Re: [ccp4bb] Help needed in solving a MAD dataset
Hi Qing Lu, try Autorickshaw: http://www.embl-hamburg.de/Auto-Rickshaw/ It can perform the complete structure solution procedure if the quality of your data is sufficient and I consider it very user-friendly, especially for beginners . Regards, Uli Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu
Re: [ccp4bb] Help needed in solving a MAD dataset
Dear All, Not only for beginners, but also for experts who want to solve structures in hurry at the beamline and who want to complete model starting from X-ray data at resolution better than 3.0 A resolution. Santosh Quoting Ulrich Zander ulrich.zan...@strubio.uni-kiel.de: Hi Qing Lu, try Autorickshaw: http://www.embl-hamburg.de/Auto-Rickshaw/ It can perform the complete structure solution procedure if the quality of your data is sufficient and I consider it very user-friendly, especially for beginners . Regards, Uli Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu Santosh Panjikar, Ph.D. Staff Scientist EMBL-Hamburg Outstation C/o DESY Notkestrasse 85 22603 Hamburg (Germany) panjikar at embl-hamburg.de http://www.embl-hamburg.de/~panjikar
Re: [ccp4bb] Help needed in solving a MAD dataset
Dear Jürgen, The road to perfection is a long one ... . Thank you for the feedback! With best wishes, Gerard. -- On Thu, May 20, 2010 at 10:31:37PM -0400, Jürgen Bosch wrote: I don't like the site finding option in autosharp, takes too long in most of my cases. So my approach is locate sites via SHELX, then feed them into Sharp. Sorry Gerard :-) Jürgen On May 20, 2010, at 10:02 PM, Jeremiah Farelli wrote: I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ -- === * * * 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 * * * ===
Re: [ccp4bb] Help needed in solving a MAD dataset
Crank is a good tool for doing this automatically. Follow the instructions here: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_experimental_phasing_with_Crank Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu
Re: [ccp4bb] Help needed in solving a MAD dataset
Minor correction: SHELX software are not part of CCP4 but if you have them installed as part of your crystallograhic software, you can call them from the CCP4 GUI. You can obtain the SHELX suite free to academic labs from Ggeorge Sheldrickbe Email George Sheldrick. George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de Jürgen Bosch wrote: CCP4 way: locate the Se sites with SHELX (if you use the CCP4I gui it's technically a ccp4 program :-) ) Try using only your peak data set first. If you can't locate your sites with the single wavelength then add remote (DAD) and if that doesn't work go MAD. non-ccp4 way run hkl2map as frontend to SHELX, do the same thing. After 10 minutes go and open a bottle of your favourite sparkling cider* and start tracing the structure. Jürgen * can be replaced by other sparkling product containing trace amounts of EtOH supplemented with flavours On May 19, 2010, at 12:01 PM, Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Help needed in solving a MAD dataset
Dear Qing Lu, Now that several suggestions, both ccp4 and non-ccp4, have been made, may I suggest that you (also) try autoSHARP, available free of charge at http://www.globalphasing.com/sharp/ It includes the invocation of SHELXD to solve the substructure, and takes you all the way to autobuilding with ARP/wARP if you have it installed and your data resolution is sufficient. It has been around for quite a while and has many happy users. With best wishes, Gerard. -- On Wed, May 19, 2010 at 09:06:54AM -0700, Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu -- === * * * 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 * * * ===
Re: [ccp4bb] Help needed in solving a MAD dataset
I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it.
Re: [ccp4bb] Help needed in solving a MAD dataset
I don't like the site finding option in autosharp, takes too long in most of my cases. So my approach is locate sites via SHELX, then feed them into Sharp. Sorry Gerard :-) Jürgen On May 20, 2010, at 10:02 PM, Jeremiah Farelli wrote: I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Help needed in solving a MAD dataset
CCP4 way: locate the Se sites with SHELX (if you use the CCP4I gui it's technically a ccp4 program :-) ) Try using only your peak data set first. If you can't locate your sites with the single wavelength then add remote (DAD) and if that doesn't work go MAD. non-ccp4 way run hkl2map as frontend to SHELX, do the same thing. After 10 minutes go and open a bottle of your favourite sparkling cider* and start tracing the structure. Jürgen * can be replaced by other sparkling product containing trace amounts of EtOH supplemented with flavours On May 19, 2010, at 12:01 PM, Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Help needed in solving a MAD dataset
First, you will need CCP4 installed and set up properly. You will also need to know your protein sequence. Put the latter into a text file (FASTA format will do). Next, download the file Elves from: http://ucxray.berkeley.edu/~jamesh/elves/download.html then type: chmod a+x Elves Elves /path/to/data/frames/ ./proteinsequence.txt If you don't know how to answer any of the questions Elves ask you, then the default is usually the best choice. If the structure can be solved from the data, this will do the trick most of the time (~80% in my tests). Things they don't handle well are twinning and severe radiation damage. -James Holton MAD Scientist Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu
