Re: [ccp4bb] phaser oprn error
You may have called the version of phaser installed in the phenix path. Type wich phaser in a terminal to check it. Daniel yang li a écrit : Hi: I am using CCP4 6.0.2, it has phaser contained in this package. When I use it to do mr, error occured: * *** Phaser Module: READ DATA FROM MTZ FILE2.0 *** * - FILE OPENING ERROR: "/home/work/MR/mader/mad_peak.mtz" - EXIT STATUS: FAILURE I donnot know what is wrong with the mtz file, it is simply converted from a sca file with scalepack2mtz, and now I am using molrep, it didnot give such wrong information. What is the problem? Thanks! Li Yang
Re: [ccp4bb] Nature policy update regarding source code
In any case, does Nature Methods actually publish any papers that fall into the category (quote) "custom-designed software necessary for the method's implementation" where "a software program is the focus of the report", at least in the area of macromolecular structure determination? Come to that, are its sister journals Nature or even Nature Structural & Molecular Biology well-known for publishing such papers, and is this the reason that there is not the same requirement for them? Recently we were looking for a journal to publish precisely such a paper and on looking at the "Aims and scope of journal" (http://www.nature.com/nmeth/authors/index.html) we saw "Biomolecular structural analysis technologies, including NMR and crystallography", but then looking through the past issues we couldn't find any papers remotely similar to ours so it was way down the list of options. There is actually no absolute requirement by Nature Methods that the software be Open Source, quote "The guiding principle is that enough information must be provided so that users can reproduce the procedure and use the method in their own research at reasonable cost." and that closed-source software "may be acceptable if the operations performed by the software are sufficiently clear.". If however "the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it" then "releasing the code may not be a requirement for publication". Actually I would be rather more concerned with the statement: "a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available to readers promptly on request". "Materials" would appear to include purified and crystallised protein, at least they aren't specifically excluded, so does this really mean I'm obliged to give the 10mg of pure protein that has taken me 6 months to isolate to anyone that asks for it, even though I'm apparently allowed to charge "reasonable" costs (presumably in this case 6 months salary + overheads + all materials used). Even so, losing all my protein in this way would be a major set-back to my research program! I concede this is an extreme example but where does one draw the line? Cheers -- Ian > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Nadir T. Mrabet > Sent: 23 March 2007 18:57 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Nature policy update regarding source code > > Hi, > > I believe such requirements concern only "Nature Methods" rather than > "Nature" by and large. > Regards, > > Nadir Mrabet > > Pr. Nadir T. Mrabet > Cellular & Molecular Biochemistry > INSERM U-724 > UHP - Nancy 1, School of Medicine > Avenue de la Foret de Haye, BP 184 > 54505 Vandoeuvre-les-Nancy Cedex > France > Phone: +33 (0)3.83.68.32.73 > Fax: +33 (0)3.83.68.32.79 > E-mail: [EMAIL PROTECTED] > > > > [EMAIL PROTECTED] wrote: > > I thought that some of you might be interested that the > journal Nature > > has clarified the publication requirements regarding source code > > accessibility. It is likely that some of you deserve congrats > > for this. Cheers! > > > > http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html > > > > Although there are still some small problems, I think that this is a > > big step forward, and certainly an interesting read, if you are > > interested in FOSS and science. > > > > Regards, > > Michael L. Love Ph.D > > Department of Biophysics and Biophysical Chemistry > > School of Medicine > > Johns Hopkins University > > 725 N. Wolfe Street > > Room 608B WBSB > > Baltimore MD 21205-2185 > > > > Interoffice Mail: 608B WBSB, SoM > > > > office: 410-614-2267 > > lab:410-614-3179 > > fax:410-502-6910 > > cell: 443-824-3451 > > http://www.gnu-darwin.org/ > > > > > > > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therape
Re: [ccp4bb] Solving a structure by MR with a pseudo-translation vector
These structures are horrible.. Remember you do not know your spacegroup. Absences along 0k0 and 00l will be very influenced by the translation. Sp you need to test all: P21 2 2 P21 21 2P21 2 21 P21 21 21 Run MOLREP using the pseudo translation vector - it is an option in the GUI under search parameters. There wont be a clear distinction of course because they are all going to be almost equivalent but maybe there will be a marginal difference.. The features of the data you describe are the consequence of this translation.. Eleanor Peter J Stogios wrote: Hello, I posted a message about this a month ago and thanks to everyone for their responses. At the time, I did not fully appreciate the problem I was dealing with so this time my question is much more specific. I would very much appreciate your help as this structure is turning out to be very difficult to solve! I am trying to solve a structure by MR that should be easy, given that I have solved multiple structures of homologous proteins by the same means. This crystal is 2.6 angstrom, apparently P212121, with two molecules in the asymmetric unit that are related by the pseudo-translation vector (0, 0.47, 0.5). This vector was identified from the Patterson map, it is a peak 45% the height of the origin peak. As well, I have looked at all the reflection parity groups. Based on I/sigmaI values output by Truncate, the k+l = 2n reflections are as high as 2-fold greater in I/sigI vs. k+l = 2n+1 reflections from 16 to 5.1 angstrom. From 5.1 to 2.9 angstrom, the reverse is true: the k+l = 2n reflections are as high as 0.62-fold LOWER in I/sigI vs. k+l = 2n+1. Then, from 2.9 to 2.6 angstrom, each reflection class is approximately equal in intensity. MR using Molrep's multi-copy search, using all reflections, consistently reproduces the pseudo-translation vector as the dyad vector between the two molecules. However, these solutions are not easily noticeable (Molrep just picks the highest score but this score does not stick out from the pack), and these solutions do not refine well via rigid body or restrained refinement in Refmac. I have found some papers that show successful structure determinations by MR with pseudo-translation, but I am not sure which approach to take to solve my structure. Do I need to remove the pseudo-weak or pseudo-strong reflections? Or do I actually use the pseudo-weak or pseudo-strong reflections for the MR since they will contain the information from the pseudo-translation? Which reflections should I refine against? Should I reindex to C222 to reflect the pseudo-face centering from the (0, 0.47, 0.5) vector? Or am I missing something completely? Any help would be very very much appreciated Thanks! Peter ~ Peter J Stogios Ph.D. candidate, Privé Lab Dept. of Medical Biophysics, University of Toronto Toronto Medical Discoveries Tower (TMDT) at MaRS 101 College St., Rm. 4-308 Toronto, Ontario M5G 1L7 e: [EMAIL PROTECTED] w: http://xtal.uhnres.utoronto.ca/prive p: (416) 581-7543
Re: [ccp4bb] Highest shell standards
On Fri, 23 Mar 2007, Edward Berry wrote: > I believe fft does not by default do this- only if you use the "fillin" > keyword? One place where it might be important is in density > modification/ molecular averaging. Molecular averaging can be seen > as a numerical solution of the MR equations, finding a density map > which (A) obeys the NCS/intercrystal symmetry and (B) yields the > observed F's upon Fourier transformation. Now if on each cycle > you set the missing F's to zero, you are requiring it to have > as part of (B) zero amplitude for the missing reflections, which is > more restrictive and incorrect. If instead you allow the missing F's > to "float", calculating them on each cycle from the previous map > using the fillin option, someone has shown (don't have the > reference handy at the moment) that the F's tend toward the true F's > (in the case that they weren't really missing but omitted as part > of the test). > > Ed You have phase scatter plots in Acta Cryst. D51, 575-589 (1995) that show just that: the map inversion phases from NCS averaging tend toward the true phases. Since F's are phased quantities and since phases are more important than amplitudes, non random amplitudes plus non random phases (both from map inversion of averaged maps) lead to better electron density maps. Fred. -- Fred. Vellieux, esq. = IBS J.-P. Ebel CEA CNRS UJF / LBM 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 =
Re: [ccp4bb] Inclusion body
We have tried them and had them work for a few proteins that didn't look hopeful other ways. The chaperones express well and obviously by gel and, in fact, we had one protein that was difficult to separate from the Cpn60. We very carefully follow the instructions on induction that come with the cells (they are a little odd) and do the expression at 10°C. We have added the ArcticExpress into our standard list of things to try for rescuing insoluble proteins. We just started testing it out a few weeks ago and it hasn't saved all of problem proteins by any means. I don't have the numbers right now, but I think we got something like 3 of 10 that looked insoluble at 15°C in BL21. Best of luck, Cynthia On Mar 24, 2007, at 9:51 AM, Hongmin Li wrote: Hi Weijun and all, Anyone tried the Stratagene's ArcticExpress™ Competent Cells for expression of proteins at low temperature (13 degree). The company claims that the cells encode chaperonins Cpn60 and Cpn10 and they can enhance the protein folding and solubility. Hongmin >Dear All, >I got enclusion body in many cases when I tried to express human >proteins in E coli. I would like some suggestions on how to go about >it. I would also like to try co-expression of GroEL/GroES or >DnaJ/DnaK, and would like to know where to get the plasmids. >Any help or comments would be appreciated. >Weijun Cynthia Kinsland, Ph.D. Cornell University Protein Facility Director 607-255-8844
Re: [ccp4bb] Nature policy update regarding source code
Hi, >From a very narrow point of view of a crystallographer/protein expressionist, this is an overkill. Obviously if you're dealing with articles in materials science, physics, etc. - not everything is as simple as getting some DNA. Generally speaking, if someone wants to reproduce nearly any crystallographic results all they need is the source DNA in whatever form. An obvious exception to that would be the case where the protein is purified from a natural source. Special cases excluded; cloning, expression, purification and so forth should be reproducible from source DNA onward. In fact, with the advent and proliferation of synthetic DNA even that requirement is not really all that important - all you need is the sequence, provided that the 'materials and methods' section of the work is well written and no significant details are omitted. The latter is (in my experience) the more common problem than the availability of sarting materials. It is very hard to include absolutely everything into the Materials and Methods. At least half of the published protocols we've reproduced required very significant investment of effort to get right (sometimes even changing expression systems from what's reported). The end point is clear - the crystal structures DO reproduce quite faithfully even if extra work has to be done to get there. For many industrial scientists the following sentence is basically the end of the road as far as publication is concerned: "One preferred form of disclosure is a link from the methods section to a copy of the relevant Material Transfer Agreement (MTA) form, which is hosted as Supplementary Information on the journal's web site." Pharma/biotech companies are typically very reluctant to make blanket provisions of this kind. Are the journals trying to exclude industrial submissions? Artem
Re: [ccp4bb] Nature policy update regarding source code
It seems to me to be important in this context to draw the distinction between _software_ which is about the most ephemeral thing I can think of (OK maybe butterflies are more so) - e.g. try compiling code published > 5 years ago - and _algorithms_ which if well constructed are potentially everlasting (how many programmers still use Knuth's data structure & sorting algorithms?). One assumes that the only lasting commitment of the author is to supply the version of the code _as_it_was_ when the paper was published (for the purpose of replicating the results in the paper), he's not committed to maintaining the program so that it's still guaranteed to work _now_ (but may well not replicate the results), i.e. he's not committed to supplying updates for ever! So unless of course the code was designated Open Source and kept maintained by the community, the old code may not be much use to anyone for very long without the programming expertise needed to adapt it to new versions of OS's etc. But note that Nature Methods doesn't stipulate that the code must be Open Source, only that the code or executable is made "available to readers promptly on request". The problem is that the important features of an algorithm tend to get obscured by the nitty-gritty details of its implementation in code. On the other hand, even a programmer who knows nothing about the underlying science should be able to code a well-written algorithm using whatever is the language flavour-of-the-day. So it seems to me that it's just as important to establish good algorithmic standards in order to ensure that the methodology is completely and correctly expressed in the published algorithm, as it is to enforce software availability. Cheers -- Ian > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Nat Echols > Sent: 26 March 2007 00:12 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Nature policy update regarding source code > > > I thought that some of you might be interested that the > journal Nature > > has clarified the publication requirements regarding source code > > accessibility. It is likely that some of you deserve congrats > > for this. Cheers! > > > > http://www.nature.com/nmeth/journal/v4/n3/full/nmeth0307-189.html > > > > Although there are still some small problems, I think that this is a > > big step forward, and certainly an interesting read, if you are > > interested in FOSS and science. > > Any chance of getting the IUCR to implement some policy like > this? (Or > the public funding agencies?) > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Highest shell standards
You are probably referring to the following works: Caliandro et al, Acta Cryst. D61 (2005) 556-565 and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087 in which they used density modification to calculate phases for unmeasured reflections, and used the phases to extend the resolution by calculating rough estimates unmeasured amplitudes. Using this technique they actually could improve the electron density. If I'm not mistaken, George Sheldrick has implemented this "Free Lunch" algorithm in SHELXE. /Michel On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote: > If instead you allow the missing F's > to "float", calculating them on each cycle from the previous map > using the fillin option, someone has shown (don't have the > reference handy at the moment) that the F's tend toward the true F's > (in the case that they weren't really missing but omitted as part > of the test). > > Ed
[ccp4bb] SHARP question
Hi all, I am a first time SHARP user. I have it installed on SUse 10.0 OS and configured to ccp4-6.0.2. I do not see the option for inputting known phase information from my .mtz file on the "Global" page, even if the mtz file has the Hendrickson-Lattman coefficients. Also, in the "Phase improvement panel", for Density Modification, only "solvent fraction" and "including available partial Model" options are active. I was assuming that the defaults would be used. So even though "starting DM run/" is set to "no", DM runs anyway, outputting Fdm, Phidm, HL..dm etc. Is it mandatory that the program be configured to ccp4 version 5? Is this an installation problem? Appreciate any help. Thank. Arti Pandey Chemistry & Biochemistry Montana State University Bozeman MT 59715
Re: [ccp4bb] Highest shell standards
Actually I was thinking of a somewhat earlier paper: Rayment,I. Molecular relacement method at low resolution: optimum strategy and intrinsic limitations as determined by calculations on icosahedral virus models. Acta Crystallogr. A 39, 102 116 (1983). But thanks for bringing the Caliandro et al. paper to my attention. Thanks also to Fred. Vellieux for his comments, and to Pete Dunton for explaining to me that while fft doesn't do fillin by default, the 2MFo-DFc map coefficients from refmac5 do have fillin values for the missing reflection, making model bias a problem when many missing residues are included. Now I understand Petrus's question. Ed Michel Fodje wrote: You are probably referring to the following works: Caliandro et al, Acta Cryst. D61 (2005) 556-565 and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087 in which they used density modification to calculate phases for unmeasured reflections, and used the phases to extend the resolution by calculating rough estimates unmeasured amplitudes. Using this technique they actually could improve the electron density. If I'm not mistaken, George Sheldrick has implemented this "Free Lunch" algorithm in SHELXE. /Michel On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote: If instead you allow the missing F's to "float", calculating them on each cycle from the previous map using the fillin option, someone has shown (don't have the reference handy at the moment) that the F's tend toward the true F's (in the case that they weren't really missing but omitted as part of the test). Ed
Re: [ccp4bb] Highest shell standards -oops-
-oops- many missing REFLECTIONS are included.
Re: [ccp4bb] SHARP question
Hello Arti, To be able to input external phases as HL you have to set the "User level" in the "Preferences" to "Advanced" or "Expert". I think that also changes the options you have in the "phase improvement panel". Sabine Sabine Schneider School of Pharmacy and Centre for Biomolecular Sciences Clifton Boulevard University of Nottingham NG7 2RD Phone: +44 115 8468009 Fax: +44 115 8468002 > -Original Message- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > [EMAIL PROTECTED] > Sent: 26 March 2007 19:09 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] SHARP question > > Hi all, > I am a first time SHARP user. I have it installed on SUse 10.0 OS and > configured to ccp4-6.0.2. I do not see the option for inputting known > phase information from my .mtz file on the "Global" page, even if the mtz > file has the Hendrickson-Lattman coefficients. Also, in the "Phase > improvement panel", for Density Modification, only "solvent fraction" and > "including available partial Model" options are active. I was assuming > that the defaults would be used. So even though "starting DM run/" is set > to "no", DM runs anyway, outputting Fdm, Phidm, HL..dm etc. > Is it mandatory that the program be configured to ccp4 version 5? > Is this an installation problem? > Appreciate any help. > Thank. > Arti Pandey > Chemistry & Biochemistry > Montana State University > Bozeman MT 59715 This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Re: [ccp4bb] Highest shell standards
Isn't automatically included fabricated data for missing reflections a really bad idea for anisotropic data where most reflections are "missing" at high resolution? Shouldn't there be a big flashing red flag alerting the user to what's been done? Phoebe At 01:22 PM 3/26/2007, Edward A. Berry wrote: Actually I was thinking of a somewhat earlier paper: Rayment,I. Molecular relacement method at low resolution: optimum strategy and intrinsic limitations as determined by calculations on icosahedral virus models. Acta Crystallogr. A 39, 102 116 (1983). But thanks for bringing the Caliandro et al. paper to my attention. Thanks also to Fred. Vellieux for his comments, and to Pete Dunton for explaining to me that while fft doesn't do fillin by default, the 2MFo-DFc map coefficients from refmac5 do have fillin values for the missing reflection, making model bias a problem when many missing residues are included. Now I understand Petrus's question. Ed Michel Fodje wrote: You are probably referring to the following works: Caliandro et al, Acta Cryst. D61 (2005) 556-565 and Caliandro et al, Acta Cryst. D61 (2005) 1080-1087 in which they used density modification to calculate phases for unmeasured reflections, and used the phases to extend the resolution by calculating rough estimates unmeasured amplitudes. Using this technique they actually could improve the electron density. If I'm not mistaken, George Sheldrick has implemented this "Free Lunch" algorithm in SHELXE. /Michel On Fri, 2007-03-23 at 08:05 -0800, Edward Berry wrote: If instead you allow the missing F's to "float", calculating them on each cycle from the previous map using the fillin option, someone has shown (don't have the reference handy at the moment) that the F's tend toward the true F's (in the case that they weren't really missing but omitted as part of the test). Ed --- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/index.html http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
[ccp4bb] phaser in ccp46.0.2
Hi, Anyone has used phser in ccp46.0.2 which is automatically installed with ccp4? In previous ccp4 edition I installed phaser seperately and it worked well, but now it seems has some problems, it cannot read the input mtz file, I tried several data, all gave the same error information like below: * *** Phaser Module: READ DATA FROM MTZ FILE2.0 *** * --- FILE OPENING ERROR: "/root/work/1she/1she.mtz" --- EXIT STATUS: FAILURE I donnot think all these data are bad, and these data can be read in other mr programs. I wonder if I should install phaser again? The phaser install package for CCP4-5.0 still can be used in this edition? Thanks!
Re: [ccp4bb] phaser in ccp46.0.2
Hi, You are almost certainly not using phaser that came with ccp4, but some other version, e.g. phenix. From the window you start ccp4i from, type 'which phaser'. It should say '/your/path/to/ccp4-6.0.2/bin/phaser', but it will say something different in your case (e.g. '/your/path/to/phenix/bin/phaser'). Make sure your path variable has CBIN before the path of the other phenix-path, or rename the phenix-version if you do not use it. Probably the best way would be to start up ccp4i from a script that sources the ccp4i environment first and then starts ccp4i - that way your environment settings do not affect the other programs (would that be a suggestion to the ccp4-developers?) so create a script saying something like #!/bin/sh source /your/path/to/ccp4-6.0.2/include/ccp4.setup exec ccp4i and make sure ccp4.setup puts CBIN first in the PATH variable. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Tue, 27 Mar 2007, yang li wrote: Hi, Anyone has used phser in ccp46.0.2 which is automatically installed with ccp4? In previous ccp4 edition I installed phaser seperately and it worked well, but now it seems has some problems, it cannot read the input mtz file, I tried several data, all gave the same error information like below: * *** Phaser Module: READ DATA FROM MTZ FILE2.0 *** * --- FILE OPENING ERROR: "/root/work/1she/1she.mtz" --- EXIT STATUS: FAILURE I donnot think all these data are bad, and these data can be read in other mr programs. I wonder if I should install phaser again? The phaser install package for CCP4-5.0 still can be used in this edition? Thanks!
