote: Hello Folks, My enquiry pertains to membrane proteins. If you have been able to successfully express a eukaryotic integral MEMBRANE protein in E. coli or know of such a case, would you please provide some details. Thanks. Raji Dr. Karen McLuskey Glasgow Biomedical Research Centre University of Glasgow G12 8TA Tel: +44 141 330 4476 -
Re: [ccp4bb] .phs file conversion
Paul Emsley wrote: And for those who like the command line to convert .res to .pdb (and have Coot): [see attached] Oh curses - sorry. Not everyone develops coot. s?\./coot-real?coot? Paul.
Re: [ccp4bb] Eukaryotic Membrane Proteins
Hi Raji- A number of GPCRs have been overexpressed in E. coli. Examples are Reinhard Grishammer's work with neurotensin receptor and Christopher Tate's work with B2-adrenergic and adenosine 2a receptors. The problem was not necessarily expression but proper outer membrane targeting of *active* receptors. This seems to have been overcome for the most part by the use of either helpful lipid additives like cholesterol analogs or by brute-force mutagenesis to find more stable and active receptors. However, I don't know of any crystals or structures from any GPCR system generated from bacteria. Hope this helps... Brad On Thu, Mar 5, 2009 at 8:04 AM, Raji Edayathumangalam r...@brandeis.eduwrote: Hello Folks, My enquiry pertains to membrane proteins. If you have been able to successfully express a eukaryotic integral MEMBRANE protein in E. coli or know of such a case, would you please provide some details. Thanks. Raji
Re: [ccp4bb] express large proteins in E. coli?
David Garboczi wrote:
Have large proteins (300+ kD) been successfully produced in E. coli?
Which ones?
have a look at Suo et al., 2000, PNAS, 14188-14193; (350 kDa);
or Pan et al., 1999, NAR, 1094-1103; ('only' 190 kDa).
klaus
Dave
--
Dr. Klaus Scheffzek
European Molecular Biology Laboratory (EMBL)
Structural and Computational Biology Unit
Meyerhofstr. 1
69117 Heidelberg, Germany
Phone: (49) 6221 387 401
Fax:(49) 6221 387 306/519
E-mail: scheff...@embl.de
Web:www.embl.de
Re: [ccp4bb] Problem with setting up ccp4 gui
I had the same problem. In my case I think it was related to the part
of ccp4 configuration that redefines python path. For some reasons (it
breaks wxPython, at least in Hardy), I had it commented out and then
after starting ccp4i I got these dbccp4i warnings. When I turned python
part of ccp4 configuration script back on I got the same messages as Jan
does - ccp4i window opens and then closes.
What solved the problem for me was to delete the whole .CCP4 folder (it
may be enough just to get rid of unix subfolder). Since it was fresh
Hardy installation on a new machine, I didn't lose anything.
HTH,
Ed.
On Wed, 2009-03-04 at 17:02 +, Stein, ND (Norman) wrote:
Hi Jan
If they exist, could you please send me any of the .log files in the
following directory:
~/.CCP4/
In particular the file dbhandler.log. These should help to fix the
problem.
Thanks
Norman Stein
CCP4
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Jan Jensen
Sent: 03 March 2009 17:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Problem with setting up ccp4 gui
Hi all,
I have been struggling with installing the new CCP4 package. I run
RedHat Enterprise 4 and have previously used older packages with
success. After I untar and run ./install as root everything seems to
install just fine. When I run ccp4i -c to configure I think something
goes wrong or extensions get misdirected. If I try to run all the
scripts to test, they all seem to execute fine.
I have had luck starting the GUI as root or user but when you get to the
part where projekt directories are setup the GUI stops working and
cannot be restarted (showing the message below)
Error in startup script: wrong # args: should be dbccp4i_open_project
project args
while executing
dbccp4i_open_project
(eval body line 1)
invoked from within
eval dbccp4i_open_project $project $args
(procedure DbLoadFile line 12)
invoked from within
DbLoadFile $project
(procedure DbOpenDatabase line 13)
invoked from within
DbOpenDatabase $project
(procedure DbOpen line 30)
invoked from within
DbOpen -init
(procedure DbInitialise line 19)
invoked from within
DbInitialise
(procedure task line 14)
invoked from within
task
(configure arm line 6)
invoked from within
switch $system(RUN_MODE) \
script {
# Run a script ($CCP4I/scripts/project.script) with parameters from def
file
source [file join $env(CCP4I_...
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i.tcl line 163)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /opt/ccp4/ccp4-6.1.0/ccp4i/bin/ccp4i line 5)
Can anyone help me?
Thanks,
Jan K Jensen, Pl-R, Ph.D.
Post doctoral fellow at University of Illinois at Chicago (UIC)
Laboratory of Peter GW Gettins Department of Biochemistry and Molecular
Genetics MBRB Room 1260 900 S Ashland Chicago Il, 60607
Phone: 312 996 7664 or 773 574 9276 (mobile)
Email: j...@uic.edu
Homepage: http://www.epernicus.com/jkj
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Nadir T. Mrabet
Sent: Monday, February 16, 2009 12:37 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] PDB protein strucutrues as screen saver
Hi,
You may want to have a look at
http://www.luminorum.com/html/luminorum_ltd___extras.html.
hth
Nadir
--
Pr. Nadir T. Mrabet
Cellular Molecular Biochemistry
INSERM U-724
Nancy University, School of Medicine
9, Avenue de la Foret de Haye, BP 184
54505 Vandoeuvre-les-Nancy Cedex
France
Phone: +33 (0)3.83.68.32.73
Fax: +33 (0)3.83.68.32.79
E-mail: nadir.mra...@medecine.uhp-nancy.fr
Jayashankar wrote:
Dear Scientists,
It may be too much...
But as a biophysics student I would like to appreciate and feel happy
to have pdb structures as my computers screen savers than to have some
funny and fancy stuffs.
And it may help me as a motivator to solve my own structures in
future
I want to ask is there any existing script that grep strucutres one by
one with one line definition of that structure.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
--
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /
Re: [ccp4bb] XDS Viewer
Hi, Once you have a 2cbf in /usr/local/bin and start XDS Viewer from a terminal (/Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer) it seems to work fine. However for the diffraction image viewing I would suggest adxv. You can find it at: http://www.scripps.edu/~arvai/adxv.html. Andrzej On 5/3/09 15:21, Derek Logan wrote: Hi, I very recently downloaded and installed the Mac OS X executable of the new XDS Viewer program to inspect diffraction images. I have moved the program to /Applications. It starts up fine, but when I try to load an image it complains: Cannot open file! For image formats other than .cbf you need to install the 2cbf script. Please make sure you have added it to the executable path. Now 2cbf is in /usr/local/bin, which is in my path. I use /bin/tcsh as shell. Is there some confusion between the shell used by XDS Viewer (if any) and my preferred shell? Looking in the XDS Viewer.app directory I can't find any obvious clues. Thanks Derek __ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden
Re: [ccp4bb] XDS Viewer
Hi Andrzej, Thanks for the tip. It just seemed to me that since the package installed as a typical Mac OS X clickable program, then it was meant to run that way. Thanks also for info about adxv. I wasn't aware that there was a Mac executable for this program. Kay, the image I was trying to read was a .mar2560 file frpm the mar555 flat panel detector, which I had previously processed using XDS. Cheers Derek On Mar 6, 2009, week10, at 8:10, Andrzej Lyskowski wrote: Hi, Once you have a 2cbf in /usr/local/bin and start XDS Viewer from a terminal (/Applications/XDS-Viewer.app/Contents/MacOS/XDS-Viewer) it seems to work fine. However for the diffraction image viewing I would suggest adxv. You can find it at: http://www.scripps.edu/~arvai/adxv.html. Andrzej On 5/3/09 15:21, Derek Logan wrote: Hi, I very recently downloaded and installed the Mac OS X executable of the new XDS Viewer program to inspect diffraction images. I have moved the program to /Applications. It starts up fine, but when I try to load an image it complains: Cannot open file! For image formats other than .cbf you need to install the 2cbf script. Please make sure you have added it to the executable path. Now 2cbf is in /usr/local/bin, which is in my path. I use /bin/tcsh as shell. Is there some confusion between the shell used by XDS Viewer (if any) and my preferred shell? Looking in the XDS Viewer.app directory I can't find any obvious clues. Thanks Derek __ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden __ Derek Logan tel: +46 46 222 1443 Associate Professor fax: +46 46 222 4692 Molecular Biophysics mob: +46 76 8585 707 Centre for Molecular Protein Science Lund University, Box 124, 221 00 Lund, Sweden
