From: Theresa H. Hsu
Date: 17 February 2012 11:31
Dear crystallographers
I would like to get some opinion. For someone beginning to learn basic crystallography including indexing, scaling ..., should I start with automated tool like Xia2? Or is manual method for each step better for learning?
Thank you.
Theresa
----------
From: Poul Nissen
Dear theresa
xia2 does a great job so it can be used as your reference when processing your data manually, either for learning or improvement. When comparing different processing programs and protocols try to judge data quality by some objectice criteria like HA site identification, anomalous patterson or fourier peak strength, mr solution or model refinement.
Poul
----------
From: Graeme Winter
Dear Theresa,
My answer would be - it depends.
If you are in the business of learning crystallography, then I would
absolutely suggest you start from doing everything by hand. Indeed, if
you really want to get "stuck in" I would suggest starting with the
programs you need (mosflm, scala, truncate etc) and scripts so you can
get a proper idea what the programs are doing. There is of course
CCP4i, but this can "hide" some of the details which may be
instructive to know about.
If however you're in the business of getting on with biological
research, well I would say that automated tools (be they for data
reduction or phasing / model building) are exceedingly useful.
If you can find the time, I would always encourage people to do things
with automation and by hand, to allow comparison of the results. If
nothing else this may give you confidence in the automation software.
Best wishes,
Graeme
----------
From: Liz Potterton
Hello Teresa,
I need to disagree with Graeme over the idea that ccp4i 'hides' what is happening. If you care to you can see all the gorey details of command files, log files etc.. You can run the programs one step at a time and with various modes with ccp4i and iMosflm and learn something of what is going on at each stage but the gui layer at least gives you a much quicker user-friendly way to control them rather than going back to prehistoric scripts.
On the other hand pipelines such as xia2 will usually do the job and save you much time.
Liz
----------
From: Harry Powell
Hi
In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration & scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes...
"to read is to forget, to write is to remember, to do is to understand" .
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
----------
From: <eugene.krissinel
This is actually very true, I simply want to support/enforce Liz's statement by adding that ccp4i indeed provides for both ends: from elementary scripts, useful for experts, to a rather large-scale automated processing where low-level details are not on the front page, which is more useful for a general user. By far, not every piece of software offer such range of granularity :)
Eugene
----------
From: jens Preben Morth
After putting up your quote in the lab, a student quickly replied "To do and fail is to remember and to understand" :-)
--
J. Preben Morth, Ph.D
Date: 17 February 2012 11:31
Dear crystallographers
I would like to get some opinion. For someone beginning to learn basic crystallography including indexing, scaling ..., should I start with automated tool like Xia2? Or is manual method for each step better for learning?
Thank you.
Theresa
----------
From: Poul Nissen
Dear theresa
xia2 does a great job so it can be used as your reference when processing your data manually, either for learning or improvement. When comparing different processing programs and protocols try to judge data quality by some objectice criteria like HA site identification, anomalous patterson or fourier peak strength, mr solution or model refinement.
Poul
----------
From: Graeme Winter
Dear Theresa,
My answer would be - it depends.
If you are in the business of learning crystallography, then I would
absolutely suggest you start from doing everything by hand. Indeed, if
you really want to get "stuck in" I would suggest starting with the
programs you need (mosflm, scala, truncate etc) and scripts so you can
get a proper idea what the programs are doing. There is of course
CCP4i, but this can "hide" some of the details which may be
instructive to know about.
If however you're in the business of getting on with biological
research, well I would say that automated tools (be they for data
reduction or phasing / model building) are exceedingly useful.
If you can find the time, I would always encourage people to do things
with automation and by hand, to allow comparison of the results. If
nothing else this may give you confidence in the automation software.
Best wishes,
Graeme
----------
From: Liz Potterton
Hello Teresa,
I need to disagree with Graeme over the idea that ccp4i 'hides' what is happening. If you care to you can see all the gorey details of command files, log files etc.. You can run the programs one step at a time and with various modes with ccp4i and iMosflm and learn something of what is going on at each stage but the gui layer at least gives you a much quicker user-friendly way to control them rather than going back to prehistoric scripts.
On the other hand pipelines such as xia2 will usually do the job and save you much time.
Liz
----------
From: Harry Powell
Hi
In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration & scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes...
"to read is to forget, to write is to remember, to do is to understand" .
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
----------
From: <eugene.krissinel
This is actually very true, I simply want to support/enforce Liz's statement by adding that ccp4i indeed provides for both ends: from elementary scripts, useful for experts, to a rather large-scale automated processing where low-level details are not on the front page, which is more useful for a general user. By far, not every piece of software offer such range of granularity :)
Eugene
----------
From: jens Preben Morth
After putting up your quote in the lab, a student quickly replied "To do and fail is to remember and to understand" :-)
Hi
In addition to what Poul and Graeme have said, it may be worthwhile attending one of the fine protein crystallography schools that are run, where you will hear lectures on integration& scaling etc that attempt to explain the basics of what's being done, and probably have a couple of practical sessions where you get to use the programs under the watchful eye of an expert. Or you could ask someone who has taught on (or attended) one of these schools if you could see their lecture slides and notes...
--
J. Preben Morth, Ph.D
----------
From: Bosch, Juergen
You would hope one learns something from failed experiments.
I feel prehistoric now after Liz comment.
Jürgen
......................
Jürgen Bosch
----------
From: Sanishvili, Ruslan
Hi Harry,
Are you advertising our CCP4 Summer School coming up in June at APS?
If not, then I'll shamelessly plug in: http://www.ccp4.ac.uk/schools/APS-school/
And if one visits previous years' school links, there are plenty of lectures posted.
Thanks,
N.
Ruslan Sanishvili (Nukri), Ph.D.
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