[ccp4bb] Is it possible to predict the kinase when knowing a phosphorylated substrate sequence?
Dear all, Sorry for the non-CCP4 question. Could anyone please tell me is there a way to predict the kinase when knowing a phosphorylated substrate sequence? Thanks in advance! Cheers Tiancen Hu Ph.D. Shanghai Institute of Materia Medica Chinese Academy of Sciences
Re: [ccp4bb] buster-tnt on OSX ?
Dear Bill,, On Sun, Oct 26, 2008 at 07:18:05PM -0700, William G. Scott wrote: > I'm actually one of those whom has struggled unsuccessfully to install > Sharp. I can't even remember why, and I am certain it was entirely my > fault, but this did get me wondering... I guess this is often a more general problem: when we're dealing with a crystallographic problem that our current set of practices doesn't deal satisfactorily with and we would like to try out another program, this is usually also a time of great stress and pressure (competitors, supervisors, finishing PhD etc). Ideally one would want to install and learn how to use a new software package when there is a half day or day time ... seldom happens. Without getting into details of installation, usually (> 90%) it is enough to download our packages and then run "./installSHARP -F". I might be wrong - but this could be a problem of not getting enough feedback about failed attempts (time pressure?). So please tell us about installation problems (or any problems) - hopefully this is a small price to pay for getting the software for free. If you feel like sending us positive feedback - even better (especially since crystallographic software doesn't get citations anymore these days ... maybe hidden in supplementary material that isn't easily visible through any search system I know of). > mlphare and MIR/MAD phasing seems to me the weak point in the ccp4 > distribution. (I've often switched over to CNS to calculate phases and > solvent-flatten them.) > > Is there any chance your team might be inspired, persuaded or bribed to > create a drop-in replacement for mlphare, maybe a "sharp light" for > boneheads like me? Something that uses the same I/O and interface as ccp4? A drop-in replacement would be very tricky: the concepts of SHARP are quite different (there is no such thing as 'native' or 'derivative') - but this adds a huge amount of flexibility. However, in the next 6.1 release there will be a autoSHARP CCP4i interface already in the CCP4 distribution (it's already there in the latest 6.0.99 prerelease or the CVS sources). Although this will still require the installation of SHARP/autoSHARP itself, at least one could run autoSHARP without the need of running a httpd. But be aware that using the CCP4i interface does limit you somewhat - a lot of the additional tools (regarding density modification, checking/finding sites via LLG maps, fine-tuning SHARP and viewing maps directly) aren't easily accessible this way. But autoSHARP should deal with all the situations that mlphare etc are dealing with: SIRAS, SAD, MIRAS, MAD etc. And if you want to do (or need to do) MAD+native+derivative or TaBr-cluster phasing or site-specific radiation damage or other more complex phasing scenarios: SHARP itself is the tool for doing all that. 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] poor density after phase extension
Dear Joe, On Mon, Oct 27, 2008 at 06:04:38AM +, joe wrote: > Hi, all: > > I have a poor density after phase extension problem. > Usually I use HKL2000 to scale the data and use the macro at the integrate > and scale steps. I got a good native data( P6422 130 130 150 , 90 90 120) at > 3.0A (completeness >90%, I/sigma >5, redandance>10, Linear R-fac<0.5, but > square R-fac >0.6; one problem is Linear R-fac smaller than squear R-fac in > my scaled data. I used macro: sigma cutoff 0 during scaling stage. if i > don't > use macro, the data will be getting bad less than 4.0A) and my reflection > data has strong anisotropy. > > I used this native data to do phase extension from 3.6A to 3.0A by CCP4i DM > program(the phase got from sharp program), but I cannot find any density is > improved.(density of sidechain cannot be seen) Two points that I would try: - if your data is very anisotropic, try and remove that anisotropy from your data before going into the (real-space) density modification part. I found over the last 1-2 years that this can have an impact. autoSHARP will do that automatically for you - but only if the reference dataset has at least 2.5A resolution. This might be a very conservative limit and you could run SHARP itself instead: specify to estimate (but not refine) the anisotropic scale of the first (reference) dataset. This will then give you 'isotropic' amplitudes in the output eden.mtz file. - when coming from SHARP I would recommend using the SOLOMON procedure we have inside our system: it is tightly connected to the SHARP output, makes sure to use the right columns and information from the SHARP file and generally gives as good density (and very often better) than running DM outside our system. However, if you have NCS and want to do NCS averaging you should still use something different (our SOLOMON procedure doesn't deal with NCS yet): but you should start these density modification and averaging jobs from a map coming out of SHARP+SOLOMON. There are obviously also other programs out there you could try: parrot and pirate from Kevin Cowtan or resove from Tom Terwilliger/Phenix. Make sure to use the correct column labels from the eden.mtz file though (if in doubt: drop me a line)! 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] buster-tnt on OSX ?
I would like to add my comments that Sharp & autoSharp are great programs that produce excellent phases, and that installation isn't too hard (even though the whole setup does seem unnecessarily complicated :-) ) I would also like to say that the Global Phasing people, in particular Clemens Vonrhein, are extraordinarily helpful and respond quickly to any query about the software On the original question that started this thread, as far as I can see there doesn't seem to be a Mac OSX intel version available, publicly at least Thanks Phil Evans On 27 Oct 2008, at 08:22, Clemens Vonrhein wrote: Dear Bill,, On Sun, Oct 26, 2008 at 07:18:05PM -0700, William G. Scott wrote: I'm actually one of those whom has struggled unsuccessfully to install Sharp. I can't even remember why, and I am certain it was entirely my fault, but this did get me wondering... I guess this is often a more general problem: when we're dealing with a crystallographic problem that our current set of practices doesn't deal satisfactorily with and we would like to try out another program, this is usually also a time of great stress and pressure (competitors, supervisors, finishing PhD etc). Ideally one would want to install and learn how to use a new software package when there is a half day or day time ... seldom happens. Without getting into details of installation, usually (> 90%) it is enough to download our packages and then run "./installSHARP -F". I might be wrong - but this could be a problem of not getting enough feedback about failed attempts (time pressure?). So please tell us about installation problems (or any problems) - hopefully this is a small price to pay for getting the software for free. If you feel like sending us positive feedback - even better (especially since crystallographic software doesn't get citations anymore these days ... maybe hidden in supplementary material that isn't easily visible through any search system I know of). mlphare and MIR/MAD phasing seems to me the weak point in the ccp4 distribution. (I've often switched over to CNS to calculate phases and solvent-flatten them.) Is there any chance your team might be inspired, persuaded or bribed to create a drop-in replacement for mlphare, maybe a "sharp light" for boneheads like me? Something that uses the same I/O and interface as ccp4? A drop-in replacement would be very tricky: the concepts of SHARP are quite different (there is no such thing as 'native' or 'derivative') - but this adds a huge amount of flexibility. However, in the next 6.1 release there will be a autoSHARP CCP4i interface already in the CCP4 distribution (it's already there in the latest 6.0.99 prerelease or the CVS sources). Although this will still require the installation of SHARP/autoSHARP itself, at least one could run autoSHARP without the need of running a httpd. But be aware that using the CCP4i interface does limit you somewhat - a lot of the additional tools (regarding density modification, checking/finding sites via LLG maps, fine-tuning SHARP and viewing maps directly) aren't easily accessible this way. But autoSHARP should deal with all the situations that mlphare etc are dealing with: SIRAS, SAD, MIRAS, MAD etc. And if you want to do (or need to do) MAD+native+derivative or TaBr-cluster phasing or site-specific radiation damage or other more complex phasing scenarios: SHARP itself is the tool for doing all that. 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] buster-tnt on OSX ?
Yikes! Apologies if that was over the top. I guess the chisanbop comment did not properly convey the hyperbole, and hence humor, I was trying to achieve. Hopefully my comments can still be taken as the constructive criticism they were intended to be. James On Oct 26, 2008, at 4:57 PM, Gerard Bricogne wrote: Dear James, I am rather surprised and disappointed to find such an intemperate, ill-judged and almost slanderous statement from you, especially in a posting to a bulletin board that is intended for the sharing of experience and good will and to which you have been such a regular and valued contributor. To deal with slander first: Global phasing has been operating for over 10 years without ever being, or intending to be, anyone's chance to "just try and make a buck". We develop our software thank to a mix of funding that does include industrial sponsors, but we distribute it free of charge to academic users (since 2002 we have issued over 3500 licence keys for SHARP to academic users). We even give support to academic users, and spare no pains in doing so, as many users can testify: this is not exactly the most lucrative occupation if one is looking to make a buck. Global Phasing's staff consists of eight scientists, plus one part-time person to keep the books and get the annual accounts audited. The company has never had any investors, and spends all its income on scientists' salaries and running costs. Perhaps the ".com" suffix has acquired a bad smell in other parts of the world, but in this case your insinuations are badly misguided. If you have had difficulties installing software from us, a more constructive form of feedback would be to write to us at sharp- develop or buster-develop (both @globalphasing.com) and explain the nature of those difficulties. We have often found that the worst problems occur when people, instead of writing to us, start to try and hack the scripts themselves and end up tying themselves in inextricable knots. One of your remarks seems to want to imply that we have taken a perverse pleasure in making installations difficult. It is true that we still carry a legacy from earlier days when some of our sponsors wanted to be able to distribute jobs over heterogeneous clusters of machines and to view the results from any other machine on that network, while most users today just want to run everything on one machine. Our installation procedures have kept evolving to become simpler and more robust, although the need to link up with several third-party packages makes it hard to suppress complexity entirely. If you happen to have constructive suggestions to make in this direction, we will be only too happy to listen to them and will do our best to make use of them. We do have, however, to weigh up how much time to devote to these issues, vs. how much to developing and implementing new methods. I hope you will take the time to write to either of the mailing lists I indicated above to explain what simplifications you would like to see in our current installation procedures, and look forward to reading them. With best wishes, Gerard. -- On Sun, Oct 26, 2008 at 01:40:35AM -0700, James Stroud wrote: The info at http://www.globalphasing.com/buster/installation/index.html#requirements will give you some hints about whether it will be successful on OS X. As per the Global Phasing modus operandi, any instruction involving installation of their software is muddled in riddle and ambiguity. They have made an art of making their software difficult to install. I guess the philosophy is that if you can somehow get their software installed, then you have earned your phase information. Personally, I'd rather solve my structure with using chisanbop and a pencil than attempt to install Global Phasing software. Speaking from experience, this is my 2c. Apologies if I hurt anyone's feelings who are "just trying to make a buck". James On Oct 24, 2008, at 9:39 AM, jacques-philippe colletier wrote: Hi everydoby, I`d like to know if there is a version of BUSTER-TNT available on MacOSX ? Anyone knows ? * Dr. Jacques-Philippe Colletier UCLA / DOE Institute for Genomics and Proteomics 90095 Los Angeles, CA, USA * [EMAIL PROTECTED] [EMAIL PROTECTED] * -- James Stroud UCLA-DOE Institute for Genomics and Proteomics Box 951570 Los Angeles, CA 90095 http://www.jamesstroud.com -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park
Re: [ccp4bb] installing Phaser EP
Well, in case of installation difficulties, you can always contact the friendly and helpful staff at [EMAIL PROTECTED] . ;-) Unfortunately, our friendly and helpful Mac expert is away at the moment, but I can try to help. If you follow through to the Mac download page, you have a few choices. Which ones did you try? The ftp site also has a few combinations which are not linked on the downloads page. If you do have the right package, it may be that the update of ccp4i went wrong for some reason. You may need to do a manual System Administration -> Install/uninstall Tasks HTH Martyn -Original Message- From: CCP4 bulletin board on behalf of James Whittle Sent: Sun 10/26/2008 4:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] installing Phaser EP Hi all- I'm trying to get Phaser EP working through ccp4i on an intel Mac. I've tried re-installing both ccp4 and phaser from the automatic downloads section of the website, but Phaser EP still does not appear in the program list. Can anyone suggest how to fix this? --James
[ccp4bb] Invisible but intact disulphides?
Hello everyone, We are working on a protein in which a long loop is held in place by a disulphide bond. All the biochemistry and biophysics of this protein indicates that the disulphide bond should be intact, but we only see one end of it in the crystal structure. The protein has not been exposed to any reductants. The data were collected at a medium intensity synchrotron source (MAX-lab in Lund) and the total dose should thus not have been extremely high. We have even looked at maps calculated from the first half of the dataset (45 minutes exposure vs. 90) and there is no difference. We have tried to react the free cysteine with 1mM MeHgCl2 and 10mM iodacetamide, to no avail. Thus we really think the disulphide is intact even in the crystal. Has anyone seen a similar case, where all evidence pointed to an intact disulphide but it was not visible in the density? 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] Invisible but intact disulphides?
Fox GC, Shafiq M, Briggs DC, Knowles PP, Collister M, Didmon MJ, Makrantoni V, Dickinson RJ, Hanrahan S, Totty N, Stark MJ, Keyse SM, McDonald NQ. Abstract Redox-mediated substrate recognition by Sdp1 defines a new group of tyrosine phosphatases. Nature. 2007 May 24;447(7143):487-92. Epub 2007 May 9. PMID: 17495930 (ahem) We have something similar to what you describe - a disulphide linked N-terminal extension that was invisible, but part of it (including the disulphide bond) was necessary for substrate recognition. We had datasets ± DTT, and were able to confirm the presence of a disulphide my mass spec and free-thiol assays. HTH, David 2008/10/27 Derek Logan <[EMAIL PROTECTED]>: > Hello everyone, > We are working on a protein in which a long loop is held in place by a > disulphide bond. All the biochemistry and biophysics of this protein > indicates that the disulphide bond should be intact, but we only see one end > of it in the crystal structure. The protein has not been exposed to any > reductants. The data were collected at a medium intensity synchrotron source > (MAX-lab in Lund) and the total dose should thus not have been extremely > high. We have even looked at maps calculated from the first half of the > dataset (45 minutes exposure vs. 90) and there is no difference. We have > tried to react the free cysteine with 1mM MeHgCl2 and 10mM iodacetamide, to > no avail. Thus we really think the disulphide is intact even in the > crystal. > Has anyone seen a similar case, where all evidence pointed to an intact > disulphide but it was not visible in the density? > 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 > -- David C. Briggs PhD Father & Crystallographer http://drdavidcbriggs.googlepages.com/home AIM ID: dbassophile
Re: [ccp4bb] buster-tnt on OSX ?
Dear James, Thank you for your reply. Again, I invite you to share with us the details of the problems you encountered, through the appropriate mailing list at Global Phasing. I failed, however, to see either humour or constructiveness in your claim that we were "just trying to make a buck", and could not leave such a statement hang in the air unanswered. With best wishes, Gerard. -- On Mon, Oct 27, 2008 at 02:52:16AM -0700, James Stroud wrote: > Yikes! > > Apologies if that was over the top. I guess the chisanbop comment did not > properly convey the hyperbole, and hence humor, I was trying to achieve. > Hopefully my comments can still be taken as the constructive criticism they > were intended to be. > > James > > On Oct 26, 2008, at 4:57 PM, Gerard Bricogne wrote: > >> Dear James, >> >> I am rather surprised and disappointed to find such an intemperate, >> ill-judged and almost slanderous statement from you, especially in a >> posting >> to a bulletin board that is intended for the sharing of experience and >> good >> will and to which you have been such a regular and valued contributor. >> >> To deal with slander first: Global phasing has been operating for over >> 10 years without ever being, or intending to be, anyone's chance to "just >> try and make a buck". We develop our software thank to a mix of funding >> that >> does include industrial sponsors, but we distribute it free of charge to >> academic users (since 2002 we have issued over 3500 licence keys for SHARP >> to academic users). We even give support to academic users, and spare no >> pains in doing so, as many users can testify: this is not exactly the most >> lucrative occupation if one is looking to make a buck. Global Phasing's >> staff consists of eight scientists, plus one part-time person to keep the >> books and get the annual accounts audited. The company has never had any >> investors, and spends all its income on scientists' salaries and running >> costs. Perhaps the ".com" suffix has acquired a bad smell in other parts >> of >> the world, but in this case your insinuations are badly misguided. >> >> If you have had difficulties installing software from us, a more >> constructive form of feedback would be to write to us at sharp-develop or >> buster-develop (both @globalphasing.com) and explain the nature of those >> difficulties. We have often found that the worst problems occur when >> people, >> instead of writing to us, start to try and hack the scripts themselves and >> end up tying themselves in inextricable knots. One of your remarks seems >> to >> want to imply that we have taken a perverse pleasure in making >> installations >> difficult. It is true that we still carry a legacy from earlier days when >> some of our sponsors wanted to be able to distribute jobs over >> heterogeneous >> clusters of machines and to view the results from any other machine on >> that >> network, while most users today just want to run everything on one >> machine. >> Our installation procedures have kept evolving to become simpler and more >> robust, although the need to link up with several third-party packages >> makes >> it hard to suppress complexity entirely. If you happen to have >> constructive >> suggestions to make in this direction, we will be only too happy to listen >> to them and will do our best to make use of them. We do have, however, to >> weigh up how much time to devote to these issues, vs. how much to >> developing >> and implementing new methods. >> >> I hope you will take the time to write to either of the mailing lists >> I >> indicated above to explain what simplifications you would like to see in >> our >> current installation procedures, and look forward to reading them. >> >> >> With best wishes, >> >> Gerard. >> >> >> -- >> On Sun, Oct 26, 2008 at 01:40:35AM -0700, James Stroud wrote: >>> The info at >>> >>> http://www.globalphasing.com/buster/installation/index.html#requirements >>> >>> will give you some hints about whether it will be successful on OS X. As >>> per the Global Phasing modus operandi, any instruction involving >>> installation of their software is muddled in riddle and ambiguity. They >>> have made an art of making their software difficult to install. I guess >>> the >>> philosophy is that if you can somehow get their software installed, then >>> you have earned your phase information. Personally, I'd rather solve my >>> structure with using chisanbop and a pencil than attempt to install >>> Global >>> Phasing software. >>> >>> Speaking from experience, this is my 2c. Apologies if I hurt anyone's >>> feelings who are "just trying to make a buck". >>> >>> James >>> >>> >>> >>> >>> >>> On Oct 24, 2008, at 9:39 AM, jacques-philippe colletier wrote: >>> Hi everydoby, I`d like to know if there is a version of BUSTER-TNT available on MacOSX ? Anyone knows ? **
Re: [ccp4bb] buster-tnt on OSX ?
Dear Jacques-Philippe, Sorry to have been distracted into responding to comments on your question rather than answering your question itself. We will shortly be announcing an academic release of a new version of BUSTER-TNT, which contains several major improvements over the previous one. It has been under beta-testing since July and has also been made available to a few academic labs with whom we have a beta-testing arrangement. This new version is in the last stages of being ported to MacOSX, but for the Intel processor only. I hope this release will come in time for your needs. You are welcome to get in touch for more details through the mailing list "[EMAIL PROTECTED]" . With best wishes, Gerard. -- On Fri, Oct 24, 2008 at 09:39:03AM -0700, jacques-philippe colletier wrote: > Hi everydoby, > I`d like to know if there is a version of BUSTER-TNT available on MacOSX ? > Anyone knows ? > > > * > Dr. Jacques-Philippe Colletier > UCLA / DOE Institute for Genomics and Proteomics > 90095 Los Angeles, CA, USA > * > [EMAIL PROTECTED] > [EMAIL PROTECTED] > * -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] buster-tnt on OSX ?
Apologies for going slightly further off-topic... Last time I had a free half-day to look into sharp, I noticed that the academic license prohibits reverse-engineering. This seemed to put any comparative testing into a slightly grey area. For example, if I find that sharp does the best job refining sites, but bp3 outputs better phases for a dataset due to different representation of phase probabilities*, I've implicitly constructed a primitive model of how sharp is working. This seems close enough to a first step of reverse-engineering that I was concerned. Could someone confirm that I'm worrying about things I don't need to here? Pete * Purely hypothetical example. Clemens Vonrhein wrote: > Dear Bill,, > > On Sun, Oct 26, 2008 at 07:18:05PM -0700, William G. Scott wrote: >> I'm actually one of those whom has struggled unsuccessfully to install >> Sharp. I can't even remember why, and I am certain it was entirely my >> fault, but this did get me wondering... > > I guess this is often a more general problem: when we're dealing with > a crystallographic problem that our current set of practices doesn't > deal satisfactorily with and we would like to try out another program, > this is usually also a time of great stress and pressure (competitors, > supervisors, finishing PhD etc). Ideally one would want to install and > learn how to use a new software package when there is a half day or > day time ... seldom happens. > > Without getting into details of installation, usually (> 90%) it is > enough to download our packages and then run "./installSHARP -F". I > might be wrong - but this could be a problem of not getting enough > feedback about failed attempts (time pressure?). So please tell us > about installation problems (or any problems) - hopefully this is a > small price to pay for getting the software for free. If you feel like > sending us positive feedback - even better (especially since > crystallographic software doesn't get citations anymore these days > ... maybe hidden in supplementary material that isn't easily visible > through any search system I know of). > >> mlphare and MIR/MAD phasing seems to me the weak point in the ccp4 >> distribution. (I've often switched over to CNS to calculate phases and >> solvent-flatten them.) >> >> Is there any chance your team might be inspired, persuaded or bribed to >> create a drop-in replacement for mlphare, maybe a "sharp light" for >> boneheads like me? Something that uses the same I/O and interface as ccp4? > > A drop-in replacement would be very tricky: the concepts of SHARP are > quite different (there is no such thing as 'native' or 'derivative') - > but this adds a huge amount of flexibility. > > However, in the next 6.1 release there will be a autoSHARP CCP4i > interface already in the CCP4 distribution (it's already there in the > latest 6.0.99 prerelease or the CVS sources). Although this will still > require the installation of SHARP/autoSHARP itself, at least one could > run autoSHARP without the need of running a httpd. But be aware that > using the CCP4i interface does limit you somewhat - a lot of the > additional tools (regarding density modification, checking/finding > sites via LLG maps, fine-tuning SHARP and viewing maps directly) > aren't easily accessible this way. > > But autoSHARP should deal with all the situations that mlphare etc are > dealing with: SIRAS, SAD, MIRAS, MAD etc. And if you want to do (or > need to do) MAD+native+derivative or TaBr-cluster phasing or > site-specific radiation damage or other more complex phasing > scenarios: SHARP itself is the tool for doing all that. > > Cheers > > Clemens >
Re: [ccp4bb] buster-tnt on OSX ?
Dear Pete, just my personal view on this (so don't take this as a legal expertise regarding our SHARP licence). I don't have any problems with people comparing software programs - I do that all the time. I doubt this can be seen as reverse engineering. The tricky part comes when comparisons are being published: ideally it would be nice if every developer of a particular piece of software is given the chance to comment - maybe he/she could even give a few simple advices how to run the program. After all, different programs might have different set of defaults (conservative versus adventurous) for particular problems. It's similar to a problem we discover e.g. in a PDB entry: contacting the authors of that PDB entry first to give them a chance to comment (and correct) I think is the apropriate initial step. Or actually - lets rephrase that: it's not like an error in a PDB entry! Improvements in software benefit a lot more crystallographers whereas a fixed PDB entry usually concerns a much smaller group of us. Anyway, I think we're doing actually fairly well compared to other scientific fields: crystallographic method developers are a very friendly bunch I must say, even if we're in a kind of 'competition'. Cheers Clemens On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote: > Apologies for going slightly further off-topic... > > Last time I had a free half-day to look into sharp, I noticed that the > academic license prohibits reverse-engineering. This seemed to put any > comparative testing into a slightly grey area. For example, if I find > that sharp does the best job refining sites, but bp3 outputs better > phases for a dataset due to different representation of phase > probabilities*, I've implicitly constructed a primitive model of how > sharp is working. This seems close enough to a first step of > reverse-engineering that I was concerned. > > Could someone confirm that I'm worrying about things I don't need to here? > > Pete > > * Purely hypothetical example. -- *** * 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] buster-tnt on OSX ?
James, If I may chime in here, as the head of a similar effort half as old and one quarter the size of Global Phasing... We scientists heading up private crystallography & related software efforts tend to be hypersensitive to such criticisms because of certain unfortunate past behaviors of commercial entities, who clearly were "just trying to make a buck", rather than trying to help their colleagues or advance science. So even the suggestion that one of us might be becoming that which initially drove us to achieve independence from the "academic-to-industrial software licensing complex" is an anathema guaranteed to engender a strong reaction. But there is more to it than that: For one thing, if we were "just trying to make a buck" from software, then we would all be idiots for attempting to do so in a field increasingly dominated by excellent free, academic, and open-source solutions. But we're not idiots -- we're in this area by desire and by choice, not by necessity. There are far more software bucks to be made downstream of basic research... For another thing, most of our businesses engage in practices deliberately inconsistent with making as many bucks as possible, such as: giving source code away unconditionally, making executables available at no cost to some users, and providing certain types of support at no charge -- so long as we can continue to make ends meet. That is compelling evidence that we all care more about helping our colleagues and about advancing science than about raking in the dough. Of course, knowing you personally, I don't think you meant anything with that hyperbole, but I can understand Gerard's reaction to it. So, in summary, going after us small private businesses for weak documentation, complex installations, sporadic crashes, or lack of undo -- that stuff is all fair game. But calling us just "buck makers"? Now that's below the belt, even in jest! Cheers, Warren DeLano Scientific LLC [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of James Stroud Sent: Monday, October 27, 2008 5:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] buster-tnt on OSX ? Yikes! Apologies if that was over the top. I guess the chisanbop comment did not properly convey the hyperbole, and hence humor, I was trying to achieve. Hopefully my comments can still be taken as the constructive criticism they were intended to be. James On Oct 26, 2008, at 4:57 PM, Gerard Bricogne wrote: > Dear James, > > I am rather surprised and disappointed to find such an > intemperate, > ill-judged and almost slanderous statement from you, especially in a > posting > to a bulletin board that is intended for the sharing of experience > and good > will and to which you have been such a regular and valued contributor. > > To deal with slander first: Global phasing has been operating > for over > 10 years without ever being, or intending to be, anyone's chance to > "just > try and make a buck". We develop our software thank to a mix of > funding that > does include industrial sponsors, but we distribute it free of > charge to > academic users (since 2002 we have issued over 3500 licence keys for > SHARP > to academic users). We even give support to academic users, and > spare no > pains in doing so, as many users can testify: this is not exactly > the most > lucrative occupation if one is looking to make a buck. Global > Phasing's > staff consists of eight scientists, plus one part-time person to > keep the > books and get the annual accounts audited. The company has never had > any > investors, and spends all its income on scientists' salaries and > running > costs. Perhaps the ".com" suffix has acquired a bad smell in other > parts of > the world, but in this case your insinuations are badly misguided. > > If you have had difficulties installing software from us, a more > constructive form of feedback would be to write to us at sharp- > develop or > buster-develop (both @globalphasing.com) and explain the nature of > those > difficulties. We have often found that the worst problems occur when > people, > instead of writing to us, start to try and hack the scripts > themselves and > end up tying themselves in inextricable knots. One of your remarks > seems to > want to imply that we have taken a perverse pleasure in making > installations > difficult. It is true that we still carry a legacy from earlier days > when > some of our sponsors wanted to be able to distribute jobs over > heterogeneous > clusters of machines and to view the results from any other machine > on that > network, while most users today just want to run everything on one > machine. > Our installation procedures have kept evolving to become simpler and > more > robust, although the need to link up with several third-party > packages makes > it hard to suppress complexity entirely. If you happen to have > con
Re: [ccp4bb] buster-tnt on OSX ?
@all, we've been comparing various programs during our SGPP times (that was about 2 years ago) Sharp, Shelx, bp3, mlphare, SnB (BnP). If I remember it correctly at that time Sharp was the winner, although the site finding was the major bottleneck/problem. What we ended doing was finding sites (SeMet) by an external program (most of the time Shelx) and feeding them into Sharp. I do remember long time ago the setup on a G5 MacPro which worked fine, I did have quite some exchange with Clemens to get it running though - mostly because I'm a user and not a programmer. On a side note we also looked at HKL, Mosflm, XDS processing of data, we observed differences in the ability of e.g. Shelx to locate SeMet sites depending on the processing program you used. Of course perfect data was undistinguishable, but some datasets which were more tricky to process showed significant differences in locating the SeMet positions. In those cases XDS was better. This is of course running all programs with their default parameters and not tweaking them. Jürgen On 27 Oct 2008, at 08:30, Clemens Vonrhein wrote: Dear Pete, just my personal view on this (so don't take this as a legal expertise regarding our SHARP licence). I don't have any problems with people comparing software programs - I do that all the time. I doubt this can be seen as reverse engineering. The tricky part comes when comparisons are being published: ideally it would be nice if every developer of a particular piece of software is given the chance to comment - maybe he/she could even give a few simple advices how to run the program. After all, different programs might have different set of defaults (conservative versus adventurous) for particular problems. It's similar to a problem we discover e.g. in a PDB entry: contacting the authors of that PDB entry first to give them a chance to comment (and correct) I think is the apropriate initial step. Or actually - lets rephrase that: it's not like an error in a PDB entry! Improvements in software benefit a lot more crystallographers whereas a fixed PDB entry usually concerns a much smaller group of us. Anyway, I think we're doing actually fairly well compared to other scientific fields: crystallographic method developers are a very friendly bunch I must say, even if we're in a kind of 'competition'. Cheers Clemens On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote: Apologies for going slightly further off-topic... Last time I had a free half-day to look into sharp, I noticed that the academic license prohibits reverse-engineering. This seemed to put any comparative testing into a slightly grey area. For example, if I find that sharp does the best job refining sites, but bp3 outputs better phases for a dataset due to different representation of phase probabilities*, I've implicitly constructed a primitive model of how sharp is working. This seems close enough to a first step of reverse-engineering that I was concerned. Could someone confirm that I'm worrying about things I don't need to here? Pete * Purely hypothetical example. -- *** * 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) *** - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch
[ccp4bb] Post-doctoral position in IBS, Grenoble, France
Post-doctoral position: Kinetic protein crystallography of photo-activatable fluorescent proteins. A two-year post-doctoral fellowship is available in the “kinetic protein crystallography” team of the Institute for Structural Biology (IBS), Grenoble, France (http://www.ibs.fr/content/ibs_eng/presentation/lab/lccp/cinetique/). It consists in studying the fluorescence mechanisms of fluorescent proteins (FP’s) from the Green Fluorescent Protein (GFP) family (cf 2008 Chemistry Nobel price), by combining X-ray crystallography with UV-visible and Raman microspectrophotometry. Fluorescent proteins are used as markers in fluorescence cell imaging. Recently discovered photo-activatable FP’s (PAFP’s) undergo multiple photo-conversion processes, which make them invaluable tools to study cell dynamics and develop super-resolution imaging methods. Such proteins also offer fascinating perspectives for biotechnological applications such as the development of high-capacity storage devices. The work aims at improving our fundamental knowledge of the photophysics of PAFP’s, and at rationally designing new PAFP’s with enhanced properties. It will involve both local and international collaborations with teams specialized in molecular biology, ab-initio quantum calculations and cell imaging. The project will be performed in the context of a very tight collaboration with the ESRF synchrotron and will make intense usage of the Cryobench, a laboratory dedicated to in crystallo spectroscopic techniques (http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench/). Photo-activation will be triggered in PAFP crystals following the methods of kinetic crystallography, so as to determine the induced conformational changes along the switching pathway. Neutron crystallography of a PAFP will also be undertaken. Candidates should have a strong expertise in crystallography, biochemistry and UV-visible spectroscopy. A general background in bio-physics and an interest for imaging applications is recommended to conduct this highly pluri-disciplinary project. Administrative rules state that candidates should preferably be less than 30 years and have defended their phD in the last 2 years. The monthly gross salary will amount to ~2750 €. Applications should be sent to Dominique Bourgeois ([EMAIL PROTECTED]). -- Dominique BOURGEOIS /\ Dominique Bourgeois/\/\ / \ LCCP IBS/\/ /\ /\/\ UMR 5075 / \/ \ / \ \ 41 Rue Jules Horowitz \ \ \ \ 38027 GRENOBLE Cedex 1\ \ \ \ FRANCE \ \ ** phone: (+33) (0)4 38 78 96 44 ** ** fax: (+33) (0)4 38 78 51 22 ** ** e-mail: [EMAIL PROTECTED] ***
Re: [ccp4bb] buster-tnt on OSX ?
>On a side note we also looked at HKL, Mosflm, XDS processing of data, >we observed differences in the ability of e.g. Shelx to locate SeMet >sites depending on the processing program you used. Of course perfect >data was undistinguishable, but some datasets which were more tricky >to process showed significant differences in locating the SeMet >positions. In those cases XDS was better. This is of course running >all programs with their default parameters and not tweaking them. Has this (or anything like this) been published? It may be interesting to look at this in a systematic way. You often hear that certain data processing packages are better than others for problematic datasets, but I have never found anything concrete about this. Bert
Re: [ccp4bb] buster-tnt on OSX ?
Dear Pete, Thank you for your message. I can confirm that you need not worry about this clause: it is meant to prohibit the aggressive use of code decompilers with the intention of stealing the content of the source code. What you have described in your hypothetical example is nothing of the sort, but instead a very useful kind of comparative evaluation. With best wishes, Gerard. -- On Mon, Oct 27, 2008 at 09:53:19AM -0500, Pete Meyer wrote: > Apologies for going slightly further off-topic... > > Last time I had a free half-day to look into sharp, I noticed that the > academic license prohibits reverse-engineering. This seemed to put any > comparative testing into a slightly grey area. For example, if I find > that sharp does the best job refining sites, but bp3 outputs better > phases for a dataset due to different representation of phase > probabilities*, I've implicitly constructed a primitive model of how > sharp is working. This seems close enough to a first step of > reverse-engineering that I was concerned. > > Could someone confirm that I'm worrying about things I don't need to here? > > Pete > > * Purely hypothetical example. > -- === * * * Gerard Bricogne [EMAIL PROTECTED] * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] OXION Postdoc fellowships and DPhil/PhD studentships
OXION is a research initiative grouping 25 UK laboratories based in Oxford, Cambridge and London and aimed at structural and functional characterisation of ion channels (http://oxion.dpag.ox.ac.uk/). Two training fellowships (at the junior or senior postdoctoral level, application deadline: Nov 14th, 2008) and up to four graduate studentships (application deadline: Jan 9th, 2009), generously funded by the Wellcome Trust, have been recently advertised. More details can be found at: http://oxion.dpag.ox.ac.uk/fellowshipsandstudentships Candidates with experience in membrane protein expression, purification and crystallization are warmly invited to apply :-) Best wishes, radu -- A. Radu Aricescu, PhD University of Oxford Wellcome Trust Centre for Human Genetics Division of Structural Biology Roosevelt Drive, Oxford OX3 7BN United Kingdom Phone: +44-1865-287551 Fax: +44-1865-287564
[ccp4bb] H32 use
Dear All, I wonder whether it is a good idea to still accept H32 as a space group in the PDB CRYST1 record, despite it may be used internally by programs. * The combination of hexagonal cell parameters and R32 clearly indicates a hexagonal (obverse) axis setting in the R centered cell. * The H-M R32 symbol with rhombohedral setting a, alpha, is inconsistent anyhow because the cell is then primitive and not centered. * The ITCA (and most data mining programs?) seem to be unaware of a Bravais symbol H. The practice of using H32 anywhere in published data should be strongly discouraged. Internally please feel free to use whatever works. What is the current opinion on this? Best, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.ruppweb.org/ - The hard part about playing chicken is to know when to flinch -
Re: [ccp4bb] Is it possible to predict the kinase when knowing a phosphorylated substrate sequence?
Tiancen, While not entirely impossible - this is a formidable task. The answer to your quesiton depends on the specifics of your situation and on what additional information you are able to procure. Quite a few kinases have specific sites; equal or greater numbers are only partially specific to a greater or lesser extent. For instance, unregulated PKA will phosphorylate as many Ser and Thr residues as it can find, provided that steric hindrance isn't an issue. This is of course somewhat of an extreme example. What other information is available to you? Artem _ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of TC Hu Sent: Monday, October 27, 2008 4:17 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Is it possible to predict the kinase when knowing a phosphorylated substrate sequence? Dear all, Sorry for the non-CCP4 question. Could anyone please tell me is there a way to predict the kinase when knowing a phosphorylated substrate sequence? Thanks in advance! Cheers Tiancen Hu Ph.D. Shanghai Institute of Materia Medica Chinese Academy of Sciences
Re: [ccp4bb] H32 use
In fact there's another good reason not to use H3 etc when you mean R3: the H lattice symbol is already in use to mean something completely different! - namely H-centring in *trigonal & hexagonal* (i.e. *not rhombohedral*) space groups such as P3, P3/1 etc & supergroups, so e.g. H3 is actually a supergroup of P3 not R3. See here: http://books.google.co.uk/books?id=ilVvOYOFCx8C&pg=PA96 and here: http://img.chem.ucl.ac.uk/sgp/large/trigonal.htm and the above is consistent with the definition now adopted in the new ITC-A1: http://it.iucr.org/cgi-bin/itsearch?query=DC.creator%3D%22H.%22%20AND%20 DC.creator%3D%22Wondratschek%22&metaname=swishdefault&IT.group=2.1.4&IUC r.volume=A1 It would be interesting to know if the PDB consulted the IUCr on this change! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp > Sent: 27 October 2008 22:50 > To: CCP4BB@JISCMAIL.AC.UK > Subject: H32 use > > Dear All, > > I wonder whether it is a good idea to still accept H32 as > a space group in the PDB CRYST1 record, despite it may be used > internally by programs. > > * The combination of hexagonal cell parameters and R32 clearly > indicates a hexagonal (obverse) axis setting in the R centered cell. > > * The H-M R32 symbol with rhombohedral setting a, alpha, is > inconsistent > anyhow because the cell is then primitive and not centered. > > * The ITCA (and most data mining programs?) seem to be > unaware of a Bravais symbol H. > > The practice of using H32 anywhere in published data should be > strongly discouraged. Internally please feel free to use whatever > works. > > What is the current opinion on this? > > Best, BR > - > Bernhard Rupp > 001 (925) 209-7429 > +43 (676) 571-0536 > [EMAIL PROTECTED] > [EMAIL PROTECTED] > http://www.ruppweb.org/ > - > The hard part about playing chicken > is to know when to flinch > - > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] H32 use
Good point. Btw, also these nonstandard, triple ab-plane centered H3x cells can be readily reindexed standard primitive, so no new space groups are needed...let's not give the PDB new ideas... BR -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Ian Tickle Sent: Monday, October 27, 2008 7:59 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] H32 use In fact there's another good reason not to use H3 etc when you mean R3: the H lattice symbol is already in use to mean something completely different! - namely H-centring in *trigonal & hexagonal* (i.e. *not rhombohedral*) space groups such as P3, P3/1 etc & supergroups, so e.g. H3 is actually a supergroup of P3 not R3. See here: http://books.google.co.uk/books?id=ilVvOYOFCx8C&pg=PA96 and here: http://img.chem.ucl.ac.uk/sgp/large/trigonal.htm and the above is consistent with the definition now adopted in the new ITC-A1: http://it.iucr.org/cgi-bin/itsearch?query=DC.creator%3D%22H.%22%20AND%20 DC.creator%3D%22Wondratschek%22&metaname=swishdefault&IT.group=2.1.4&IUC r.volume=A1 It would be interesting to know if the PDB consulted the IUCr on this change! -- Ian > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Rupp > Sent: 27 October 2008 22:50 > To: CCP4BB@JISCMAIL.AC.UK > Subject: H32 use > > Dear All, > > I wonder whether it is a good idea to still accept H32 as a space > group in the PDB CRYST1 record, despite it may be used internally by > programs. > > * The combination of hexagonal cell parameters and R32 clearly > indicates a hexagonal (obverse) axis setting in the R centered cell. > > * The H-M R32 symbol with rhombohedral setting a, alpha, is > inconsistent > anyhow because the cell is then primitive and not centered. > > * The ITCA (and most data mining programs?) seem to be unaware of a > Bravais symbol H. > > The practice of using H32 anywhere in published data should be > strongly discouraged. Internally please feel free to use whatever > works. > > What is the current opinion on this? > > Best, BR > - > Bernhard Rupp > 001 (925) 209-7429 > +43 (676) 571-0536 > [EMAIL PROTECTED] > [EMAIL PROTECTED] > http://www.ruppweb.org/ > - > The hard part about playing chicken > is to know when to flinch > - > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
[ccp4bb] about the PEG molecules in crystals
Dear all, Are there some articles or reviews discussing about the PEG molecules in crystals or the biochemical features of PEG? Thanks. -- Jiamu Du, Ph.D. State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 P. R. China Tel: +86-21-5492-1117 E-mail: [EMAIL PROTECTED]
