Re: [ccp4bb] BUSTER on CCP4 Cloud
Dear Dave, Thank you for the answer. There is only one way to first import phases in projects — using hop-on mode or task. Hop-on task can be run in existing projects but should be started from the top of the tree. There is a way to replace already existing phases with Import & Replace task, but it's a different story. Dear Shawn, As Dave wrote. if your structure is already phased and built and you want to continue working in CCP4 Cloud you should use the hop-on task to import your data. In this case, you won't be needed to run ASU task. In case you are starting a new project you will need to get phase estimation first before running Buster. Let me know if you still have issues. Warm regards, Maria Fando CCP4 Core team UKRI Science and Technology Facilities Council Rutherford Appleton Laboratory Harwell Campus Didcot, Oxfordshire OX11 0QX UK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] BUSTER on CCP4 Cloud
HI Shawn, the asymmetric unit contents task tells Cloud how many copies of your model exist in the ASU, but not necessarily that they are in the correct position (think, prior to Molecular replacement - no phase information). Depending upon where you are in your workflow, you can run a quick MR job, or start a new project with the "hop on" mode specifying an already partially refined structure. I am certain you can do this within an existing project, (maybe by importing phases?) but I can't recall the right task to do this at the moment (in my defence it is still quite early here). Perhaps someone else can help with that? (please reply to the list because I'd like to know as well!) Best, Dave -- Dr David C. Briggs CSci MRSB (he/him) Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK Working hours: Mon-Fri 0900-1700 == about.me/david_briggs<https://about.me/david_briggs> | OrcID<https://orcid.org/-0002-9793-7339> | Google Scholar <https://scholar.google.co.uk/citations?user=DRKG5KwJ> From: CCP4 bulletin board on behalf of Shawn R <a7787de0adf6-dmarc-requ...@jiscmail.ac.uk> Sent: 09 July 2023 05:02 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] BUSTER on CCP4 Cloud External Sender: Use caution. Dear All, I would like to run Buster refinement using CCP4 Cloud. However, the task says I am missing a structure revision. This is despite having generated the structure revision using the Asymmetric Unit Content task. I can see the output of AU Content task is the structure revision, so I am a little confused why it does not allow me to run the refinement. Perhaps I am missing some small detail? Thanks for your thoughts! To unsubscribe from the CCP4BB list, click the following link: https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7C%7C1756a803ee7c42d8560308db80316d55%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638244722008953538%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=FPjAMXqUiVWivTD8KqirBywuzeLtcKiJCFF3l1Ll4uQ%3D=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB=05%7C01%7C%7C1756a803ee7c42d8560308db80316d55%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638244722008953538%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=Wk%2BWIoXGZgmzbiFk2nPzJD8Up%2BOEhQrhLj6I0QZVswU%3D=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F=05%7C01%7C%7C1756a803ee7c42d8560308db80316d55%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638244722008953538%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=h3KN8TPBNBrduH2NJe2RbzgCHjFLXhg8peUtVnipni0%3D=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F=05%7C01%7C%7C1756a803ee7c42d8560308db80316d55%7C4eed7807ebad415aa7a99170947f4eae%7C0%7C1%7C638244722008953538%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=oqqthLf7d3lZSVrK9fVbhNkdL3S4E8YY5EGil0G6Dck%3D=0<https://www.jiscmail.ac.uk/policyandsecurity/> The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] BUSTER on CCP4 Cloud
Dear All, I would like to run Buster refinement using CCP4 Cloud. However, the task says I am missing a structure revision. This is despite having generated the structure revision using the Asymmetric Unit Content task. I can see the output of AU Content task is the structure revision, so I am a little confused why it does not allow me to run the refinement. Perhaps I am missing some small detail? Thanks for your thoughts! To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Buster
Dear Xavier, I am very sorry that I didn't respond instantly to your query about this strange observation at the beginning of the month. After that, it was sitting rather invisibly in my mailbox, given that its subject line said Re: [ccp4bb] Dehydration treatments :-) . We are just about to release a new version of BUSTER in conjunction with the final session of the ACA meeting. However, let us deal with your question off-list, as it isn't related to ccp4. I will be in touch. With best wishes, Gerard. -- On Fri, May 27, 2011 at 04:57:04PM +0200, F.Xavier Gomis-Rüth wrote: Dear CCP4ers, I start apologizing for this off-topic question but I could not get an answer knocking at other doors... We have installed version 1.6.0. from July 18,2009 of BUSTER, which apparently has a slight problem: after each refinement step, I need to re-center the model within the new electron density map. Is there any means to circumvent this ? Is there any newer version available somewhere ? I could not find any indication in the web page of Global Phasing but think it is rather strange that there has been no release since almost two years. Thanks a lot in advance, Xavier -- -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] buster-tnt on OSX ?
Dear All Thank you all a lot for your answers, and sorry for the trouble that my question has generated. Gerard B. : Thanks a lot to you and your colleagues for releasing, in the forthcoming time, an OSX version of BUSTER-TNT. Best from LA Jacques 2008/10/28 Pete Meyer [EMAIL PROTECTED] Gerard, Thank you very much for clearing that up. It's always good to hear that there's one less things I need to worry about. Pete Gerard Bricogne wrote: 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.
Re: [ccp4bb] buster-tnt on OSX ?
Clemens Vonrhein schrieb: ... A nice task would be to compare different integration/scaling packages at various stages: for finding the sites e.g. in SHELXD and separately (using known sites) for giving best phases e.g. in SHARP. there could be differences. Yes, maybe it is finally time to get past the rumour stage of software comparison. The only way I can think of is to start with a standard set of data that cover the range of typical experimental situations. The Quality Control article in XDSwiki ( http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Quality_Control ) is meant to enable users and developers to do exactly what Clemens proposes. Users/developers can download the datasets that this article talks about, and run them through their favourite data reduction program(s), and report the results in new articles linked to the Quality Control one. But one word of warning: comparisons of complex pieces of software are not entirely straightforward; e.g. different people may obtain different results with the same software package, and different versions of the same software may behave differently. So this is a never-ending project. Nevertheless I do believe that one can learn a lot about using software in the right way, for a given project, and generalize from that. best, Kay -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: [EMAIL PROTECTED]Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilites, please ignore the attached signature smime.p7s. smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] Comparison of Integration Programs (was: Re: [ccp4bb] buster-tnt on OSX ?)
Hi Folks, The idea of comparing different data reduction packages is an interesting one. It is not however without challenges as alluded to by Kay. As far as I can see there are two main challenges - the first is that different users when given the same tools will do different things - in challenging cases this will be very significant [Kay's point]. The second is to be able to express why a given package did better than others for a specific case, then bootstrap your way back to some general rules (i.e. expertise) about the packages for future reference. For a single case this was looked at in (ahem): Acta Cryst. (2007). F63, 168-172 Structure of 5-formyltetrahydrofolate cyclo-ligase from Bacillus anthracis (BA4489) C. Meier , L. G. Carter, G. Winter, R. J. Owens, D. I. Stuart and R. M. Esnouf Where we concluded that XDS did a better job than Mosflm or Denzo because the mosaic spread was rather high and the oscillations a little narrow. We did not try d*TREK but I would anticipate it would work well as the method of integration is similar to XDS. The better job in question though was to give a data set which would give a refinable molecular replacement solution, where the others did not. Now something which I have been interested in doing but which is almost certainly prohibitively expensive in terms of time is to take a number of data sets of varying levels of challenge and get the program authors (or delegated experts) to do their absolute best with the data reduction with that program, then compare the results. This will help to reduce the impact of lesser known but very helpful options (i.e. outlier recycling in XDS CORRECT, say) and perhaps generate a more fair comparison. In the example above there may have been some tweaks which could have been made to improve the results substantially for the 2D integration packages. For most (easy) cases however the best tool for the job is the one you know best. If you have the spare CPU horsepower and time, you can always reduce the data with all available packages and see which one gives the best results for your case - something which would be perfectly reasonable for substructure determination but much more unusual for data reduction. From my testing of xia2 against structural genomics data I can say that, for easy data, there is not much to call between Mosflm / Scala and XDS / XSCALE. Just my 2c. Cheers, Graeme
Re: [ccp4bb] buster-tnt on OSX ?
Gerard, Thank you very much for clearing that up. It's always good to hear that there's one less things I need to worry about. Pete Gerard Bricogne wrote: 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.
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] 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] 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 ?
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 constructive suggestions to make in this direction, we will be only too happy
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] buster-tnt on OSX ?
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] *
Re: [ccp4bb] buster-tnt on OSX ?
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
Re: [ccp4bb] buster-tnt on OSX ?
Having solved a few structures using AutoSHARP, I feel compelled to comment on the CCP4BB that I really like the software, never had a major problem installing or using it, feel extremely grateful to the guys at Global Phasing for making this available to us all, and for (in my case at least) responding to my queries quickly and helpfully. cheers Ashley On 26/10/2008, at 7:40 PM, 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 Associate Professor Ashley M Buckle NHMRC Senior Research Fellow The Department of Biochemistry and Molecular Biology School of Biomedical Sciences, Faculty of Medicine Victorian Bioinformatics Consortium (VBC) Monash University, Clayton, Vic 3800 Australia http://www.med.monash.edu.au/biochem/staff/abuckle.html iChat/AIM: blindcaptaincat skype: ashley.buckle Tel: (613) 9902 0269 (office) Tel: (613) 9905 1653 (lab) Fax : (613) 9905 4699
Re: [ccp4bb] buster-tnt on OSX ?
Dear Gerard et al: 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... 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? Like me, James might have what Edward Abbey (one of the very few decent American writers since Mark Twain) once referred to as a tendency to over-exaggerate in his rhetorical flourishes. I hope mine are viewed charitably and are designed for entertainment purposes only. All the best. Bill
Re: [ccp4bb] buster-tnt on OSX ?
I heartily agree with Ash and Gerald - Autosharp (which we routinely use for experimental phasing) is free for academics and in my opinion is an outstanding package. Further, we have always found the people at Global Phasing are always extremely helpful with all sorts of phasing questions not just installation! From a personal perspective I would always rather have free or low cost packages that require a little bit of setup than being charged like a wounded bull for a commercial package. J Ashley Buckle [EMAIL PROTECTED] wrote: Having solved a few structures using AutoSHARP, I feel compelled to comment on the CCP4BB that I really like the software, never had a major problem installing or using it, feel extremely grateful to the guys at Global Phasing for making this available to us all, and for (in my case at least) responding to my queries quickly and helpfully. cheers Ashley On 26/10/2008, at 7:40 PM, 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 Associate Professor Ashley M Buckle NHMRC Senior Research Fellow The Department of Biochemistry and Molecular Biology School of Biomedical Sciences, Faculty of Medicine Victorian Bioinformatics Consortium (VBC) Monash University, Clayton, Vic 3800 Australia http://www.med.monash.edu.au/biochem/staff/abuckle.html iChat/AIM: blindcaptaincat skype: ashley.buckle Tel: (613) 9902 0269 (office) Tel: (613) 9905 1653 (lab) Fax : (613) 9905 4699 -- 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 +613 9905 3747 (Phone) +613 9905 4699 (Fax) +61 418 170 585 (Mobile)
