Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac
I didn’t see the following solution in any other responses. It’s probably the most reasonable one given the constraints of collaboration and publishing. In the absence of using the best software, I found it practical to write the equations in MathType and save them as MathType PDF equations and then add these equations to the document. It is a portable, cross-platform-ish solution. Others only need to install a MathType player, which is free. The advantage is that if your equation gets hosed in the document, you still have the original, editable equation in the PDF. In such cases, you must re-embed it in your document, but it’s better than fully rewriting it. With that said, if you want to work behind a full-featured word processor and have access to the wonders of TeX typesetting, LibreOffice (OpenOffice) + TexMaths is the best for the author during preparation of a manuscript. At this point it is bug free (to my experience), embeds vector equations (SVG) or raster (PNG), is editable, and looks spectacular both when editing and when publishing/printing. The downside is that you have to collaborate with people you can’t force into using the best software. Worse, journals seem to use proprietary publishing software and they want MathType or equation editor with Microsoft word, hence my first solution. James On May 18, 2015, at 5:10 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: There is the possibility of using one of the open-source versions, like openOffice, but those I guess also have their issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Monday, May 18, 2015 4:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Equation Editor woes with Office 2011 for Mac Rather off-topic, but maybe someone on the list has found a way to work around this! There's a problem with the Equation Editor in Office 2011 for Mac (i.e. the one that is based on a stripped-down version of MathType, which you get with Insert-Object-Microsoft Equation). You can insert an equation, re-open it and edit it several times, and then suddenly (and seemingly randomly) the equation object will be replaced by a picture showing the equation, which can no longer be edited. I'm writing a rather equation-heavy paper at the moment, and this is driving me crazy. This seems to be a known bug, which has existed from the release of Office 2011. Apparently it happens, unpredictably, when an AutoSave copy of the document is saved, so you can avoid it by turning off the AutoSave feature. The last time this drove me crazy, several years ago, I did try turning off AutoSave. For a while, I was very good about manually saving frequently, but I got into bad habits and eventually Word crashed after I had worked for several hours on a grant proposal without manually saving. So I turned AutoSave back on. At the moment, the least-bad solution seems to be to turn off AutoSave while I'm working on a document with lots of equations and then (hopefully) remember to turn it back on after that document is finished. But it would be great if someone has come up with a better cure for this problem. No doubt someone will suggest switching from Word to LaTeX, but I need to be able to collaborate on paper-writing, and even though I might be willing to invest the effort in learning LaTeX, I can't really expect that of my collaborators. Most people in our field do use Microsoft Word, regardless of its failings. I've also tried using the professional version of MathType, but that requires your collaborators to install it as well - and I don't think that cured the equation to picture problem anyway. Thanks! - Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical ResearchTel: +44 1223 336500 Wellcome Trust/MRC Building Fax: +44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] [RANT] Reject Papers describing non-open source software
I hereby call on the broadest community of academics and researchers, including scientists, historians, economists, sociologists, psychologists, and whoever else has ever published a paper or read from the literature thereof, to reject any and all papers that describe new software that itself is not released under an open source model. I further declare that this post is designed to ruffle feathers and incite incendiary conversation, to provoke all-caps and evoke multiple exclamation marks with interposed “1”s where anger prevents one from properly holding the shift key. My rationale for this post: I have just spent a week installing software for structural biology (not crystallography) only to find that some of the key utilities needed were described in a recent publication but were not OSS. The authors have decided to stop supporting the software but have not retracted their paper, which is completely irrelevant without the availability of the software package they describe. Let’s hammer this one out and come to the rational conclusion that non-OSS software should not be awarded publications. James
Re: [ccp4bb] [RANT] Reject Papers describing non-open source software
If the software were open source, then funding would not matter. It could be supported (or at least used) by the user base. Withdrawing the use of published software because of funding issues represents a problem that can be remedied by enforcing (at the referee level) open source licenses. We allow (or rather can’t prevent) the use of other published information long after the funding that produced said knowledge dries up. The situation should be no different with software. James On May 12, 2015, at 1:08 PM, Gloria Borgstahl gborgst...@gmail.com wrote: Did they stop supporting it due to lack of renewed funding and having to cut staff that had the knowledge? I'm pretty sure you only know part of the story. On Tue, May 12, 2015 at 11:48 AM, James Stroud xtald...@gmail.com wrote: I hereby call on the broadest community of academics and researchers, including scientists, historians, economists, sociologists, psychologists, and whoever else has ever published a paper or read from the literature thereof, to reject any and all papers that describe new software that itself is not released under an open source model. I further declare that this post is designed to ruffle feathers and incite incendiary conversation, to provoke all-caps and evoke multiple exclamation marks with interposed “1”s where anger prevents one from properly holding the shift key. My rationale for this post: I have just spent a week installing software for structural biology (not crystallography) only to find that some of the key utilities needed were described in a recent publication but were not OSS. The authors have decided to stop supporting the software but have not retracted their paper, which is completely irrelevant without the availability of the software package they describe. Let’s hammer this one out and come to the rational conclusion that non-OSS software should not be awarded publications. James
Re: [ccp4bb] [RANT] Reject Papers describing non-open source software
On May 12, 2015, at 12:29 PM, Roger Rowlett rrowl...@colgate.edu wrote: Was the research publicly funded? If you receive funds from NSF, for example, you are expected to share and make widely available and usable software and inventions created under a grant (section VI.D.4. of the Award and administration guide). I don't know how enforceable that clause is, however. The funding shouldn’t matter. I suggest that a publication that has the purpose of describing non-open source software should be summarily rejected by referees. In other words, the power is in our hands, not the NSF’s.
Re: [ccp4bb] [RANT] Reject Papers describing non-open source software
Making the software OSS solves many problems. For example, it solves the problem of interdependency. Many tools these days aggregate the functions of several different software packages into pipelines. If one step in that pipeline is unavailable then the pipeline can be rendered unusable. Most OSS licenses are only restrictive in the sense of trying to supersede the license in a derivative product. They do not restrict the authors unless the institution for which they work does not permit OSS licenses, which is usually done in the name of monetizing a product. In that case it doesn’t matter whether the product is published or not, except that the publication is free advertisement. If the software eventually becomes unavailable, then the publication is false advertisement and should be retracted. If it is monetized, then pay the researches with the profit, which can buy more things than simply having one's name on an article. In terms of re-implementing tools. That is a colossal waste of time. First the idea that OSS software would be “too expensive” is not logical. Second, if OSS software does not do what you wish, you modify it, not re-implement it. I don’t want to this to degenerate into a discussion of the merits of OSS. I would rather focus on the merits of not publishing articles whose purpose it is to describe closed source software. If software is described in the context of algorithms, then the description of the software should be removed from the paper. The algorithms should stand on their own. James On May 12, 2015, at 1:19 PM, Robbie Joosten robbie_joos...@hotmail.com wrote: I strongly disagree with rejecting paper for any other reasons than scientific ones. A paper describing software should properly describe the algorithms to ensure the reproducibility. The source should be available for inspection to ensure the program does what was claimed, for all I care this can be under the Ms-RSL license or just under good-old copyright. The program should preferably be available free for academic users, but if the paper is good you should be able to re-implement the tool if it is too expensive or doesn't exactly do what you want so it isn't entirely necessary. Making the software open source (in an OSS sense) does not solve any problems that a good description of the algorithms doesn't do well already. OSS does not guarantee long-term availability, a paper will like outlive the software repository. OSS licenses (not the BSD license) can be so restrictive that you end up having to re-implement the algorithms anyway. So not having an OSS license should not be a reason to reject the paper about the software. Cheers, Robbie
Re: [ccp4bb] [RANT] Reject Papers describing non-open source software
On May 12, 2015, at 3:08 PM, Douglas Theobald dtheob...@brandeis.edu wrote: On May 12, 2015, at 4:50 PM, tom.p...@csiro.au tom.p...@csiro.au wrote: I like the open source model, but there are problems with this model along with the others. One major problem is that the authors are expected to support their software after others have gone in and modified it, which is unrealistic. I’ve never heard of such a thing. Even if it does exist, there are plenty of open source models that don’t require that. When I fork “wiki-source” software, I usually just put it into a repository that others can’t modify, unless the license restricts that. /snark
Re: [ccp4bb] Loop clashing on symmetry axis
You may want to drop the symmetry to see what is happening with the loop. James On Jun 10, 2014, at 11:48 AM, Nicholas Keep n.k...@mail.cryst.bbk.ac.uk wrote: Am refining a structure in P3(1)21 with three copies in the ASU. It is pretty close to completion R/Rfree 18/21 with 2A data. However in one copy a section that is clear in the other two is poor as it meets itself on a two fold. My interpretation is that one copy of the loop is in a visible conformation that is on the two fold axis and the symmetry related copy is disordered so it does not clash. Presumably close to half the time the ordered copy is from one side and the rest from the other to give the symmetric density. If you push the structure into the density then the symmetry related copy clashes. Is this conformation refineable in refmac5 or phenix if the occupancy is set to zero? Should I allow clashes to push both copies either side of the density as is currently happening? Any tips on dealing with this? Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] mmCIF as working format?
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote: On 08/07/2013 01:51 PM, James Stroud wrote: In the long term, the MM structure community should perhaps get its inspiration from SQL For this to work, a particular interface must monopolize access to structural data. Not necessarily, although the alternative pathway might be more idealistic and hence unrealistic. All that needs to happen is that the community agree on 1. What is the finite set of essential/useful attributes of macromolecular structural data. 2. What is the syntax of (a) accessing and (b) modifying those attributes. 3. What is the syntax of selecting subsets of structural data based on those attributes. The resulting syntax (i.e. language) itself should be terse, easy to learn, easy to use, and preferably easy to implement. If such a standard is created, then I believe awk-ing/grep-ing/sed-ing/etc PDBs and mmCIFs would quickly become historical. James
Re: [ccp4bb] mmCIF as working format?
On Aug 7, 2013, at 2:35 PM, Ed Pozharski wrote: If I understand your proposal and reference to SQL correctly, you want some scripting language that sounds like simple English. I didn't say anything about being English-like. English and other natural languages are ill-adapted to describing the well-defined operations one might perform on a data structure. Is the advantage over existing APIs here that one does not need to learn Python, C++, (or, heaven forbid, FORTRAN)? Anyone can learn Python in an hour and a half. That's not an issue (except for whitespace nuts). If one wants to use Python to modify PDB structural data, I recommend starting with the tutorial I wrote for CCTBX: http://cctbxwiki.bravais.net/CCTBX_Wiki#Working_with_pdb_Files The advantage of a language over an API is that an API requires coding overhead and must (by the definition of API) be part of an Application. SQL has no such requirement and neither would an ideal language for *selecting* and *modifying* macromolecular structural data. In SQL, one can make selections and modifications without importing libraries, defining a main function, declaring variables, etc. Low overhead is probably the reason so many crystallographers (myself not included) are fluent in the likes of awk. I.e. programs would look like this --- GRAB protein FROM FILE best_model_ever.cif; SELECT CHAIN A FROM protein AS chA; SET chA BFACTORS TO 30.0; GRAB data FROM FILE best_data_ever.cif; BIND protein TO data; REFINE protein USING BUSTER WITH TLS+ANISO; DROP protein INTO FILE better_model_yet.cif; --- Not necessarily a bad idea but now through the fog of time I remember something oddly reminiscent... ah, CNS! (for those googling for it it's not the central nervous system :). Although a little too much like natural language, it is not a bad idea. But, where is the link describing the layer of CNS that looks like that? In my X-Plor 3.1 manual (Yale University Press, 1987) I see nothing remotely like what you describe. CNS, according to the most recent tutorial for 1.3, looks like this: topology evaluate ($counter=1) evaluate ($done=false) while ( $done = false ) loop read if ( exist_topology_infile_$counter = true ) then if ( BLANK%topology_infile_$counter = false ) then @@topology_infile_$counter end if else evaluate ($done=true) end if evaluate ($counter=$counter+1) end loop read end This example makes a point about the problems of APIs. Namely, they require loops and tests, and lack a true selection mechanism, except perhaps for the scripting layer of CNS. But even with CNS, once you have a selection, you must loop over it to modify the data. Although it is likely the best library for working with structural data, CCTBX requires a loop just to change a specific chain ID (to the best of my knowledge): pdb_inp = pdb.input(file_name=best-model.pdb) hierarchy = pdb_inp.construct_hierarchy() for model in hierarchy.models(): for chain in model.chains(): if chain.id == A: chain.id = B I don't intend to pick on CCTBX specifically (because the CCTBX developers have specific needs to which they program), but loop/test mechanisms are awkward for selecting and modifying structural data, and get much more awkward as selections get more complex (e.g. selecting the C-alpha of every alanine of chain A, etc.). James
Re: [ccp4bb] Extracting .pdb info with python
On Jun 5, 2013, at 10:41 PM, Nat Echols wrote: On Thu, Jun 6, 2013 at 2:37 PM, GRANT MILLS gdmi...@students.latrobe.edu.au wrote: My script seems to miscount the columns and read the two as one column, does anyone know how to avoid this? (PS, I've googled this like crazy but I either don't understand or the link is irrelevant) You should resist the temptation to write your own PDB parser; that way lies pain and suffering. There are multiple free libraries for Python that can be used for this task - I recommend either CCTBX or BioPython (probably the latter if you don't need to do very much with the models). -Nat Resist the urge to duplicate the work of others should be the first rule of programming if its not already (although it's the hardest rule to follow). I wrote a PDB tutorial for cctbx, which has probably the most powerful python PDB parsing library: http://cctbxwiki.bravais.net/CCTBX_Wiki#CCTBX_Basics James
Re: [ccp4bb] how to make the crystal thicker
I think there are some mitegen loops that are flat. They will probably be useful for your crystals given what you say about the 2.2 Å anisotropic diffraction, which is probably caused by deformation of your plates in conventional loops. Some others on the list may have a more specific recommendation about this brand of loops. Also, you may want to check the mitegen website for specific products and applications. James On May 28, 2013, at 7:18 PM, 姜艳 wrote: Dear professors, I get my crystal in 0.1M Tris, PH7.5, 200mM (NH4)2SO4, and 20% PEG3350, however, it is very thin. From one side, the diffraction is perfect, about 2.2A, but from the other side, diffraction is too bad, the spots look like a thread! Process cannot be done by HKL2000. As top guns of this field, could you give me some suggestion to make the crystal thicker? I will be grateful for your kind help. Best, Jiang Yan Institute of Biophysics, Chinese Academy of Sciences Beijing, Chaoyang District
Re: [ccp4bb] DNA structures superimpose
The concept of a domain in a DNA structure is a bit obscure. Could you be more explicit about what you are trying to do? Do you mean protein domains in a protein-DNA complex? James On Apr 12, 2013, at 12:18 AM, Veerendra Kumar (Dr) wrote: Dear CCP4 members, Is there any program to superimpose the DNA structures? I also want to measure the relative domain rotation angle. I tried using DynDom but it does not work for me. Can someone suggest a program which can output the rotation angles? Thank you Best Regards Veerendra kumar CONFIDENTIALITY:This email is intended solely for the person(s) named and may be confidential and/or privileged.If you are not the intended recipient,please delete it,notify us and do not copy,use,or disclose its content. Towards A Sustainable Earth:Print Only When Necessary.Thank you.
Re: [ccp4bb] CCP4 Update victim of own success
On Apr 12, 2013, at 12:44 PM, eugene.krissi...@stfc.ac.uk wrote: What, I'm afraid, people rarely realise these days, is that their desktops are, essentially, GUIs to various OS features, so they obviously use GUI more frequently than they think :) After all, this is all matter of habits and training, and the reality is that people get more and more GUI-oriented these days, like it or not. Whether to fight the reality or try to use it for benefit is, certainly, every developer's own choice. I still remember payroll officers saying that hand calculators (and even their predecessors) were much more convenient and robust than modern software, but do not hear this for some 15 years already ... Eugene There is nothing intrinsically wrong with a GUI. The problem, for those who like to take advantage of automation, is that a GUI is a bottleneck if it can't be automated in some way. In my opinion, the best automation is based on an API (in my favorite scripting language, of course). The original unix tools were built with automation in mind, using pipes, redirects, and file I/O to control the flow of information. This automation wasn't designed because the architects couldn't conceive of a GUI, but because it was and is efficient. A utility can easily lock a user into a GUI. The usual cruel method is by spawning a dialog box the forces the user to acknowledge whatever triviality the program is trying to communicate (instead of sending the information to a log file where it belongs). If a program locks the user into a GUI, by whatever means, then the program can't be automated. And if it can't be automated it becomes a source of inefficiency. I think this is James Holton's point. Most of CCP4 can be automated by using the utilities from the command line, taking advantage of pipes, redirects, and file I/O as envisioned by the unix architects. CCP4 can also be run via a GUI, which I take advantage of in certain situations. It's a great model for user interaction. Long may it live (and may modal dialog boxes die a horrible and quick death). James On 12 Apr 2013, at 19:09, James Holton wrote: I agree with Nat. There are good GUIs and bad GUIs, just like there are good command-line programs and bad command-line programs. Bad programs are easy to write and good ones are hard. Conservation of work I think. -James Holton MAD Scientist On 4/12/2013 10:38 AM, Nat Echols wrote: On Fri, Apr 12, 2013 at 10:27 AM, James Holton jmhol...@lbl.govmailto:jmhol...@lbl.gov wrote: But, when it comes to GUIs, I have always found them counterproductive. In my humble opinion, the purpose of computers and other machines is to DO work for me, not create work for me, and I already have enough buttons to push each day. This is a very defensible position with regards to your normal workflow (or mine) - but beamline scientists (or software developers) are not very representative of crystallographers as a group. I've seen a lot of reflexive anti-GUI mentality from users who don't fall into either category, presumably because a senior postdoc or PI told them real crystallographers use the command line, when in reality they'd be better served by figuring out on their own what workflow is most efficient for them. -Nat -- Scanned by iCritical.
Re: [ccp4bb] CCP4 Update victim of own success
On Apr 11, 2013, at 6:17 AM, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote: Sorry that this was unclear. We assume that updater is used primarily from ccp4i, where nothing changed (and why it should be used from command line at all ?:)). Scriptability. On Apr 11, 2013, at 10:34 AM, Jim Pflugrath wrote: I think James gets to 'fight' like in the old game of rogue by pressing the h, j, k, l keys on his keyboard (not a detachable one either). While Eugene gets to use a modern game controller or a Wii. Ooops, game is already over and James [Holton] has lost. But he wrote the game. James
[ccp4bb] CCP4 Update victim of own success
Hello All, I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update? James
Re: [ccp4bb] CCP4 Update victim of own success
On Apr 10, 2013, at 9:30 PM, eugene.krissi...@stfc.ac.uk eugene.krissi...@stfc.ac.uk wrote:No, it got renamed to ccp4um :) That should have been written in update descriptions, was it not?There was only one mention of "ccp4um" that I could find in all update descriptions that I found (6.3.0-020). I only figured out what information was trying to be communicated because of your message (see attachment).JamesOn 11 Apr 2013, at 03:54, James Stroud wrote:Hello All,I downloaded a crispy new version of CCP4 and ran update until the update update script disappeared. Is the reason that CCP4 has reached its final update?James
Re: [ccp4bb] SHELX-2013 release and homepage
The underlying issue is that the implementation of OS X dynamic linking is dependent system architecture. As I understand it, OS X 10.5.8 has a 32 bit kernel, so its dynamic linking is not forward-compatible with 64 bit OS X versions, for which SHELX-2013 seems to built. Also, to be fair, it's not as if Linux users have ever been able to migrate from from 32 bit to 64 bit without a complete system overhaul. So while I believe that OS X may not be the optimal OS of the future, the 32/64 bit incompatibility should not be blamed as the reason. James p.s. What I don't understand is why the dynamic loader was ever needed in the first place. As a zero dependency program, wouldn't it make sense just to statically compile all of the SHEL* programs at the cost of a little bigger downloads? On Feb 27, 2013, at 3:10 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 phew - and people claim, macs were user-friendly. On Linux you just add '-static' (at least for command line tools as the shelx programs) and make the sane assumption that the kernel is less than say 10 years old... Tim On 02/26/2013 04:50 PM, Guangyu Zhu wrote: I just downloaded it. I'm using Mac 10.5.8 and getting error messages: dyld: unknown required load command 0x8022 Trace/BPT trap Google search shows that: You should contact the developer of this application. Only the developer can fix this. The application was incorrectly built on a OS X 10.6 machine for a OS X 10.5 machine. The developer can fix this by considering three things: 1. Using the correct compiler parameters: gcc-4.2 -mmacosx-version-min=10.5 -isysroot /Developer/SDKs/MacOSX10.5.sdk ... 2. Using the correct linker settings (setting environment variable before link command). This is required, so that the OS X 10.6 linker will not use the loader command 'LC_DYLD_INFO_ONLY' (=0x8022), because OS X 10.5 does not understand this command: export MACOSX_DEPLOYMENT_TARGET=10.5 (or setenv MACOSX_DEPLOYMENT_TARGET=10.5) After this is fixed, one can check if the application was correctly built for OS X 10.5 by running 'otool': otool -l binary The correct binary should not contain any 'LC_DYLD_INFO_ONLY' load commands (only 'LC_DYLD_INFO' commands). (also see my blog article http://grauonline.de/wordpress/?p=71 ) Is it possible to build one for Mac 10.5.8? Thanks! Guangyu Zhu On 2/26/13 3:32 AM, George Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: As some of you have already discovered, there is a major new release of the whole of SHELX (the first since 1997) complete with a new homepage that should make downloads easier. To obtain the programs, please point your browser to: http://shelx.uni-ac.gwdg.de/SHELX/ and then 'register' (top of blue menu, upper left). You will then receive the password immediately by email and can then go to 'downloads'. The procedure has been designed to make life difficult for spammers etc. A little program (in FORTRAN of course) turns the registrations into a sorted users' list, which I hand-edit where necessary before it appears on the homepage, this may take a few days. The homepage also provides access to extensive documentation, FAQs etc. Please let me know of any problems (even typos) with the homepage and programs, with so much new material there are sure to be some bugs. The new versions replace all previous versions including beta-tests and almost all the programs have been improved since their last beta-test version (see 'recent changes'). In particular, the new shelxe_2013/2 corrects a couple of serious bugs in the autotracing from MR models and MRSAD present in the beta-test 2013/1. George -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFRLduMUxlJ7aRr7hoRAkNUAJ99nANlYCXYmlOqTpvKnDJyg+A1bwCdF7GA Ag8n9o/IzBAkuX+HBfH8cMw= =WBV3 -END PGP SIGNATURE-
Re: [ccp4bb] off topic - legacy hardware help needed
It seems like the problem is that the Indigo has an IP address that is not part of the subnet that it is on, so this makes network access impossible. Is this correct? If so, you can just spoof the proper subnet in isolation. You can run dd-wrt on a compatible router and assign any subnet you want (ensuring to disconnect it from the WAN, lest a disgruntled IT guy shows up at your office). Then, just access the SGI via IP as you normally would from another machine on the isolated subnet and edit the config files to change the IP address. This doesn't require tracking down any legacy hardware. James On Jan 23, 2013, at 5:07 PM, Dave Roberts wrote: Hi all, By the way, thanks for all the suggestions on the linux versions. I went against my better judgement and just stuck with Fedora, mainly because I'm familiar with it. I have to admit, I kind of like it. I was able to get it up and running, run nfs to mount local drives, and install all the necessary crystallography software with no hitch - quick. It's kind of nice. And it set up my wireless printer automatically - so all is great. Anyway, we have an old Indigo SGI that runs our NMR. It's a console only system, and we access it via the network from another old SGI (toaster model - blue). The console does not have a video card (nor space for one), so I can't plug in to it and see what's happening. Anyway, our network was recently updated, and in doing so it has made access to our console system unavailable. We can't get there because the IP's that used to be needed are no more. So, I can get the disk out, and I have a variety of unix/linux systems that I could plug it in to. But, alas, I have no motherboards or systems that take SCSI (that I have a sled for or a way to put it in). I need to be able to mount the drive on some sort of system, edit a few config files to fix the network, then plug it all back in. All without messing up boot tables and such (not a big deal, just thought I'd throw that out there). Is there a cable that simply allows me to plug in the back of a SCSI drive then connect to an IDE port on a newer motherboard (or better yet, an external USB port)? Just curious - that would be worth it to me. Any thoughts? Thanks Dave
Re: [ccp4bb] Mac mini advice
On Jan 22, 2013, at 11:20 PM, Nat Echols wrote: The real difficulty is integrating Macs into a Linux-centric environment, for example configuring NFS, NIS, etc. That's because NFS and NIS are antiquities left over from the days of mainframes. Distributed file systems and user information databases are designed for an environment of many workers and few machines, when the typical graphics workstation cost $50,000. These days, we argue whether to spend an extra $200 on a $500 computer. We have moved to a new paradigm: many workers with many more machines, with each machine having essentially mainframe levels of storage and computing power. In other words, instead of NFS, you should run git. James
Re: [ccp4bb] Mac mini advice
Get a quad-core. If you have iTunes going, some website running javascript without your knowing it, and you have a computational job running, then you've used up your dual core and things get sluggish. It happens to me all the time on my c. 1996 iMac, which is still (barely) good enough for me. On Mac v. Linux where calculations come secondary to office-type calculations, you have to weigh your level of vendor lock-in. Do you run Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? Etc. If you are locked-in to commercial products and haven't migrated to open source, then you may want to think twice about a Linux box. Macs are very seamless for an office environment, but I don't know if they are appropriate for heavy-duty calculations given that you'll trade horsepower for the Mac experience. James On Jan 22, 2013, at 10:59 AM, Cara Vaughan wrote: Dear CCP4BB I'm thinking about buying a Mac Mini and was looking for advice from people who have used these for crystallography. We don't need the computer to do serious number-crunching as we have back-end servers that can do this for us, so it is primarily for running coot for model building, etc. and low intensity crystallography jobs. I've seen from the archive that some people do use the Mac Mini for crystallography and I've got two questions: 1. Do I need the Quad core or is a Dual core processor enough? 2. Is the intergrated Intel HD graphics card OK for crystallography requirements? All the best, Cara. Cara Vaughan Lecturer in Structural Biology Institute of Structural and Molecular Biology Birkbeck College and UCL London UK This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] Mac mini advice
I meant c.2006 iMac, of course. James On Jan 22, 2013, at 11:05 PM, James Stroud wrote: Get a quad-core. If you have iTunes going, some website running javascript without your knowing it, and you have a computational job running, then you've used up your dual core and things get sluggish. It happens to me all the time on my c. 1996 iMac, which is still (barely) good enough for me. On Mac v. Linux where calculations come secondary to office-type calculations, you have to weigh your level of vendor lock-in. Do you run Libreoffice or Microsoft Office? Inkscape or Illustrator? Gimp or Photoshop? Etc. If you are locked-in to commercial products and haven't migrated to open source, then you may want to think twice about a Linux box. Macs are very seamless for an office environment, but I don't know if they are appropriate for heavy-duty calculations given that you'll trade horsepower for the Mac experience. James On Jan 22, 2013, at 10:59 AM, Cara Vaughan wrote: Dear CCP4BB I'm thinking about buying a Mac Mini and was looking for advice from people who have used these for crystallography. We don't need the computer to do serious number-crunching as we have back-end servers that can do this for us, so it is primarily for running coot for model building, etc. and low intensity crystallography jobs. I've seen from the archive that some people do use the Mac Mini for crystallography and I've got two questions: 1. Do I need the Quad core or is a Dual core processor enough? 2. Is the intergrated Intel HD graphics card OK for crystallography requirements? All the best, Cara. Cara Vaughan Lecturer in Structural Biology Institute of Structural and Molecular Biology Birkbeck College and UCL London UK This message was sent using IMP, the Internet Messaging Program.
Re: [ccp4bb] Symmetry operator
The transformation matrix describing the symmetry is sensitive to the coordinate system origin. You should center the entire tetramer on the origin (0, 0, 0), where the origin coincides with the point symmetry element. If you have a tetramer with true point symmetry, then the center of the tetramer should be the center of mass. Then you can use lsq-expl from O or whatever the equivalent is in pymol, phenix, or coot to get the transformation matrix between any two monomers. Repeated application of that transformation matrix to any monomer of the tetramer should generate the tetramer. James On Jan 10, 2013, at 5:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
Re: [ccp4bb] Symmetry operator
I need to amend that and make a couple of corrections, after thinking about it. First, the rotation-translations shouldn't be sensitive to the origin. Second, if it has C4 (square) symmetry, then you only need one generator (rotation-translation) to make the tetramer, and the two monomers should be adjacent. If it is T4 (tetrahedral) symmetry, then you need two generators, with one generator made from a pair of monomers opposite and one generator made from a pair adjacent. James On Jan 10, 2013, at 6:05 PM, James Stroud wrote: The transformation matrix describing the symmetry is sensitive to the coordinate system origin. You should center the entire tetramer on the origin (0, 0, 0), where the origin coincides with the point symmetry element. If you have a tetramer with true point symmetry, then the center of the tetramer should be the center of mass. Then you can use lsq-expl from O or whatever the equivalent is in pymol, phenix, or coot to get the transformation matrix between any two monomers. Repeated application of that transformation matrix to any monomer of the tetramer should generate the tetramer. James On Jan 10, 2013, at 5:48 PM, james09 pruza wrote: Hi, Which program outputs the symmetry operator (rotation and translation)? I have a dimer in the asymmetric unit and need to know the symmetry operator to get a tetramer, the active molecule. James
Re: [ccp4bb] Off topic: Selecting atoms within a given distance from a target atom
In O, the command is called symm_sphere. http://xray.bmc.uu.se/alwyn/A-Z_of_O/everything_s.html#anchor536668 James On Nov 18, 2012, at 10:14 AM, Bosch, Juergen wrote: Hi Pavel, does this also work for symmetry related atoms ? Jürgen .. Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://lupo.jhsph.edu On Nov 17, 2012, at 14:26, Pavel Afonine pafon...@gmail.com wrote: Hi Rex, as easy as: phenix.pdb_atom_selection model.pdb within(3, chain L and resseq 9 and name CA) --write-pdb-file=cut.pdb which in the above example selects all atoms within 3 A from CA atom in chain A of residue number 9, and writes them into cut.pdb file. Pavel On Sat, Nov 17, 2012 at 12:04 PM, Rex Palmer rex.pal...@btinternet.com wrote: I would like to specify a target atom in a pdb file and then isolate all atoms within a given distance of the target. The selected atoms are then to be placed in a new pdb file. Any suggestions please. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
Re: [ccp4bb] vitrification vs freezing
On Nov 16, 2012, at 12:01 PM, Ed Pozharski wrote: On 11/16/2012 12:54 PM, Kendall Nettles wrote: I wouldn't go into the lab and say did you cryo-cool those crystals yet? or check out this nice crystal. Its ready for vitrification. If we speak the way scientific articles are written... By Bernard Dixon, published in New Scientist, 11 April 1968, p.73, an imaginary conversation at breakfast: Daddy, I want cornflakes this morning. Must I have porridge? Yes. It has been suggested by mummy that, in view of the external coldness, the eating of porridge by you will cause an increase in bodily temperature. Furthermore, in regard to the already-mentioned temperature considerations, your grandma-knitted gloves and wool-lining-hooded coat will have to be worn. The imprecision of this language is staggering. For instance, the meaning of the word worn is completely ambiguous and should be clarified. Does the author mean that the coat (what kind?) should be draped over the child's head, tied around the child's waste, or should his arms be placed through the sleeves. If the latter, should the fasteners (what kind?) be dorsal or ventral? James
Re: [ccp4bb] vitrification vs freezing
Isn't cryo-cooled redundant? James On Nov 15, 2012, at 11:34 AM, Phil Jeffrey wrote: Perhaps it's an artisan organic locavore fruit cake. Either way, your *crystal* is not vitrified. The solvent in your crystal might be glassy but your protein better still hold crystalline order (cf. ice) or you've wasted your time. Ergo, cryo-cooled is the description to use. Phil Jeffrey Princeton On 11/15/12 1:14 PM, Nukri Sanishvili wrote: s: An alternative way to avoid the argument and discussion all together is to use cryo-cooled. Tim: You go to a restaurant, spend all that time and money and order a fruitcake? Cheers, N.
Re: [ccp4bb] Assemble Protein-DNA complex
This sounds like a job for ammonium acetate. Use it as your salt. Purify your complex in it and then set up drops where they wells have the amount of ammonium acetate needed to keep your protein stable and the wells have none, or a range of concentrations. The ammonium acetate will equilibrate by vapor diffusion, lowering the concentration in the drop and causing your complex to come out of solution. James On Nov 9, 2012, at 9:14 AM, Wei Huang wrote: Dear CCP4BBers, I have a problem in purifying protein-DNA complex for a protein that I am interested in. The purification of protein only has been optimized and I've get enough yield for what I need (10 mg/2.4 L growth). And I've measured DNA binding using Fluorescence Anisotropy. The results show that my protein has the tightest binding (Kd=8 nM) to the DNA at low salt condition (30 mM KCl) in 20 mM HEPES (pH 7.5). However, I came across several problems when I assemble protein-DNA complex in large scale. First, my protein is unstable at low salt condition. When I dialyzes my protein into low salt buffer (tried 30 mM and 100 mM KCl) for binding DNA, the protein precipitates. What I don't quite understand is that the DNA binding assay performed at low salt condition doesn't seem to be affected by this instability of protein. I guess it may be due to the assay was performed at very diluted protein concentration (in nM). Second, I can not purify protein-DNA complex at high salt condition with gel filtration column. Because of the first problem, I tried to assemble the complex at high salt condition (150 mM KCl, 150 mM NaCl). However, the elution profile shows no binding of DNA to my protein (no increase in the observation of protein peak and a large peak around expected position for DNA). This may be due to weaker binding at high salt as my DNA binding assay shows that the Kd under this buffer condition is ~1100 nM. Third, a lot of protein is lost during dialysis of protein-DNA complex into low salt condition. I tried add DNA directly into protein in high salt buffer, then dialyze very slowly against low salt buffer. However, I still lost quite a lot of protein due to precipitation. I was able to load some sample onto the gel filtration column with low salt running buffer. And I saw the shift of protein peak in the elution profile, also protein concentration measured by Bradford assay shows that the protein concentration is much less than that expected from uv trace, suggesting the contribution to the absorbance from DNA. But the yield is very low, less than 0.2 mg of protein is left and the complex seems to be unhappy when I concentrate it. So I can not get protein sample concentrated enough for my study. My previous experience with another DNA binding protein is much better. I purified it in high salt, dialyzed into low salt to binding DNA and finally purify with gel filtration column. However, the one I am currently working on seems to be very picky. If you have any suggestion regarding to my problems, I will be thankful. Best regards, -- Wei Huang, PhD Postdoctoral Associate Center for Proteomics and Bioinformatics Case Western Reserve University Cleveland, OH 44106
Re: [ccp4bb] Assemble Protein-DNA complex
I meant where the drops have the concentration of ammonium acetate needed. James On Nov 9, 2012, at 10:06 AM, James Stroud wrote: This sounds like a job for ammonium acetate. Use it as your salt. Purify your complex in it and then set up drops where they wells have the amount of ammonium acetate needed to keep your protein stable and the wells have none, or a range of concentrations. The ammonium acetate will equilibrate by vapor diffusion, lowering the concentration in the drop and causing your complex to come out of solution. James On Nov 9, 2012, at 9:14 AM, Wei Huang wrote: Dear CCP4BBers, I have a problem in purifying protein-DNA complex for a protein that I am interested in. The purification of protein only has been optimized and I've get enough yield for what I need (10 mg/2.4 L growth). And I've measured DNA binding using Fluorescence Anisotropy. The results show that my protein has the tightest binding (Kd=8 nM) to the DNA at low salt condition (30 mM KCl) in 20 mM HEPES (pH 7.5). However, I came across several problems when I assemble protein-DNA complex in large scale. First, my protein is unstable at low salt condition. When I dialyzes my protein into low salt buffer (tried 30 mM and 100 mM KCl) for binding DNA, the protein precipitates. What I don't quite understand is that the DNA binding assay performed at low salt condition doesn't seem to be affected by this instability of protein. I guess it may be due to the assay was performed at very diluted protein concentration (in nM). Second, I can not purify protein-DNA complex at high salt condition with gel filtration column. Because of the first problem, I tried to assemble the complex at high salt condition (150 mM KCl, 150 mM NaCl). However, the elution profile shows no binding of DNA to my protein (no increase in the observation of protein peak and a large peak around expected position for DNA). This may be due to weaker binding at high salt as my DNA binding assay shows that the Kd under this buffer condition is ~1100 nM. Third, a lot of protein is lost during dialysis of protein-DNA complex into low salt condition. I tried add DNA directly into protein in high salt buffer, then dialyze very slowly against low salt buffer. However, I still lost quite a lot of protein due to precipitation. I was able to load some sample onto the gel filtration column with low salt running buffer. And I saw the shift of protein peak in the elution profile, also protein concentration measured by Bradford assay shows that the protein concentration is much less than that expected from uv trace, suggesting the contribution to the absorbance from DNA. But the yield is very low, less than 0.2 mg of protein is left and the complex seems to be unhappy when I concentrate it. So I can not get protein sample concentrated enough for my study. My previous experience with another DNA binding protein is much better. I purified it in high salt, dialyzed into low salt to binding DNA and finally purify with gel filtration column. However, the one I am currently working on seems to be very picky. If you have any suggestion regarding to my problems, I will be thankful. Best regards, -- Wei Huang, PhD Postdoctoral Associate Center for Proteomics and Bioinformatics Case Western Reserve University Cleveland, OH 44106
[ccp4bb] PyMOL/Python CGObjects interest
Related to PDB embedded objects, I'm wondering if there would be much interest in my releasing an implementation of a language designed to make fairly elaborate illustrations in PyMOL. The reason I ask is because it would take some time to document and distribute, but I would do it if the demand was there. The implementation is written and battle-tested in my own projects, but undocumented. At this moment, I call the language CGObjects. Here are a couple of examples of what it can do: http://www.jamesstroud.com/pictures/site-pictures/cgobjects-example/image http://www.jamesstroud.com/site-multimedia/site-mp4-movies/example-mp4-movie (The movie is just a bunch of still images created using the library.) CGObjects is a hierarchical and purely declarative language that is based on yaml structure. For example, the (superfluous) helices in the picture in the first link are specified like this: - a_helix : - show : True - object : doublehelix args : pitch : 5 phase : 30 handedness : left p : [1, -15, 0] p1 : [0, -15, 0] p2 : [0, 15, 0] rgb1 : [1, 1, 0] rgb2 : [0, 1, 1] step : 0.1 radius : 0.075 head_size : 0.225 nsec : 30 center_on : atoms cyl D 4:6 CA align_to : my_moment : [0, 0, 1] frame: atoms cyl D 4:6 CA frame_moment : [1, 0, 0] Although this example looks complicated, it is mostly styling information (rgb1, rgb2, radius, head_size, etc.). The doublehelix is created by winding point p around the axis specified by p1 and p2 with a pitch of 5. Points can be specified as vectors (e.g. [1, -15, 0]) or by atom selections (e.g. atoms cyl D 4 CA). The selection syntax allows for very terse and intuitive selections for single atoms or atom ranges. For example, the CA atoms of residues 4 through 6 of chain D of the pdb abbreviated as cyl are selected with the expression atoms cyl D 4:6 CA Selections are not limited, however, in that they can be arbitrarily complicated using an S-expression (LISP-like) syntax that is easy to use once you get the hang of it. Here is an example: or (and (one_of segID A000 A002 B00B B00D C000 C002) ( resSeq 25)) (and (one_of segID A00C A00E B001 B003 C00A C00C) ( resSeq 22)) This expression selects all residues numbered less than 25 from segments named A000, A002, etc., and also all residues greater than 22 from segments A00C, A00E, etc. Although S-expressions look funny or confusing at first, once you get the hang of them, you might agree with me that any other selection syntax seems barbaric by comparison. (Note that atoms cyl D 4:6 CA is actually an S-expression, where atoms is the operator and the rest of the expression contains the arguments to the operator.) In the first link above, note that the helices are perfectly aligned with the so-called figure axes (green, blue, and yellow double-headed arrows). These figure axes align with the principle moments of the triangle made by atoms cyl D 4:6. Similarly, the helix is made to align with these moments by first centering on the triangle formed by the atom centers of atoms cyl D 4:6 and then by aligning the last moment of the helix with the principal moment of the triangle. All of this high-level geometry is specified by only five simple lines: center_on : atoms cyl D 4:6 CA align_to : my_moment : [0, 0, 1] frame: atoms cyl D 4:6 CA frame_moment : [1, 0, 0] The use of atom selections and moments frees the user from performing manual alignments, extracting coordinates, or doing math. This means that if your model coordinates change, then your illustrations change with them. CGObjects has many different types of objects like surfaces, polytubes, and arrows. It also supports reusable, hierarchical styling and even variable declarations, making it possible to change the appearance of an entire set of illustrations in a centralized and uniform way. James On Oct 26, 2012, at 2:32 PM, Pete Meyer wrote: Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks
Re: [ccp4bb] adding some user-defined graphical objects in a PDB file (and displaying them)
This sounds like something that a PDB file is not intended to do. I think everyone has universally agreed to the PDB specification at the RCSB, which makes no provisions for arbitrary objects, as cool as they would be. But you could put your information into REMARK records, which are free-form. Maybe you could then find some people to honor your specification or build an implementation yourself... 21st century solution The simplest way, would be to write a converter that embeds a pymol script into REMARK records and a preprocessor for pymol that extracts them and feeds them into the pymol stream. If you write the implementation then you have a de facto standard. It would take a handful of lines of code. Write it in python and claim the mantle of coolness and the disdain of python detractors everywhere! You could set up a home page using wikispaces or even the pymol wiki, pointing to your implementation that you keep on github. James On Oct 25, 2012, at 7:25 PM, Francois Berenger wrote: Hello, For some new project, I'd like to be able to generate things and store them in PDB format. For example, a triangle, a line segment, a square, a cube, a sphere, an arrow, etc. Being able to change the color and line width would be nice. Is there some official recommended way of doing this? Is there some software able to read and display such graphical annotations of PDB files? I'll also need the format description in that case. I want to be able to process a PDB file and store the result of my processing in the same PDB file as some kind of annotation. My current way of doing this is to discretize my objects as H atoms in some other output PDB file, but that's just a temporary workaround. My current search got me this: http://www.cgl.ucsf.edu/eccc1/ So, maybe there is some support for what I am looking for into Chimera. Thanks a lot for your suggestions, Francois.
Re: [ccp4bb] off topic: a Python online course and others
The design of python was influenced by the ABC language which itself was meant to be a replacement for BASIC. So the similarities you observe are not by chance. If you are looking for a free online experience that will stretch your computer literacy, try this: http://mitpress.mit.edu/sicp/full-text/book/book.html James On Oct 21, 2012, at 7:38 AM, Edward Berry wrote: I took a look at the first four lessons at the first link, and I think there must be some mistake- this site is actually teaching BASIC. All these commands are valid syntax under say microsoft GWBasic or QuickBasic. But I think this Zed Shaw has been studying shell programming also and got mixed up because he uses this octa-#-thorpe instead of apostrophe or REM to denote comments. Remember when parents used to send their kids to computer boot camp to learn BASIC for fear they would be computer-illiterate and couldn't function in the modern age if they couldn't program a computer? Sean Seaver s...@p212121.com 10/20/12 1:43 PM I'd also recommend: Learn Python The Hard Way By Zed A. Shaw http://learnpythonthehardway.org/ Online Python Tutor http://pythontutor.com/ Take Care, Sean Seaver, PhD P212121 http://store.p212121.com/
Re: [ccp4bb] PNAS on fraud
The fit seems to be driven by the high number of points in the area of the graph where many points overlap. The points that catch your eye and establish the visible balance probably do not contribute much. Maybe this one should have been plotted as log in the abscissa for appearances. James On Oct 18, 2012, at 11:52 AM, DUMAS Philippe (UDS) wrote: Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com a écrit: I had a look to this PNAS paper by Fang et al. I am a bit surprised by their interpretation of their Fig. 3: they claim that here exists a highly signficant correlation between Impact factor and number of retractations. Personnaly, I would have concluded to a complete lack of correlation... Should I retract this judgment? Philippe Dumas Dear CCP4 followers, Maybe you are already aware of this interesting study in PNAS regarding the prevalence of fraud vs. 'real' error in paper retractions: Fang FC, Steen RG and Casadevall A (2012) Misconduct accounts for the majority of retracted scientific publications. Proc Natl Acad Sci U S A 109(42): 17028-33. http://www.pnas.org/content/109/42/17028.abstract There were also a few comments on related stuff such as fake peer review in the Chronicle of Higher Education. As not all may have access to that journal, I have put the 3 relevant pdf links on my web http://www.ruppweb.org/CHE_Misconduct_PNAS_Stuft_Oct_2012.pdf http://www.ruppweb.org/CHE_DYI_reviews_Sept_30_2012.pdf http://www.ruppweb.org/CHE_The-Great-Pretender_Oct_8_2012.pdf Best regards, BR - Bernhard Rupp 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -
Re: [ccp4bb] Plate crystals
You might get better help if you post links (not attachments) to diffraction images from several angles and an image of the crystal that gave the image, and maybe several images of typical crystals. Also, you could post dimensions of the crystal, and if your lab is set up for it, a picture of the crystal in the loop. 4 Å diffraction for a plate crystal could be promising, but plate crystals require proper handling and optimization. You should also try to work with your 4 Å data and see if you can get a structure with MR (or even MIR), if that is at all possible. You might find that you can trim some extra sequence from one or both ends that hinder good crystallization. James On Oct 15, 2012, at 4:01 PM, Jahan Alikhajeh wrote: Dear Friends, I am trying to crystalize a 70 kDa nasty protein but I got plate shape crystals with high mosaicity and useless diffraction (up to 4A). I tried to improve/optimize crystallization but either I got the same or nothing. I tried seeding but I had so many crystals without any improvement. Does anyone have better idea than routine optimization method in the lab? Thanks in advance. Jahan
Re: [ccp4bb] electrostatic potential and charged residues
You could do homology modeling of several homologs using http://protein.cribi.unipd.it/Homer/ . Then calculate the electrostatics of the homologs. Better though would be actual structures. How much identity do the homologues have? If they are so close that homology modeling works, then you may be able to crystallize a few with the information available from the structure you already have. Imagine how powerfully a range of experimental structures would be to support your argument that the electrostatics are a conserved feature of the protein. James On Sep 14, 2012, at 12:37 PM, Qiang Chen wrote: Hi all, I'm working on a protein structure which showed a special electrostatic potential on its surface: positive on one end and negative on the other end. I wonder to what extent I can say this pattern is determined by the charged residues? If the residues are conserved, could I make a conclusion that its homologues also have such pattern? Thanks! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 13, 2012, at 3:24 AM, Tim Gruene wrote: I have the impression that python programmers spend a lot of effort in trying to convince others that python is a good choice. Why bother rather than let people make their own decision? Someone asked. Plus, python programmers put no more effort than any other programmer. It's just that python has more advocates (for good reason) so the apparent effort is amplified. Don't hate us because our preferred programming language is beautiful. James -- James Stroud http://www.jamesstroud.com
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 13, 2012, at 11:02 AM, Patrick Shaw Stewart wrote: Like most computer users and many scientists I don't write scripts to organize or analyse my data unless I get desperate. I've used both Python and Perl a few years ago, but it would take quite a lot of time and effort and staring at on-line tutorials to get back into either of them right now. So I end up using massive Excel files that kind of work, but are a pain. I've noticed that quite a few structural biologists have the same problem. I've never understood why there can't be a simple programming language that is completely self-explanatory bercause it uses English sentences. Yeah. They tried that. It's called AppleScript and is a complete disaster for programmers simply because of its vague resemblance to natural language. There are essays on this issue [1, 2], but other than the message stay away from programming languages that try to be natural languages, these essays are mostly academic. It turns out that the syntax and semantics of all reasonable programming languages are very similar, or fall into only a few classes (e.g. C-like, S-expressions, etc.), so once you are fluent in one from a class, it's easy to pick up the others. This can't be said of natural languages, which are full of idioms and grammatical exceptions, even in closely related dialects. James [1] http://www.codinghorror.com/blog/2006/08/computer-languages-arent-human-languages.html [2] http://daringfireball.net/2005/09/englishlikeness_monster
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 12, 2012, at 9:11 AM, Pete Meyer wrote: That said, I'd take a look at python, octave or R. Python's relatively easy to learn, and more flexible than octave/R; but it doesn't have the built-in statistic functions that octave and R do. import scipy Now it does!
Re: [ccp4bb] Off-topic: Best Scripting Language
Python sorting 1 records of 1 floats for each record, finding the max,
min, and mean of entire 100,000,000 32 bit float array (400 MB) on a 6 year old
white imac.
*11.6 seconds.
*This doesn't include the time to generate the 400 MB of random (normal) data.
Try it on your own computer. Here's the copy-paste from mine:
py import timeit
py timeit.timeit('big_data.sort(axis=0), big_data.mean(); big_data.max();
big_data.min();',
'import numpy; big_data=numpy.random.normal(10,
size=1e8).reshape((1e4,1e4)); print random data made, starting...',
number=1)
random data made, starting...
11.597978115081787
James
On Sep 12, 2012, at 8:32 AM, Jacob Keller wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of tab-delimited data on
which I would like to do some math (averaging, sigmas, simple arithmetic,
etc) as well as some sorting and rejecting. It can be done in Excel, but this
is exceedingly slow even in 64-bit, so I am looking to do it through some
scripting. Just as an example, a sort which takes 10 min in Excel takes
~10 sec max with the unix command sort (seems crazy, no?). Any suggestions?
Thanks, and sorry for being off-topic,
Jacob
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***
Re: [ccp4bb] Off-topic: Best Scripting Language
On Sep 12, 2012, at 1:00 PM, George Sheldrick wrote: It is the lack of compatibility between different versions mentioned by Ethan that really put me off learning PYTHON. Python is backwards compatible. I have reams of code I wrote in python 2.3 that still works in 2.7 without modification. Also, python (aka python 2) and python 3000 (aka python 3) are considered two different languages. It's not reasonable to consider them one language and then complain that they are incompatible. Python 3 was created as a new language (and should be treated as such) precisely because it breaks compatibility with python 2. That was the intent of the language authors. You blame the authors for recognizing limitations of a language and inventing a new one to overcome those limitations. If the FORTRAN authors would have done that about 30 years ago, we all might be programming in FORTRAN. James
Re: [ccp4bb] Does anyone have used DelPhi to calculate the Electrostatic potentials of DNA ？
I think delphi doesn't need to know about connectivity, only the atom identities. So the distinction between DNA and protein should be irrelevant and thus the input files would be the same. If you just want to visualize the delphi EP, try this page: http://structure.usc.edu/howto/delphi-surface-pymol.html James On Jul 10, 2012, at 8:36 PM, dengzq1987 wrote: Hi all, recently，I want to use DelPhi to calculate the Electrostatic potentials of DNA.but in the manual,i can not find the method to create the inputfile fort.11 、fort.12 and fort.13.Does anyone have experience on this? Please suggest Thank you in advance Sincerely dengzq
Re: [ccp4bb] One little clash
It looks like dityrosine, usually caused by radiation damage (I think UV is the usual culprit).http://www.nugowiki.org/images/thumb/c/ca/HMDB06045.png/220px-HMDB06045.pngJamesOn Jul 11, 2012, at 1:37 PM, Lukacs, Christine wrote:Hi all-I have a protein that crystallizes in I422, and diffracts well, between 1.3-1.7A. Beautiful density, slightly higher final R-factors than you might expect at this resolution (low to mid 20s). The density is all beautiful, except that I have this one little clash, between a few atoms from a tyrosine and its symmetry mate. In this picture I have it modeled as an Alanine and you can see the two tyrosine rings interlocking; and there is clearly no alternate conformation.image003.pngSince it is not near my site of interest, I have been pretty much ignoring it, going through refinement with it as an alanine, then changing it at the very end to a tyrosine and just minimizing B-s, no positional. Now that I plan to publish a bunch of these, I should probably figure out what is really going on. Any insights?ThanksChristineChristine LukacsRocheThis message is intended for the use of the named recipient(s) only and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.
Re: [ccp4bb] One little clash
The hydroxyls were on the wrong carbons in the previous picture I sent. These are correct.JamesOn Jul 11, 2012, at 1:37 PM, Lukacs, Christine wrote:Hi all-I have a protein that crystallizes in I422, and diffracts well, between 1.3-1.7A. Beautiful density, slightly higher final R-factors than you might expect at this resolution (low to mid 20s). The density is all beautiful, except that I have this one little clash, between a few atoms from a tyrosine and its symmetry mate. In this picture I have it modeled as an Alanine and you can see the two tyrosine rings interlocking; and there is clearly no alternate conformation.image003.pngSince it is not near my site of interest, I have been pretty much ignoring it, going through refinement with it as an alanine, then changing it at the very end to a tyrosine and just minimizing B-s, no positional. Now that I plan to publish a bunch of these, I should probably figure out what is really going on. Any insights?ThanksChristineChristine LukacsRocheThis message is intended for the use of the named recipient(s) only and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete this message. Any unauthorized use of the information contained in this message is prohibited.
Re: [ccp4bb] SOMoRe
On Jul 9, 2012, at 11:02 AM, Tim Gruene wrote: Dear Fulvio, http://lmgtfy.com/?q=somore+molecular+replacement should help you out, especially the but last paragraph of the first link provided. Not Found The requested URL /~djamrog/somore.html was not found on this server.
Re: [ccp4bb] Help with curves+
The star is usually for sugar atoms, not for the bases. I don't remember what curves wants. Does your PDB have apostrophes instead of stars? If so you should just do a global search and replace. If you still have a problem, you should copy-paste the error message. James On Jul 2, 2012, at 12:44 PM, Nikolai Suslov wrote: Hello, I am trying to analyze an RNA helix with curves+. I keep receiving an error message that base atom C1* is missing from the pdb. C1 atoms are certainly all there. Any advice on how to troubleshoot this will be much appreciated. Sincerely, Nikolai Suslov
[ccp4bb] Layer Groups: B2 recognized?
Hello Everyone and especially symmetry experts, I found at http://img.chem.ucl.ac.uk/sgp/medium/003dy1.htm that B2 (SG #2) is a recognized space group that has a basis rotated from P2 (and as a result has two new positions). I'm wondering whether a similar B2 for P2 (LG #3) is recognized for the layer groups? I checked wikipedia (http://en.wikipedia.org/wiki/Layer_group) and the Bilbao server (http://www.cryst.ehu.es/subperiodic/get_sub_gen.html) and could find no evidence of a B2 layer group being recognized, but I can also come up with no logical reason why it shouldn't be recognized. Thank you for any input, James -- James Stroud http://www.jamesstroud.com
[ccp4bb] Question on Symmetry Axis Notation Convention
Hello All,
I would like to discuss symmetry axes, but I'm not sure what the notation
convention is. For example, I'd like to say something about a 2(1) along the
x-axis, but the phrase the 2(1) symmetry axis along x is a bit cumbersome to
repeat many times or to put in a table. So I'd like a shorthand, maybe
something like x(2_1) (where the preceding _ means that the 1 is
subscript. Another way I like is x_{2(1)} (where the curly braces mean that
all of 2(1) is subscript).
Does anyone know what the convention is or if there is one?
Thanks in advance for any help.
James
Re: [ccp4bb] how to get phase of huge complex
If you want to use se-Met, you might want to start by labeling only one protein at a time. For example, if you have A,B,C,D, grow crystals like this: se-A, B, C, D A, se-B, C, D, etc. Then try combinations of 2, then 3, then if you haven't got the phases you need, try all 4. And remember, if 2 different combinations diffract and they are isomorphous, then you can try MIR too. Also, if your complex can stay intact on a gel shift, look at this paper: http://www.ncbi.nlm.nih.gov/pubmed/10903954 James On Jun 12, 2012, at 8:46 PM, LISA wrote: Hi all, My work is to solve huge complex containing 4 different proteins and total molecular weight is about 300 KD. I can purify the complex by co-expression them in E.coli. This complex contains 8 protein A, 2 protein B and 1 protein C and D. protein B and protein C have homology structures deposited in PDB database. No homology structure available for protein A and D, which contribute 60% of the whole molecular weight for the complex. Now I am trying to find a way to solve the phase of this complex. I am thinking of use sad or mad with se-Met. There total 111 Met residues in this complex. Is it possible to solve this complex by se-Met? Does someone have experience to solve huge complex structure with se-met? It is also very welcome for all the suggestion. Thank you. All the best, Lisa
Re: [ccp4bb] Who is using 64-bit Linux?
On Apr 13, 2012, at 1:24 PM, James Holton wrote: I tried downgrading the operating system to 32-bit, but that reduced the number of CPUs available in the system from 24 to 8. Still don't know why that is I'm probably wrong, but I'll guess that a 32 bit operating system can only spare 3 of those bits to address CPUs ;-) James
Re: [ccp4bb] Question about PyMol
Yes. File - Save Molecule... James On Apr 11, 2012, at 1:17 PM, Harman, Christine wrote: Hi All, Sorry for the dumb question, but if there was a way to export coordinates from PyMol. Is yes, then how? Thanks Christine
Re: [ccp4bb] very informative - Trends in Data Fabrication
On Apr 3, 2012, at 7:19 PM, Katherine Sippel wrote: I would also consider looking into adding an RSS feed to your site so that those people interested in your articles can be informed without spamming the boards. Why continue to punish him? Adding an RSS feed means installing and configuring an RSS server. Aren't there rules against cruel and inhumane punishment? There are many free newsfeed disseminators. Twitter is the most famous. There are others, maybe better, so I'm not being a twittervangelist here. My point is this: free and easy is better than difficult. James
Re: [ccp4bb] a small trick for protein and organic compound cocrystallization.
On Mar 30, 2012, at 1:04 PM, Bryan Lepore wrote: On Fri, Mar 30, 2012 at 4:02 AM, Kevin Jin kevin...@gmail.com wrote: Here is way I have used for [...] I hate to be a curmudgeon, but can a list member please explain why this is not specifically blogspam or spam - or whatever it is exactly? It's not really spam, but there are better channels to communicate these type of updates. Twitter is probably the best known channel. People get to subscribe and authors can push their contributions to willful and interested subscribers. The author posts a summary of what's behind the link and then posts the link, just as Jin is doing with his ad-hoc feed here. For example, a few days ago I created the @amyloids twitter feed (https://twitter.com/#!/amyloids) that features recent publications I have read and that I also think are of interest to amyloid researchers. Instead of being to critical, let's just direct authors to use the proper channels. Social media has moved fast in recent years, and we should be understanding as the scientific community plays catch-up. If Jin created a twitter feed for tips, it would probably get some subscribers from this board--as long as we don't begrudge the Jin an opportunity to send out an advertisement for the feed itself. James
Re: [ccp4bb] DNA length for crystallization
Use 5' overhangs of two and make the DNA 10, 11, 15, 20, 21 25, 26, 30, or 31 bases in length. Count the overhangs in the length. If you don't know where to start, try 15, 25, and 26 first because they will make 2(1) screws, which are good for crystals. James On Feb 15, 2012, at 1:06 AM, LISA wrote: Hi all, I have a DNA binding protein. I can get crystals when I mix 8-28 nt dsDNA with my protein. But neither of them has good diffraction. Some biochemical data said the longer of DNA, the tigher of the binding betwwen DNA and my protein. The binding is not sequence-specfic. Does anyone have suggestion of the optimization? What is the good length of DNA for crystallization? Thank you. Lisa
Re: [ccp4bb] Crystal Structures as Snapshots--Summary
I feel compelled to throw a few references into the ring. NFAT is a protein where you get a good sampling of snapshots: 1. Folded up as a monomer when interacting with partner proteins: http://www.ncbi.nlm.nih.gov/pubmed/9510247 http://www.ncbi.nlm.nih.gov/pubmed/16873067 2. Extended as a dimer: http://www.ncbi.nlm.nih.gov/pubmed/12949493 3. Folded up as a monomer when interacting with a partner protein which happens to be itself as an extended dimer: http://www.ncbi.nlm.nih.gov/pubmed/18462673 4. Wrapped around DNA as a monomer without partners:. http://www.ncbi.nlm.nih.gov/pubmed/14643663 In this last reference you get a sample of extended, wrapped around, and folded up all in the same unit cell! James On Feb 15, 2012, at 1:48 PM, Jacob Keller wrote: Dear Crystallographers, thanks for all of the responses and conversation. I have culled together the various references which have been sent on the BB and which I have come up with, and posted them below. Worthy of special mention, I think, is the first one (Lange et al), in which 46 (!) different crystal structures are pitted against a lot of RDC NMR data, and the match seems to be excellent (although it seems you probably have to know both methods fairly well to evaluate this properly.) Anyway, for asserting that variances between crystal structures at least in some cases represent differences between physiologically-relevant states in solution, the Lange paper is really on the mark. Thanks again, Jacob Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KF, Becker S, Meiler J, Grubmüller H, Griesinger C, de Groot BL. Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science. 2008 Jun 13;320(5882):1471-5. PubMed PMID: 18556554. Kondrashov, D.A., Zhang, W., Aranda, R.t., Stec, B., and Phillips, G.N., Jr. (2008). Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins 70, 353-362. Zhang, X. J., Wozniak, J. A., and Matthews, B. W. (1995) Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme, Journal of molecular biology 250, 527-552. Long, SB, Casey, P., Beese, LS (2002) The reaction path of protein farnesyltransferase at atomic resolution. Nature Oct 10; 419(6907):645-50. http://www.ncbi.nlm.nih.gov/pubmed?term=The%20reaction%20path%20of%20protein%20farnesyltransferase%20at%20atomic%20resolution J. R. Kiefer, C. Mao, J. C. Braman and L. S. Beese (1998) “Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal” Nature 6664:304-7. http://www.ncbi.nlm.nih.gov/pubmed?term=Visualizing%20DNA%20replication%20in%20a%20catalytically%20active%20Bacillus%20DNA%20polymerase%20crystal Mancini EJ, Kainov DE, Grimes JM, Tuma R, Bamford DH, Stuart DI (2004) Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Cell 118(6):743-55 http://www.cell.com/abstract/S0092-8674(04)00837-2 Nature. 2009 Dec 3;462(7273):669-73. Hidden alternative structures of proline isomerase essential for catalysis. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T. *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Crystal Structures as Snapshots
How could they not be snapshots of conformations adopted in solution? James On Feb 10, 2012, at 1:25 PM, Jacob Keller wrote: Dear Crystallographers, I am looking for references which discuss the validity of the assertion that multiple crystal structures of the same or similar proteins can be considered freeze-frame snapshots of actual conformations assumed in solution. In a way, the assertion seems almost definitely true to me, but on the other hand, I could imagine some objections as well. Seems there should be some classic literature here... All the best, Jacob -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Crystal Structures as Snapshots
So the implication is that some of these treatments might allow the protein to overcome energetic barriers that are prohibitive in solution--after the protein is already in the solid state and not in solution any more? Another view is that crystallization is a result of stabilizing conformations that are accessible in solution. On the point of physiological relevance, it wasn't mentioned in the original question. James On Feb 10, 2012, at 1:34 PM, Nat Echols wrote: On Fri, Feb 10, 2012 at 12:29 PM, James Stroud xtald...@gmail.com wrote: How could they not be snapshots of conformations adopted in solution? Packing billions of copies of an irregularly-shaped protein into a compact lattice and freezing it to 100K isn't necessarily representative of solution, especially when your solution contains non-physiological amounts of salt and various organics (and possibly non-physiological pH too). -Nat
Re: [ccp4bb] Crystal Structures as Snapshots
The contrast seems to boil down to the semantics of the word snapshot. In my definition, I assume that the uncertainty of a structure is an intrinsic quality of the structure and thus included in the meaning of snapshot. Part of that uncertainty comes from averaging. James On Feb 10, 2012, at 1:51 PM, Jacob Keller wrote: Interesting to juxtapose these two responses: James Stroud: How could they not be snapshots of conformations adopted in solution? David Schuller: How could that possibly be the case when any structure is an average of all the unit cells of the crystal over the timespan of the diffraction experiment? JPK
[ccp4bb] 3 Letter for 1'-deoxyribofurnaose-5'-phosphate?
Hello All, Do any of you RNA structural biologists know what is the 3 letter code for 1'-deoxyribofurnaose-5'-phosphate (abasic site in RNA)? I found that the 1'2'-dideoxy is 3DR, but could not find a lead on the 1'-deoxy. I scoured HIC-UP to no avail, which I think is the most comprehensive hetero-compound library. If I knew what the 3 and R stood for in 3DR I could probably guess. I'm pretty sure the D stands for the 2' deoxy. Thank you for any help! James
Re: [ccp4bb] 3 Letter for 1'-deoxyribofurnaose-5'-phosphate? - SOLVED!
Hello All, Two people named Rob told me that the the 3 letter code is N. http://ligand-expo.rcsb.org/reports/N/N/index.html Coincidentally, the old 3 letter name is ROB. Thank you for your help! James On Fri, Jan 27, 2012 at 2:38 PM, James Stroud xtald...@gmail.com wrote: Hello All, Do any of you RNA structural biologists know what is the 3 letter code for 1'-deoxyribofurnaose-5'-phosphate (abasic site in RNA)? I found that the 1'2'-dideoxy is 3DR, but could not find a lead on the 1'-deoxy. I scoured HIC-UP to no avail, which I think is the most comprehensive hetero-compound library. If I knew what the 3 and R stood for in 3DR I could probably guess. I'm pretty sure the D stands for the 2' deoxy. Thank you for any help! James
Re: [ccp4bb] writing scripts-off topic
I should know better than to touch a flame post, but, but here goes: flame don't use anything but python. They are nightmare languages, sloppy, and force you to format the code by inserting semantically redundant brackets and semicolons in a specific way rather than dispensing these redundancies altogether /flame On Jan 24, 2012, at 1:59 AM, Tim Gruene wrote: [flame=;-)] P.S.: don't use python. It's a nightmare language, sloppy, it forces you to format the code in a specific way rather than your own way and ... [/flame] Also, if you use python and you want to format your code in your own way, you should learn about python's I don't care if anyone, including me, can read my code parenthetical construct: print \n.join((lambda Ru,Ro,Iu,Io,IM,Sx,Sy:reduce(lambda x,y:x+y,map(lambda y, Iu=Iu,Io=Io,Ru=Ru,Ro=Ro,Sy=Sy,L=lambda yc,Iu=Iu,Io=Io,Ru=Ru,Ro=Ro,i=IM, Sx=Sx,Sy=Sy:reduce(lambda x,y:x+y,map(lambda x,xc=Ru,yc=yc,Ru=Ru,Ro=Ro, i=i,Sx=Sx,F=lambda xc,yc,x,y,k,f=lambda xc,yc,x,y,k,f:(k=0)or (x*x+y*y =4.0) or 1+f(xc,yc,x*x-y*y+xc,2.0*x*y+yc,k-1,f):f(xc,yc,x,y,k,f):chr( 64+F(Ru+x*(Ro-Ru)/Sx,yc,0,0,i)),range(Sx))):L(Iu+y*(Io-Iu)/Sy),range(Sy (-2.1, 0.7, -1.2, 1.2, 30, 60, 24)[i*60:(i+1)*60] for i in xrange(24)) (adapted from http://effbot.org/pyfaq/is-it-possible-to-write-obfuscated-one-liners-in-python.htm) James
Re: [ccp4bb] writing scripts-off topic
On Jan 24, 2012, at 11:24 AM, Ian Tickle wrote:
Maybe a Python expert will answer this
but I've often wondered, what happens if as some editors do
(particularly if as I do you have to use different editors at
different times depending on where you are working, such as on Windows
working remotely from home or Linux at work), you could have a mixture
of space and tab characters in the file?
Just have a policy of no tabs. I make sure all of my editors interpret a tab as
a set number of spaces (I like 2).
A tab was meant as a separator and not a formatting character anyway. Have you
ever edited a document where someone used 8 tabs to center a line of text
rather than simply applying centered formatting? If you have, you'll realize
that tabs are not meant to be formatting characters.
When I first picked up a python book and it told me that indent had semantic
relevance, I immediately thought of fortran, so almost gave it up. Two days
later, python's use of whitespace seemed more natural than the alternative.
Let's look at the Java hello world program again
class HelloWorldApp {
public static void main(String[] args) {
System.out.println(Hello World!);
}
}
Notice that this obviously veteran programmer has used whitespace formatting in
a natural way to improve the readability of the code. Java did not enforce
this. If a language harnesses this formatting for semantics, then all of the
brackets and the semicolon become redundant.
You probably already format your code in a way consistent with python's
whitespace rules if you have been programming for any length of time.
James
Re: [ccp4bb] secondary structure output
Try DSSP2PDB. http://structure.usc.edu/dssp2pdb/ It's a perl script. Crossover flame note: I spent a lot of time learning perl and I still don't recommend the language ;-) James On Jan 24, 2012, at 1:57 PM, Ed Pozharski wrote: I am looking for a program/server that would determine secondary structure from a pdb file and then output a new pdb file with HELIX/SHEET records. I have a model for which pymol fails to produce correct secondary structure. DSSP and STRIDE identify the secondary structure correctly but I'd need to convert their output myself to either pdb header or pymol script. So I wonder maybe something like that already exists. Gracias, Ed -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] secondary structure output
This reminds me of stride2pdb in case you want to use more than pymol with your secondary structure assignments: http://structure.usc.edu/stride2pdb/ James On Jan 24, 2012, at 2:20 PM, Martin Hällberg wrote: You can try STRIDE2PyMOL: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/stride_ss.py /Martin On Jan 24, 2012, at 9:57 PM, Ed Pozharski wrote: I am looking for a program/server that would determine secondary structure from a pdb file and then output a new pdb file with HELIX/SHEET records. I have a model for which pymol fails to produce correct secondary structure. DSSP and STRIDE identify the secondary structure correctly but I'd need to convert their output myself to either pdb header or pymol script. So I wonder maybe something like that already exists. Gracias, Ed -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] writing scripts-off topic
On Jan 23, 2012, at 9:46 PM, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Just simple calculations
from an input PDB file, B factors averages, occupancies, molecular weight, so
forth...
What should I use python,C++, visual basic?
thanks
Python is the most practical. Here is a simple python program:
print Hello World
Feel the power.
Python can be that simple or can be arbitrarily complex, nuanced, or abstract.
You can write entire applications in python or small utilities. If you practice
good habits, you will begin building reusable libraries from day one, saving
time over the long haul.
STAY AWAY from proprietary nonsense like visual basic and from languages that
do not facilitate reusability, like perl or other 1980's era shell languages.
You will find yourself porting or abandoning your code, which is not a good use
of your time.
I also do not recommend overweight languages like java, which create programs
that never seem to deploy correctly and take about 5 times more code to create
than should be necessary. Here's the java Hello World:
class HelloWorldApp {
public static void main(String[] args) {
System.out.println(Hello World!); // Display the string.
}
}
Public static void main? Don't bother.
And python can be VERY fast for calculations if you use free and popular
libraries like numpy and scipy. These librares are wrappers around optimized
fortran and C libraries that you will never have to use directly.
I recommend staying away from very low level languages like C or fortran, too.
It is good to know these languages, but not so good to use them. Your
creativity should go towards implementing cool ideas and should not be
squandered on plugging memory leaks. It's better to use high level languages
that leverage your time most effectively.
James
Re: [ccp4bb] Off-topic: ELNs
On Jan 18, 2012, at 6:17 AM, Anastassis Perrakis wrote: Here at the NKI, we had formed a committee to look at ELN solution two years ago. We had interviewed three vendors, and run two tests with twenty users. A brief description of the outcome: 1. None of the twenty test-users was satisfied with any of the two solutions - and each was annoyed for a different reason. Would you mind elaborating on any of the reasons that resonated most with you? Are these ELNs simply over-engineered? You mention the requirement to make experiment templates. This sounds cumbersome and a potential for duplicated effort. Do ELNs generally require templates or other overhead in the form of end-user effort? James
Re: [ccp4bb] artificial tetramer
This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] artificial tetramer
Coot can do this using the Rubik's Cube principle: transform to some state where the operation can be performed, perform the operation, then transform back. So, in coot, I would (1) rotate the molecule to the appropriate orientation (2) move to the appropriate place in the unit cell (3) change the symmetry to P4 (3) apply P4 symmetry (4) change the symmetry back to whatever (5) move the tetramer back to the appropriate place in the unit cell (6) rotate the molecule back Then, your original molecule will be in the original place surrounded by it's symmetry mates. James On Dec 12, 2011, at 2:36 PM, Fred wrote: Hi James, In my first post arbitrary orientation into the cell only means not parallel to any crystallographic axis, which would simplify things very much. I want to apply the 4-fold axis to the protein coordinates. If I have a cell and therefore an origin, I can take a point at any distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu: This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry operation (4-fold rotation) has 5 free parameters (translation along the symmetry axis is irrelevant). The biggest problem is determining the values for these parameters. For example, once you apply the symmetry, your molecule may clash with its symmetry mates or not even contact them. And even if you solve this latter problem automatically (which is not trivial because of irregularity), that leaves a net of 3 parameters describing the orientation of the protomer. James On Dec 12, 2011, at 1:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotation matrix. I would like to create them but don't know how and which program to use. Theoretically a have to create a axis (vector) at some distance of the molecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate' keyword. It is not clear to me whether or not you have the rotation matrix or how you define rotation. Cheers, Tim On 12/12/2011 08:49 PM, Fred wrote: Hi List, I would like to build an artificial tetramer from a monomer PBD file. All that I have is the coordinates it self with CRYST/CELL information cards. The artificial 4-fold axis has an arbitrary orientation into the cell. I mean, its not parallel to any crystallographic axis and have to be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn cqs8GHOu5M3JQahA/CofR1k= =tDUj -END PGP SIGNATURE-
Re: [ccp4bb] better way to post your density snapshots
On Dec 8, 2011, at 8:39 AM, Ed Pozharski wrote:However, I'd see noharm in posting just a small cutout of the map in the region ofinterest. It's not a difficult task (fft/mapmask or perhaps some usfmagic), but is there some user-friendly approach to cutting out a smallmap volume?There's probably a slick program somewhere, but attached is a command line tool I made several years ago and still use all of the time. To use it, you need ccp4 and mapman from USF in your path. Running the script with "mapreg -h" yields the documentation below. It can cut a map using a box, extend or cut to the ASU, extend a map to a cell, or use a pdb file to make a box. It can also cull a map around a PDB.To use it, the attachment needs to be untarred (tar zxvf mapreg.tar).One of these days I may give it a web page.James* mapreg version 0.02*** output a region of a cns map*** copyright James C. Stroud, 2008*** distributed under the GNU Public License**Usage: mapreg [-h] [-c weight] [-b border] [-s symm] [-t type] [-x 'a b c alpha beta gamma'] mapfile [x1 y1 z1 x2 y2 z2 | ASU | CELL | pdbfile ]Flags: -h print this help -b border define a border if using a pdb file to define region default is 5 (5 Angstroms) -c weight culls according to a weighting factor between 0 and 1 -x cell the sides and angles *must* be in single quotes -s symm usually symmetry number is needed (ispcgr number) -t type type of input map - default is cns -o outfile name of output file (name generated if not supplied)Description: Mapreg takes a cns map as input and outputs a new region of the map as specified at the command line. The possible region specifiers are: x1 y1 z1 x2 y2 z2 : the region defined by the two grid unit or fractional coordinate points (x1,y1,z1) and (x2,y2,z2) 'ASU' : the CCP4 default asymmetric unit 'CELL' : the whole unit cell pdbfile : a pdb file defining the limits of the regionif border is defined, then this will be the borderin Angstroms around pdbfile to define the region If the region specifier is left out, then mapreg will output the whole unit cell. CULLING === If a culling factor is supplied and a pdb file is used for trimming, then culling will be attempted. Culling trims the map to the the atoms of the pdb file if supplied. Without the pdb file, the program terminates with an error if a culling factor is supplied. The culling weighting factor is, for all practical purposes, arbitrary. Play with it to get the desired results. Start with 0.1 and go up (tighter) or down (less tight). Make sure you are aware of the caveats of culling before you use this to make figures for publication. mapreg.tar Description: Unix tar archive
[ccp4bb] [ANNOUNCEMENT] mapreg has a home page
Hello all, Since no one offered a good utility for Ed Pozharski's idea to easily cut a region of a density map, I made a permanent web location for my utility called mapreg: http://mapreg.bravais.net/ Enjoy. James
Re: [ccp4bb] Efficient way of showing residue conservation
Usually you put a statistic like this in the tempFactor field (B) and then color by B-factor in pymol or similar. I'm certain there is a facility for filling this entry somewhere. If not, then a fairly trivial server is waiting for someone to create it and claim the glory. Google something like alignment b-factor or clustal b-factor. That's my best guess. James On Dec 7, 2011, at 10:26 PM, Yuri Pompeu wrote: I once saw a figure showing the protein as surface, but instead of having it coloured by atom type or potential, it was shown by percent conservation in the family. Something like red highly conserved, all the way to white, not conserved at all... Now, I assume the figure was done by uploading aligned sequnces of several members of a family, and the colouring the generated surface accordingly. Does anyone know a way to do this more elegantly than what I tried doing? ps. I quit colouring them manually after I remebered my protein was 407 aa long...
Re: [ccp4bb] Withdrawal of subscription
With such a nice parting letter, we find it disheartening to let you go. James On Nov 29, 2011, at 7:44 PM, debanjan choudhuri wrote: To whom it may concern, I am writing this in request to the cancellation of my subscription to CCP4BB mail. It was indeed a very rewarding and a knowledgeable experience to be a part of this family. With regards Debanjan Choudhuri
Re: [ccp4bb] Movements of domains
On Nov 21, 2011, at 3:04 PM, Filip Van Petegem wrote: So the question is: how you can state that a particular movement was 'significantly large' compared to the resolution limit? I can think of a different but related question. How significant is a particular movement compared to a measured coordinate error? One way to measure the coordinate error in this example is to least-squares superpose the two instances of the domain in question and calculate the rmsd. This makes the calculation of significance independent of the resolution of the data set. James
Re: [ccp4bb] Movements of domains
On Nov 21, 2011, at 3:52 PM, Filip Van Petegem wrote: As mentioned for X-ray structures, a Luzzati analysis may give information about the positional errors, but there should be an increased resolution when comparing domain movements, because it's unlikely for all atoms to have an error in the same direction. Here's how I think about it: If you use the empirical coordinate error that I described previously, you can use simple statistics to calculate how likely you are to get a coordinated movement (relative to a fixed landmark). I can use a 1-d case as an example. In this 1-d case, let's pretend that we have a domain of N=25 atoms where atom 2 is about 1 away from atom 1 and atom 3 is 2 away from atom 1 and one away from atom 2, etc, with a standard deviation of 1 for the position of the atoms. If atom 1 for domain A is at 1, this is just A_j = j Then you can have domain B that has moved +1 compared to domain A: B_j = j+1 Since we have an alignment (B_j - A_j), then we can calculate the movement, X: X = mean(B) - mean(A) We can also calculate the error of the ensemble (aka the error of the mean): sigmaE = std( (B - mean(B)) - (A - mean(B)) ) / sqrt(25) Then, we can calculate how likely it is we observe the movement X by tail integration of the cumulative normal distribution. We will justify this for the 3-d case because the least squares superposition (from which we estimate the coordinate error) assumes normality. Here is a simulation of this scenario in python: py import numpy py from scipy.special import ndtr py a = numpy.array([numpy.random.normal(j) for j in xrange(25)]) py b = numpy.array([numpy.random.normal(j+1) for j in xrange(25)]) py a array([ 1.38125295, -0.27126096, 1.7597104 , 1.36242299, 3.88327659, 4.33063307, 5.00544708, 7.0258, 7.83945228, 9.72101719, 10.36231633, 10.29176378, 11.78497375, 12.16082056, 14.31057296, 13.25941344, 17.93779336, 18.05626047, 18.62148347, 20.52756478, 19.73362283, 21.83953268, 22.28038617, 23.24545481, 22.96192518]) py b array([ 3.32750181, 2.42664791, 3.23309368, 4.32882699, 6.59985764, 6.49597664, 5.27921723, 7.8573831 , 9.98722475, 10.65225383, 11.69970159, 11.67435798, 12.16191254, 13.69297801, 14.21845382, 17.21423427, 16.89347161, 17.68778305, 17.89371115, 18.7679351 , 20.84842496, 20.69249899, 23.97436807, 23.54011453, 26.84986504]) py X = b.mean() - a.mean() py sigma_ensemble = ((b - b.mean()) - (a - a.mean())).std() / math.sqrt(25) py X_standardized = (X - 0) / sigma_ensemble py 2 * ndtr(-abs(X_standardized)) 0.00011596192653578624 This means, for the 1-d scenario I describe, (using the random arrays generated above), the movement is expected about once for every 10,000 experiments, providing a p-value, or estimate of significance. Note that the 2 comes from the fact that the cumulative distribution has 2 tails. A 3-D calculation using the rmsd as the coordinate error would be similar except that you use Euclid's formula to calculate the distances in higher dimensions (instead of the absolute value of a simple subtraction as in 1-d). James
Re: [ccp4bb] Movements of domains
On Nov 21, 2011, at 5:23 PM, James Stroud wrote: except that you use Euclid's formula to calculate the distances in higher dimensions I meant to say Euclidian distance. Euclid's formula has a specific meaning that is different.
Re: [ccp4bb] Movements of domains
On Nov 21, 2011, at 6:34 PM, Jacob Keller wrote: I am curious how all of this can be more than splitting hairs, i.e., under what conditions can this 1Ang domain motion mean something biologically significant? To engage in the discussion, I think we had to accept this: On Nov 21, 2011, at 3:04 PM, Filip Van Petegem wrote: I'm not talking about the fact that this movement was artificially caused by crystal packing or something similar. Just for whatever the reason (whether packing, pH, ligand binding, ...), you simply observe the movement. So the point of the discussion, as I understand it, is to figure out whether the movement warrants further consideration in the first place, i.e. whether it is significant with respect to the error of the models. I think it doesn't take too much energy to discount the attempt to quantify the statistical significance by claiming that one can't imagine how such a change might be biologically significant. I'm really not privy to the structures in question, so I am in no position to make this judgement. James
Re: [ccp4bb] Archiving for fraud detection
On Nov 4, 2011, at 2:09 AM, Chris Morris wrote: One argument for archiving images has been that reprocessing could demonstrate deliberately deceptive structures. In fact, what is needed for this is not necessarily the image. It is the last data file that was produced by a trusted computer. Although this is a good idea from the perspective of storage, it is difficult to implement. For this idea to work, you need a (1) certificate system, (2) certificate authority. The certification is necessary to verify that the data file was indeed generated by a trusted computer. The chosen file needs to be certified by the authority and the certification archived on a trusted system. None of these requirements are terribly problematic. The infrastructure for a certificate system is free in the form of openSSL. Almost any lab or institution could easily become a certificate authority. The storage requirements for the certificates are trivial. For example, if a certificate were 2 KB, then, for the 8,000 structures per year, the storage requirements would be 1.6 MB. After 1000 years, we would fill up my $14.95 2 GB thumb drive. The difficulty is that certification should be done on the file before it is transferred from the trusted computer. This requires inserting the certification process somewhere in the transfer pipeline, which is difficult because it requires all the synchrotrons to actually implement it. Allowing the user to produce the certificate after transfer is as useful as having no certificate system at all. Then there is the issue of data collection on a home source. James
Re: [ccp4bb] raw data deposition
On Oct 27, 2011, at 5:22 PM, Francis E Reyes wrote: So I ask again, are there literature examples where reevaluation of the crystallographic data has directly resulted in new biological insights into the system being modeled? This is a poor criterion on which to base any conclusions or decisions. We can blame the lack of examples on unavailability of the data. Right now, I'd love to get my hands on the raw images for a particular cryoEM data set, but they are not available--only the maps. But the maps assume one symmetry and I have a hypothesis that the true symmetry is different. I could test my hypothesis by reprocessing the data were it available. James
Re: [ccp4bb] IUCr committees, depositing images
On Oct 26, 2011, at 9:59 AM, Patrick Shaw Stewart wrote: The principle is that the movie is written to the same area of memory, jumping back to the beginning when it is full (this part is not essential, but it makes the principle clear). Then, when the photographer takes his finger off the trigger, the last x seconds is permanently stored. So you keep your wits about you, and press the metaphorical store button just after you have got the movie in the can so to speak This idea seems equivalent to only storing permanently those datasets that actually yield structures worthy of deposition. James
Re: [ccp4bb] IUCr committees, depositing images
On Oct 24, 2011, at 3:56 PM, James Holton wrote: The PDB only gets about 8000 depositions per year Just to put this into dollars. If each dataset is about 17 GB in size, then that's about 14 TB of storage that needs to come online every year to store the raw data for every structure. A two second search reveals that Newegg has a 3GB hitachi for $200. So that's about $1000 / year of storage for the raw data behind PDB deposits. James
Re: [ccp4bb] Biological assembly
Since a crystallographic 3-fold generates the trimer (of dimers) then A1-B2 can be the ASU in this case.Just generate the symmetry mates with the A1-B1 dimer and then make a new PDB of A1-B2 then generate the symmetry mates of A1-B2 to see that the lattice is complete.I compulsively made and attached an illustration to show what I mean.James H3.pdf Description: Adobe PDF document On Oct 20, 2011, at 3:40 AM, Kayashree M wrote:Thank you Sir for the suggestions. Hi,If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. Normally the PDB can take care of that.The protein looks like the letter "C", So in one of the trimer it is arrangedas "C" while in the other trimer (stacked) it is arranged like "inverted C", SoThe dimer A1-B1 and A2-B2 are same while A1-B1 and A1-B2 are different.Thanking you With RegardsKavya-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Biological assembly
On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate the symmetry equivalent molecule and get that). This last sentence is a bit vague. Can you take the just dimer that PISA predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in density but retaining the dimeric relationship predicted by PISA), and then generate the complete lattice using just this fitted dimer and crystallographic symmetries? If so, that means that the PISA dimer is equivalent to the ASU you can deposit the PISA dimer as the ASU. James
Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong
The programs give me solutions with reasonable maps, but it is never possible to refine to achieve Rvalues below 0.40. This strongly suggests a space group issue. If the systematic absences are compelling, you should try to drop it down to P2 first. Look at your packing in the C222(1). If you change the direction of one of the coils relative to the other, will it break the orthorhombic symmetry and drop it to monoclinic? This may provide a clue to the space group you should try. James On Oct 17, 2011, at 11:09 AM, Napoleão Valadares wrote: Hi there! I got crystals from some synthetic peptides I bought, they are 30 residues long and are supposed to form a coiled coil. I collected various data sets (home source, Brookhaven and Diamond), including some at the resolution of 1.65 A, for which the space group appears to be C222 or C2221. The unit cell is small, 22.67, 88.06, 26.13, and the Matheus Coefficient indicates that's there's only one helix in the asymmetric unit and a 25% solvent content. I have tried A LOT of Molecular Replacement using Phaser and Phenix AutoMR. I'm using a 80% identity coiled coil helix as search model. The programs give me solutions with reasonable maps, but it is never possible to refine to achieve Rvalues below 0.40. Additionally, maps from different solutions look reasonable, so I'm thinking these are all bias. I have 5 other synthetic 30 residues peptides (that crystallize in different space groups and diffract to lower resolutions), including a SelenoMethionine (SM) derivative (but it does not have enough anomalous signal, ASU is too big, it is possible that the SM are disordered). I'm stuck on this since March. Regarding the search model, I already tried trimming some or all side chains and removing 2, 3 or 5 residues on each/both sides. I also tried other search models. Maybe some magic combination of parameters on Phaser or other programs can help me. What is your advice regarding how to proceed with MR? Is there some program, procedure, parameter, pray or human sacrifice that could help me? Thank you. Regards, Napo
Re: [ccp4bb] MR - small coiled coil, 1.65A = 1.000 solutions, all of them wrong
I should have said not compelling. James On Oct 17, 2011, at 12:40 PM, James Stroud wrote: The programs give me solutions with reasonable maps, but it is never possible to refine to achieve Rvalues below 0.40. This strongly suggests a space group issue. If the systematic absences are compelling, you should try to drop it down to P2 first. Look at your packing in the C222(1). If you change the direction of one of the coils relative to the other, will it break the orthorhombic symmetry and drop it to monoclinic? This may provide a clue to the space group you should try.
Re: [ccp4bb] data processing problem with ice rings
First of all, are you sure those are ice rings? They do not look typical. I think you might have salt crystals from dehydration *before* freezing. Otherwise, I think your freezing went well. Maybe try a humidity controlled environment when you freeze. Second, I'm not so sure the bad stats come from the contaminating rings. The lattice seems to have some sort of problem, like a split lattice. You might be able to tackle this problem by increasing your spot size or skewing it's shape to compensate for the split. You need to investigate several images throughout the run to see whether and how to manipulate your spot size. Sometimes, the split lengthens the spots in the direction of the phi axis and you get lucky. But I think the phi axis might be horizontal in this picture, which makes things a little trickier. From one image, it is difficult to tell the pathology of this crystal. In principle, if you can accurately measure the most high-resolution spots visible (which appear to be about 1.9 Å, guessing from your log file) then you will have a pretty good data set, even with the contaminating rings. Personally, I'd use Denzo for this data, but I don't know what is vogue with the community right now. I still use O, so my tastes might be somewhat antiquated. James On Oct 13, 2011, at 11:12 PM, ChenTiantian wrote: Hi there, I am processing a dataset which has bad ice rings (as you can see in the attach png file). I tried both XDS and imosflm, and got similar results, it seems that adding EXCLUDE_RESOLUTION_RANGE cannot get rid of the effects of the ice rings. the following is part of the CORRECT.LP which is the second attached file, you can find more details there. SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF RESOLUTION RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR R-FACTOR COMPARED I/SIGMA R-meas Rmrgd-F Anomal SigAno Nano LIMIT OBSERVED UNIQUE POSSIBLE OF DATA observed expected Corr 4.24 371525537 5545 99.9% 46.9% 52.7% 371502.4850.8%19.4% -28% 0.5135136 3.01 553449002 9840 91.5% 62.7% 65.1% 551161.7668.3%48.1% -28% 0.5207760 2.46 84636 12699 12703 100.0% 67.4% 84.7% 846341.5573.0%54.2% -19% 0.513 12104 2.13 97910 14743 14987 98.4% 254.5%199.3% 979080.16 276.2% 4899.9% -23% 0.473 14037 1.90 110260 16846 16940 99.4% 299.2%303.3% 1102450.06 325.0% -99.9% -17% 0.422 15995 1.74 118354 18629 18744 99.4%1062.0% 1043.6% 118317 -0.20 1156.4% -99.9% -13% 0.380 17414 1.61 122958 20193 20331 99.3% 967.5% 1571.1% 1228680.10 1059.7% 987.3%-2% 0.402 18348 1.51 125075 21554 21794 98.9% 838.9% 1355.1% 1249330.08 922.6% 1116.9%-1% 0.402 18977 1.42 72057 17042 23233 73.4% 640.8%775.3% 703910.08 732.5% 826.7%-8% 0.425 10003 total 823746 136245144117 94.5% 166.4%166.7% 8215620.40 181.1% 296.7% -15% 0.435 119774 Note that I/SIGMA of each resolution shell is 2.5, so how should I do to process the dataset properly? Any suggestion about this super ice rings? Thanks! Tiantian -- Shanghai Institute of Materia Medica, Chinese Academy of Sciences Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park, Shanghai, 201203 csrc.pngCORRECT.LP
Re: [ccp4bb] should the final model be refined against full datset
Each R-free flag corresponds a particular HKL index. Redundancy refers to the number of times a reflection corresponding to a given HKL index is observed. The final structure factor of a given HKL can be thought of as an average of these redundant observations. Related to your question, someone once mentioned that for each particular space group, there should be a preferred R-free assignment. As far as I know, nothing tangible ever came of that idea. James On Oct 14, 2011, at 5:34 PM, D Bonsor wrote: I may be missing something or someone could point out that I am wrong and why as I am curious, but with a highly redundant dataset the difference between refining the final model against the full dataset would be small based upon the random selection of reflections for Rfree?
Re: [ccp4bb] Ice rings...
I've used a technique called annealing, which amounts to holding an index card between the cryo stream and the crystal for a few seconds then removing the card quickly. In my experience, about 70% of the time the diffraction is worse and about 30% of the time the ice rings will be gone with slightly improved diffraction, allowing recovery of a significant range of data. Most of the time, though, I find another crystal that had a better initial freeze, so annealing has never been a life saver--but it could be under dire circumstances. James On Oct 11, 2011, at 9:30 AM, Dr. Thayumanasamy Somasundaram wrote: Francis, I would like to bring your attention to our paper in Acta Cryst D Volume 66 (6), 741-744 (2010) where we deal with spots under the ice-rings. We have been very successful in eliminating the ice-rings and recover the data underneath. If you are interested you can request the Python script from Michael Chapman at OHSU. De-icing: recovery of diffraction intensities in the presence of ice rings, Michael S. Chapman and Thayumanasamy Somasundaram If you need help please e-mail me outside the CCP4BB. On 10/11/2011 11:16 AM, Francis E Reyes wrote: All, So I have two intense ice rings where there appear to be lattice spots in between them. I understand that any reflections that lie directly on the ice ring are useless, however, how do software programs (HKL2000, d*Trek, mosflm, XDS) deal with these intermediate spots? It would seem to me that employing a 'resolution cut off' just before the ice ring (on the low resolution side) would be improper, as there are spots on the high resolution side of the ice. (see enclosed .tiff) In fact, how do these programs deal with spots lying on ice rings? Are they rejected by some algorithm by those programs during integration, or is it up to the scaling/merging (by SCALA for example) step to deal with them? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder -- Dr. Thayumanasamy Somasundaram [Soma] Director, X-Ray Crystallography Facility (XRF) Off. Ph: (850)644-6448 | Lab Ph: (850)645-1333 Fax:(850)644-7244 | E-mail: tsomasunda...@fsu.edu URI: www.sb.fsu.edu/~soma | URI: www.sb.fsu.edu/~xray Postal Address-- 91, Chieftan Way | KLB 414 Institute of Molecular Biophysics Florida State University Tallahassee, FL 32306-4380, USA.
Re: [ccp4bb] detect dsDNA
If you can reproduce the crystals and have the material 1. Harvest several large crystals. 2. Make several transfers to fresh mother liquor to wash. 3. Dissolve in DNA loading dye without SDS 4. Run on a native gel (e.g. 6% polyacrylamide, 0.5XTBE, etc.). 5. Include positive control lanes for protein, DNA, and complex. 6. Stain with ETBr. Take a picture. 7. Wash out the ethidium in accordance with state, local, federal, UN, laws, filling out the proper documentation ad nauseum. Take a safety class just to be sure you didn't miss something. Hug a bureaucrat. 8. Stain with coomassie. Take a picture. That should tell you more than you need to know. James On Sep 30, 2011, at 9:36 PM, zq deng wrote: Hi all, . recently,I got a crystal of protein-DNA crystal.i used silver stainto prove that it is a protein crystal.Does anyone have method to detect if there is DNA in the crystal. any suggestion will be appreciated. Regards, deng
[ccp4bb] Space Group Table
Hello All, Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count on major software packages to honor this mapping if present in a PDB file)? I notice that this web page was authored by a couple of prominent developers. Thank you, James
Re: [ccp4bb] structure based superposition
Check out Theseus: http://www.theseus3d.org/ You will need a sequence based alignment. This alignment can be provided automatically by muscle if you have it installed (http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to do an SVD to obtain the alignment. I'm not up to date on what all the other programs are using, but I think most use least-squares, so you need to provide a sequence based alignment for these programs Theseus results are always as good or better (subjectively speaking) than straight least-squares superposition. I don't know how the Theseus/muscle combo compares to pymol's use of SVD in terms of alignment quality because I haven't compared them directly. James On Aug 18, 2011, at 3:10 AM, Suda Ravindran wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] Intensity-Weighted Reciprocal Lattice
One holistic way to view a reciprocal lattice (or subset thereof) without the requirement for 3-d or moving frames is with a pole figure. http://en.wikipedia.org/wiki/Pole_figure See Palmer Ladd for a better discussion. I don't know what software can make a pole figure, though. James On Jul 21, 2011, at 6:36 PM, Michael Thompson wrote: Hello ccp4 phenix BB members, I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? I know that there are several programs out there that can generate sections (i.e. 0,k,l) of the reciprocal lattice, such as LABELIT and xrayplot. Are there any other options for doing this, perhaps within ccp4 and/or phenix? I once saw someone give a presentation and they had a little video that showed a three dimensional section of the reciprocal lattice rocking back and forth, which was really cool. I liked this because I felt like it gave a much more holistic representation as opposed to viewing a bunch of individual sections. I don't know if there is an easy way to do this, or if this person somehow managed to create this 3D depiction from a series of sections. Any tips or recommendations would be appreciated. Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Off Topic: How to delete loops from a protein
I've found that predator is one of the best services of this sort: Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997) Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator The server is slow but the service is good. James On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote: Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much it will be helpful to get a homology model of such a protein having low sequence identity. Is there any strategy to decide where the loop could be? Does anybody know any established/ rational method to do that. Waiting for your suggestions Obayed Ullah
Re: [ccp4bb] Off Topic: How to delete loops from a protein/homology modeling
Homer is one of the best services for homology modeling: http://protein.cribi.unipd.it/Homer/ James On Jul 19, 2011, at 2:06 PM, Paul Kraft wrote: Hi Obayed, even though there is 20% sequence identity you may be able to get a very good homology model, especially if there is more than one protein structure in the PDB with 20% homology. Then you can overlap the pdbs and find out what structurally needs to be preserved as opposed to what is in total homology preserved. Typically it is the position of turns residues G, D, S, P, N etc. You won't know until you thread your protein through both pdbs and compare them all. Swiss Pro's Expasy has an easy program that will take an alignment with a pdb and generate a homology model with loops spliced in and energy minimized. There are many other more or less complicated programs, but it's a good one to start with. Paul Dr. Paul Kraft Structural Biologist cell 586-596-2770 email: haresea...@yahoo.com email: kraft_proteome_resea...@yahoo.com This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. --- On Tue, 7/19/11, James Stroud xtald...@gmail.com wrote: From: James Stroud xtald...@gmail.com Subject: Re: [ccp4bb] Off Topic: How to delete loops from a protein To: CCP4BB@JISCMAIL.AC.UK Date: Tuesday, July 19, 2011, 2:37 AM I've found that predator is one of the best services of this sort: Ref: PROTEINS: Structure, Function, and Genetics 27:329–335 (1997) Server: http://mobyle.pasteur.fr/cgi-bin/portal.py?#forms::predator The server is slow but the service is good. James On Jul 18, 2011, at 10:47 PM, Francois Berenger wrote: Hi Obayed, If I understood your question well, you are looking for something called secondary structure prediction. I googled these keywords and found this server: http://bioinf.cs.ucl.ac.uk/psipred/ You may find other interesting servers on the web and some literature comparing them. I think such methods need only the sequence of your protein to predict its secondary structures. Hope this helps, Francois. On 07/19/2011 02:14 PM, Eric Larson wrote: Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein crystallization and structure determination. Nat Methods. 2007 Dec;4(12):1019-21.PMID: 17982461. (http://www.ncbi.nlm.nih.gov/pubmed/17982461) Wernimont A, Edwards A. In situ proteolysis to generate crystals for structure determination: an update. PLoS One. 2009;4(4):e5094. PMID: 19352432. (http://www.ncbi.nlm.nih.gov/pubmed/19352432) good luck, Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Mon, 18 Jul 2011, Obayed Ullah wrote: Hi all I wrote last time but got only one feedback. I know some of you guys must have this experience that how to delete loops from the protein. Please help me with suggestions. I am working with a human protein which have around 20% sequence identity with the other proteins of the same family. Structure of some of the proteins from this family have been solved. All the solved structures have around 20% identity with my protein. I am trying to crystallize the protein but it looks like very hard to get crystal. I have tried different N and C terminally truncated constructs for crystallization but no crystal. My feeling is that probably there is some flexible loops with in the protein which limiting the crystallization. So I want to delete the loops with in the protein (not to truncate in the terminal, I already have done this). I am not asking suggestion about how to delete the loop rather how to decide where the loop is. I am not sure how much
Re: [ccp4bb] Off Topic: PDB validation server
On Jul 8, 2011, at 11:13 AM, Katherine Sippel wrote: I was shocked to discover that the file with only one questionable solvent in April now has 173 of them. One word: Diffusion. James
Re: [ccp4bb] [CONCEAL]
I don't think it worked because I can still see your email address. James On Jun 16, 2011, at 10:27 AM, Peter Burkhard wrote: SET CCP4BB CONCEAL Peter Burkhard, PhD, Assoc. Prof. Nanobiotechnology The Institute of Materials Science University of Connecticut 97 North Eagleville Road Storrs, CT 06269-3136, USA Phone: +1 860 486 3830 Fax: +1 860 486 4745 E-mail: peter.burkh...@uconn.edu Web:http://www.ims.uconn.edu/~pburkhard/ This communication, including any attachments, is intended solely for the use of the addressee and may contain information which is privileged, confidential, exempt from disclosure under applicable law or subject to copyright. If you are not an intended recipient, any use, disclosure, distribution, reproduction, review or copying is unauthorized and may be unlawful. If you have received this transmission in error, please notify the sender immediately. Thank you.
Re: [ccp4bb] Question about the statistical analysis-might be a bit off topic
The short answer can be found in item 2 in this link: http://science.widener.edu/svb/stats/error.html The long answer is I highly recommend Error Analysis by John Taylor: http://science.widener.edu/svb/stats/error.html If you can find the first edition (which can fit in your pocket) then consider yourself lucky. Later editions suffer book bloat. James On Jun 4, 2011, at 10:44 AM, capricy gao wrote: If means and standard deviations of A and B are known, how to estimate the variance of A/B? Thanks.
[ccp4bb] INSERTION CODE
Just giving this thread a title. James On May 3, 2011, at 10:06 AM, Ian Tickle wrote: James, interesting that you chose residue number 32 for your example, because that is the number of one of the two active-site ASPs in the aspartic proteinase family (the other is ASP 215) that I (with Tom Blundell others) worked on for many years. So Ed, it's not just relevant to the WuKabat numbering for antibodies. The idea that one would _not_ use consistent numbering (and therefore insertion codes) across species (viral, fungal, plant and animal so there is huge sequence variability with insertions deletions everywhere), when working with these structures is frankly ludicrous. I recall some programs (FRODO was one) actually required renumbering to the ordinals, i.e. 1, 2, 3 ... - that is until I fixed it! This caused endless confusion, not least because there are often other ASPs in the vicinity of the active site which could easily get renumbered to 32. For me, it's important that when I refer to 'ASP 32' there's no possibility that I mean anything other than the active site ASP! Cheers -- Ian On Tue, May 3, 2011 at 5:17 PM, James Holton jmhol...@lbl.gov wrote: My understanding is that it was introduced for cases where an error in the sequence was discovered long after a large body of literature had accumulated for the wrong sequence. That is, imagine some enzyme where an important catalytic active site residue was number 152, and lots of people had been talking about this residue for years. Then, when you solve the 3D structure, you discover that there is actually a glycine between residues 32 and 33, what do you do? Do you change 152 to 153 and put up with all the angry letters from enzymologists, telling you that you mislabeled this important residue? In case you don't want to do this, the PDB allows you to put in a residue 32A. Deletions can happen too, but they are easier to deal with from a file format standpoint. -James Holton MAD Scientist On 5/3/2011 6:27 AM, Jahan Alikhajeh wrote: Dear Friends, I have noticed an issue in a pdb file, the term insertion code. Does anyone know anything about it? what is it used for? Thanks in Advance, Jahan Alikhajeh, Ph.D, Technical Supervisor, MAN Corporation LTD, Keshavarz Boulevard, Ghods Avenue No. 41, 5th Floor, Tehran, Iran, 14177, Tel: +982166282841 Fax: +982166282997
Re: [ccp4bb] Assigning secondary structure
Just use dssp and cite it. For cartoon figures, if you provide a disclaimer, it doesn't hurt to tweak it a bit to make it look better. The idea is that readers are supposed to know that a protein doesn't really look like a cartoon--and those who don't understand the distinction probably won't have enough knowledge to have an opinion about your assignments anyway. James On Apr 8, 2011, at 9:19 AM, Cale Dakwar wrote: Hello all, Given a PDB file of a newly solved protein structure, what is the standard procedure for assigning regions of secondary structure? And by this I mean to ask, how does one decide which residues form beta strands, which alpha helices, and so on? Is DSSP sufficient for this? Are we supposed to manually walk through the entire molecule and assign secondary structure as we deem appropriate based on hydrogen bonding behaviour? Some other procedure? And what of structures solved to ~2.7 A (or worse) where we can't be sure of H-bonding. Cheers, Cale
Re: [ccp4bb] What happened to this innovative method by MV King?
This was not so much an advance but a remarkable observation. We have since learned that these clathrates are entirely impractical. The problem is not so much their dextrorotatory properties, which are more or less a nuisance, but that they are too dense and have absolutely no affinity for other compounds. James On Apr 1, 2011, at 3:39 AM, REX PALMER wrote: Dear Protein Crystallographers I would like to share with you something I came across today. Unfortunately I was only able to copy the first 4 pages of the article by MV King as I need to post the email before 12am and the quality of the copy is somewhat lacking. I was wondering if anyone knows if anything came of the proposed method of heavy atom substitution as a Google Scholar search has failed to bring anything up. Best wishes Rex Palmer Birkbeck College, London King_1.jpgKing_2.jpgKing_3.jpgKIng_4.jpg
Re: [ccp4bb] Is there any program for specifically calculating Rvalue in CCP4
On Mar 2, 2011, at 11:13 PM, Ting-Wei Jiang wrote: I'm trying to calculate R-value (and free R) specifically which is between data and the modified structure(refined by myself without help from any program) You probably mean without help from any refinement program. Why not fix all atoms, b-factors, etc., and do one round of refinement with refmac? This probably isn't the community-approved way to refine your structure, but it should do what you want. James
Re: [ccp4bb] Harold Jeffreys
Bah...no Kindle Edition...I guess I'll have to keep reading The Grand Design. James On Mar 1, 2011, at 4:40 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote: For those who concern themselves with such matters, the 1973 edition of Sir Harold Jeffreys' Scientific Inference has just been reissued as a Cambridge paperback. Together with AFW Edwards' Likelihood this is good material for the finer aspects of inference I did only cursory touch in BMC chapter 7. Links and more on http://www.ruppweb.org/books/books_and_review_page.htm Best, BR 1. Edwards AWF (1992) Likelihood - An Account of the Statistical Concept of Likelihood and Its Application to Scientific Inference. Baltimore, MD: The Johns Hopkins University Press. 2. Jeffreys H (1973) Scientific Inference. Cambridge: Cambridge University Press. 3. Sivia DS (1996) Data Analysis - A Bayesian Tutorial. Oxford, UK: Oxford University Press. - Bernhard Hieronimus Rupp, Hofkristallrat a.D. 001 (925) 209-7429 +43 (676) 571-0536 b...@ruppweb.org hofkristall...@gmail.com http://www.ruppweb.org/ -- Knowledge: When you know a thing, to know that you know it, and when you do not know a thing, to recognize that you do not know it. Conficius. --
Re: [ccp4bb] Could someone can help me to explain why EDTA-2Na can formate salt crystals
The pH is too low and the EDTA is insoluble. You need to be above pH ~8.0. Your best bet is to try another chelator. James On Feb 21, 2011, at 2:22 PM, Yibin Lin wrote: Dear all, I got a lot of salt crystals in reservior solution (well solution), which contains 0.1 M phosphate/citrate ph 4.2, PEG200 47%, EDTA-2Na 0-22mM. Reservior solution appears crystals from 12mM EDTA. Could someone help me to explain why? Thank you very much! Yibin
