Re: [ccp4bb] process SeMet labelled data
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear ccp4bbers, I agree with Dirk. I have also noticed that much due to the way X-ray crystallography is evolving, a lot of students/early-postdocs find themselves doing crystallography in labs without a tradition in crystallography, even without real crystallographers. While we can criticise such a situation, this is a fact and students shouldn't be blamed for it. Having said so, I also think that people, students or not, should try and post, in their best interest, questions as specific as possible. As for Shivesh's question, I think this two papers (and references within) could be helpful: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=;db=PubMedcmd=searchterm=Single-wavelength%20anomalous%20diffraction%20phasing%20revisited http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmedcmd=Retrievedopt=AbstractPluslist_uids=16855302query_hl=5itool=pubmed_DocSum Cheers, Miguel Dirk Kostrewa escribió: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked for help on this board. Not everyone has always time or is always in the mood to answer such questions. In my opinion, it's then better not to respond at all than to give an answer like yours that is neither helpful nor funny! We all should try to keep a good style here. Dirk. Mark J. van Raaij wrote: why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research FellowUniversity Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFF5pSiF6oOrDvhbQIRAhVZAJ0TnW4fiBO+UGOVYkVuG3Ahe/bn0wCePWI/ owKrz/VIBcfyoVgOLLi3BTY= =OYFF -END PGP SIGNATURE-
[ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)
gruzi dirk, come on - lighten up a little! your reply wasn't funny or helpful either - just moralising. (by the way - 't is a strange fact that whenever i get any negative reactions to my own postings they stem *exclusively* from any or all of these three countries: the us, germany and switzerland. positive reactions, on the other hand, are typically from (again) the us and the uk. i think there might be a phd thesis in there for some cultural anthropologist) to address your point - we are here to try and answer queries, not to teach people crystallography from the ground up. that's what supervisors are for. and my advice to students without (access to) crystallographically trained supervisors would be to apply for a good course (e.g., the one in cold spring harbor every autumn), to move elsewhere or to not do crystallography (so as to avoid mono-, di-, tri-, tetra- or pentaretractions, which tend to be a bit of a blot on anyone's cv) i think this is the point that the people who replied carefully etc. were making, albeit more succinctly and humourously (albeit a trifle sarcastically, perhaps). moreover, these replies came from people who have contributed seriously to ccp4bb on numerous occasions! look, we're all busy, and time-waster postings are annoying. such postings, and moralisations about good style, can eventually tee off the experts who take the time to share their knowledge and expertise. if joe bloggs, who never posts anything, is annoyed by one of my posts and unsubscribes, that's his loss. if, however, people like tassos unsubscribe it's *our* loss! so, dear subscribers: before posting a question - ask your supervisor and/or your colleagues. if they can't help you, search the web with google (in many cases your question will have been asked, and answered, before). if you're still not happy, then by all means post a message to the appropriate bulletin board darn! look what you've made me do! now i'm moralising myself! guess i'd better move to switzerland then ;-) --dvd On Thu, 1 Mar 2007, Dirk Kostrewa wrote: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked for help on this board. Not everyone has always time or is always in the mood to answer such questions. In my opinion, it's then better not to respond at all than to give an answer like yours that is neither helpful nor funny! We all should try to keep a good style here. Dirk. Mark J. van Raaij wrote: why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research FellowUniversity Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: [EMAIL PROTECTED] http://sb.web.psi.ch with best regards, --gerard ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. **
Re: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)
I have found in my usenet adventures that usenet mavens often point to this link before trying to sort out among themselves exactly what level of humor to take with dubious posts: http://www.catb.org/~esr/faqs/smart-questions.html Of course usenet mavens also complain a little too much about top- posting--an aspect of ccp4bb that gives it special charm. James On Mar 1, 2007, at 1:31 AM, Gerard DVD Kleywegt wrote: gruzi dirk, come on - lighten up a little! your reply wasn't funny or helpful either - just moralising. (by the way - 't is a strange fact that whenever i get any negative reactions to my own postings they stem *exclusively* from any or all of these three countries: the us, germany and switzerland. positive reactions, on the other hand, are typically from (again) the us and the uk. i think there might be a phd thesis in there for some cultural anthropologist) to address your point - we are here to try and answer queries, not to teach people crystallography from the ground up. that's what supervisors are for. and my advice to students without (access to) crystallographically trained supervisors would be to apply for a good course (e.g., the one in cold spring harbor every autumn), to move elsewhere or to not do crystallography (so as to avoid mono-, di-, tri-, tetra- or pentaretractions, which tend to be a bit of a blot on anyone's cv) i think this is the point that the people who replied carefully etc. were making, albeit more succinctly and humourously (albeit a trifle sarcastically, perhaps). moreover, these replies came from people who have contributed seriously to ccp4bb on numerous occasions! look, we're all busy, and time-waster postings are annoying. such postings, and moralisations about good style, can eventually tee off the experts who take the time to share their knowledge and expertise. if joe bloggs, who never posts anything, is annoyed by one of my posts and unsubscribes, that's his loss. if, however, people like tassos unsubscribe it's *our* loss! so, dear subscribers: before posting a question - ask your supervisor and/or your colleagues. if they can't help you, search the web with google (in many cases your question will have been asked, and answered, before). if you're still not happy, then by all means post a message to the appropriate bulletin board darn! look what you've made me do! now i'm moralising myself! guess i'd better move to switzerland then ;-) --dvd On Thu, 1 Mar 2007, Dirk Kostrewa wrote: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked for help on this board. Not everyone has always time or is always in the mood to answer such questions. In my opinion, it's then better not to respond at all than to give an answer like yours that is neither helpful nor funny! We all should try to keep a good style here. Dirk. Mark J. van Raaij wrote: why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax:+41-56-310-5288 E-mail: [EMAIL PROTECTED] http://sb.web.psi.ch with best regards, --gerard ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity
Re: [ccp4bb] process SeMet labelled data
Dear Shivesh Below I've tried to give you some broad ideas about where to look / read and some packages / approaches to try. For a start there is a very comprehensive tutorial on the ccp4 site together with the experiemental phasing roadmaps. http://www.ccp4.ac.uk/dist/examples/tutorial/html/heavy-tutorial-mad.html which goes through the process step by step. For indexing and processing images, you are probably using MOSFLM or HKL2000?, both of which have excellent manuals that help with troubleshooting. At this stage you need to pick the appropriate bravais lattice then you need to refine and integrate. Once you have integrated (run in ccp4 for MOSFLM), then you need to scale the data using, for example, SCALA. Have a look at the following tutorial for running scala. http://www.ccp4.ac.uk/courses/ECM2004/runningscala.pdf Don't forget to seperate anomolous pairs when running scala Here, if relevant for your bravais lattice, you can also start to look at systematic absences to try to assign / narrow down the options for your space group. Remember, if your space group is incorrect, then (even though you may have a derivative) you won't be able to solve your structure. Thus if there are ambiguities, you need to systemically try out the options. Once you have scaled your data you may merge etc (see tutorial) using CAD and SCALEIT and start looking at some Anomalous Difference Patterson Maps to identify Heavy atom sites. see http://www.doe-mbi.ucla.edu/~sawaya/tutorials/Phasing/anopat.html Also, have a look at using SHARP/autoSHARP http://www.globalphasing.com/sharp/manual/index.html or SOLVE/RESOLVE http://www.solve.lanl.gov/ to analyse your data. These are both excellent packages for processing MAD / SAD datasets and calculating heavy atom positions / phases. For SHARP / autoSHARP you can supply the individual unmerged mtz's. SHARP will also alert you in a good humoured fashion to any deficiencies in your data and will try to pick the best approach (for e.g. it may try SAD depending on your data quality etc). autoSHARP will also run solvent flattening, give you final flattened maps readable in coot (which you should inspect to see if you can see features such as helices / strands etc). autoSHARP will even input your data into ARP/wARP, and if you are really fortunate you might even come in in the morning (watching ARP chain tracing can be rather addictive so its really best to go home!) and find that ARP has done a good job at a preliminary model or give you a nice starting point for manual building! Also for lower resolution and where you can clearly see features in the map for preliminary chain tracing try using Bucanneer. Hope this helps, good luck and above all have fun! Cheers James Dirk Kostrewa [EMAIL PROTECTED] wrote: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked for help on this board. Not everyone has always time or is always in the mood to answer such questions. In my opinion, it's then better not to respond at all than to give an answer like yours that is neither helpful nor funny! We all should try to keep a good style here. Dirk. Mark J. van Raaij wrote: why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research FellowUniversity Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone:+41-56-310-4722 Fax: +41-56-310-5288 E-mail: [EMAIL PROTECTED] http://sb.web.psi.ch -- Professor James Whisstock NHMRC Principal Research Fellow / Monash University Senior Logan fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia
Re: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)
Goede dag Gerard, interesting that you think my last e-mail was addressed to you ;-)! Yes, this was my first moralizing posting on this board after some 16 years. A bit sense of humor is fine, but the last posting was simply too much. We shouldn't attack people personally or discriminate against them, even if they don't follow a general policy about how to ask questions. Dirk. Gerard DVD Kleywegt wrote: gruzi dirk, come on - lighten up a little! your reply wasn't funny or helpful either - just moralising. (by the way - 't is a strange fact that whenever i get any negative reactions to my own postings they stem *exclusively* from any or all of these three countries: the us, germany and switzerland. positive reactions, on the other hand, are typically from (again) the us and the uk. i think there might be a phd thesis in there for some cultural anthropologist) to address your point - we are here to try and answer queries, not to teach people crystallography from the ground up. that's what supervisors are for. and my advice to students without (access to) crystallographically trained supervisors would be to apply for a good course (e.g., the one in cold spring harbor every autumn), to move elsewhere or to not do crystallography (so as to avoid mono-, di-, tri-, tetra- or pentaretractions, which tend to be a bit of a blot on anyone's cv) i think this is the point that the people who replied carefully etc. were making, albeit more succinctly and humourously (albeit a trifle sarcastically, perhaps). moreover, these replies came from people who have contributed seriously to ccp4bb on numerous occasions! look, we're all busy, and time-waster postings are annoying. such postings, and moralisations about good style, can eventually tee off the experts who take the time to share their knowledge and expertise. if joe bloggs, who never posts anything, is annoyed by one of my posts and unsubscribes, that's his loss. if, however, people like tassos unsubscribe it's *our* loss! so, dear subscribers: before posting a question - ask your supervisor and/or your colleagues. if they can't help you, search the web with google (in many cases your question will have been asked, and answered, before). if you're still not happy, then by all means post a message to the appropriate bulletin board darn! look what you've made me do! now i'm moralising myself! guess i'd better move to switzerland then ;-) --dvd On Thu, 1 Mar 2007, Dirk Kostrewa wrote: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked for help on this board. Not everyone has always time or is always in the mood to answer such questions. In my opinion, it's then better not to respond at all than to give an answer like yours that is neither helpful nor funny! We all should try to keep a good style here. Dirk. Mark J. van Raaij wrote: why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research FellowUniversity Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/ -- Dirk Kostrewa Paul Scherrer Institut Biomolecular Research, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail:[EMAIL PROTECTED] http://sb.web.psi.ch with best regards, --gerard ** Gerard J. Kleywegt [Research Fellow of the Royal Swedish Academy of Sciences] Dept. of Cell Molecular Biology University of Uppsala Biomedical Centre Box 596 SE-751 24 Uppsala SWEDEN http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is
Re: [ccp4bb] process SeMet labelled data
shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data.Thanx for the help. Shivesh I think you should ask your local crystallographer for help. There are several programs ( MOSFLM in CCP4, DENZO, XDS, D*TREK ) but you will need some guideance to find them and get started. Eleanor
[ccp4bb] Fwd: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)
Greetings (or in correct Swiss German Grüezi wohl, with Umlaut=vowel mutation) to all CCP4BB subscribers, being a CCP4BB reader (and sometimes writer) since something like 15 years, I realized today that the comment of Gerard was the first one I read since then containing a side-swipe regarding the nationality or the national character of authors. I think, within a multinational scientific community with a very long lasting tradition of internationalism such comments should be beyond this forum. On the other hand Gerard's comment contains a somewhat humorous (Swiss, Swedish, German, Dutch, ... kind of?) aspect, since it refers partly to Switzerland, a country where many foreigners live and work, including Germans like Dirk. I would guess a situation similar like in Sweden or The Netherlands, isn't it? Sorry being German too I could not resist making such a moralizing comment. Coming back to the original question from Shivesh Kumar, I believe Dirk is right. Shivas' question was not very specific. He probably simply wanted to know how to process MAD data correctly e.g. regarding the anomalous signal, which resulted sometimes in sign problems when using CCP4 programs (at least with previous versions), if I remember it correctly. Such questions came up frequently in the past and were not answered in a nasty/sarcastic way. --cd Dr. Klaus Piontek Albert-Ludwigs-University Freiburg -ALU-FR- (ALU-FR is an equal opportunity employer dedicated to the goal of building a culturally diverse and pluralistic community with a multicultural environment) Institute of Organic Chemistry and Biochemistry, Room 401 H Albertstrasse 21 D-79104 Freiburg Germany Phone: ++49-761-203-6036 Fax: ++49-761-203-8714 Email: [EMAIL PROTECTED] Web: http://www.chemie.uni-freiburg.de/orgbio/w3platt/ X-Real-To: [EMAIL PROTECTED] X-RAL-MFrom: [EMAIL PROTECTED] X-RAL-Connect: elvira.its.uu.se [130.238.164.5] X-CCLRC-SPAM-report: 0 : Date: Thu, 1 Mar 2007 10:31:06 +0100 Reply-To: Gerard DVD Kleywegt [EMAIL PROTECTED] Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK From: Gerard DVD Kleywegt [EMAIL PROTECTED] Subject: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data) Comments: To: Dirk Kostrewa [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK List-Help: http://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB, mailto:[EMAIL PROTECTED] CCP4BB List-Unsubscribe: mailto:[EMAIL PROTECTED] List-Subscribe: mailto:[EMAIL PROTECTED] List-Owner: mailto:[EMAIL PROTECTED] List-Archive: http://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB gruzi dirk, come on - lighten up a little! your reply wasn't funny or helpful either - just moralising. (by the way - 't is a strange fact that whenever i get any negative reactions to my own postings they stem *exclusively* from any or all of these three countries: the us, germany and switzerland. positive reactions, on the other hand, are typically from (again) the us and the uk. i think there might be a phd thesis in there for some cultural anthropologist) to address your point - we are here to try and answer queries, not to teach people crystallography from the ground up. that's what supervisors are for. and my advice to students without (access to) crystallographically trained supervisors would be to apply for a good course (e.g., the one in cold spring harbor every autumn), to move elsewhere or to not do crystallography (so as to avoid mono-, di-, tri-, tetra- or pentaretractions, which tend to be a bit of a blot on anyone's cv) i think this is the point that the people who replied carefully etc. were making, albeit more succinctly and humourously (albeit a trifle sarcastically, perhaps). moreover, these replies came from people who have contributed seriously to ccp4bb on numerous occasions! look, we're all busy, and time-waster postings are annoying. such postings, and moralisations about good style, can eventually tee off the experts who take the time to share their knowledge and expertise. if joe bloggs, who never posts anything, is annoyed by one of my posts and unsubscribes, that's his loss. if, however, people like tassos unsubscribe it's *our* loss! so, dear subscribers: before posting a question - ask your supervisor and/or your colleagues. if they can't help you, search the web with google (in many cases your question will have been asked, and answered, before). if you're still not happy, then by all means post a message to the appropriate bulletin board darn! look what you've made me do! now i'm moralising myself! guess i'd better move to switzerland then ;-) --dvd On Thu, 1 Mar 2007, Dirk Kostrewa wrote: Hi Mark, although Shivesh's question was not very specific, and he should have clearly given some more informations about what he would like to know, he is probably a beginner in crystallography and simply asked
Re: [ccp4bb] process SeMet labelled data
Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Properly
Re: [ccp4bb] process SeMet labelled data
Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
Re: [ccp4bb] process SeMet labelled data
On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Some hopefully useful remarks (fairly random and not complete and exhaustive): 1. make sure to mask out the backstop and beamstop holder correctly. Although various integration software claims to do this fairly automatic it is always better to do a good job on this. 2. check the rejected reflections (at the scaling/merging step): is there some system in those rejections? The two files produced by SCALA (ROGUES and a xmgr file that plots the detector position of rejected reflections) are very helpful. It can show ice-rings, bad beamstop-masking (see point 1) etc. 3. heavy atom detection/phasing software will also write out some helpful information about outliers: if there are some suspicious messages (e.g. warnings in autoSHARP) they usually point back to problems in data processing (see point 1). 4. if you collected several datasets/wavelengths: you can give those to SCALA for some 'local scaling'. This will also show you those really helpful CC(Dano) plots. But be careful with absorption correction: all datasets/sweeps need to be indexed identically. 5. always remember what your first reaction was when looking at the images: 'great' images should give you good statistics further down the pipeline. But if 'awfull' images give you good statistics I would be suspicious ... 6. unless you really know what's going on: stick with program defaults. Usually the developers have a very good idea why the program is doing things in a specific way. Cheers Clemens -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] process SeMet labelled data
why don't you just send all your images to the ccp4bb, then we'll process them, solve the structure and publish it for you. And we might put you in the acknowledgements, if you are lucky. Mark On 28 Feb 2007, at 16:35, Jonathan Grimes wrote: Anastassis Perrakis wrote: On Feb 28, 2007, at 14:37, shivesh kumar wrote: Dear all, I have a data set at 2.2A, of the selenomethionene labelled protein.How should I process the data. Carefully ! Thanx for the help. Shivesh Tassos i am sure what tassos really meant was Very Carefully ! jon -- Dr. Jonathan M. Grimes, Royal Society Research Fellow University Research Lecturer Division of Structural Biology Wellcome Trust Centre for Human Genetics University of Oxford Roosevelt Drive, Oxford OX3 7BN, UK Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547 Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/
