[ccp4bb] anomalous difference fourier
I suppose I should have expected this, but I still was led astray.. Ir atom - strong anomalous signal.. Good peak in anom diff fourier phased from protein. So I add it to the model with occ = 1.00 and refine.. The B factor is very high and it seems clear that the occupancy should be <<1.0 And one side effect is that now the anomalous difference fourier has a large HOLE where I have placed the Ir. Hmmm. Eleanor
Re: [ccp4bb] anomalous difference fourier maps
Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] anomalous difference fourier maps
Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk. Am 19.02.10 15:04, schrieb Gerard Bricogne: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] anomalous difference fourier maps
Hi Dirk, When it happens that I reply to a ccp4bb message and that the answer, or solution I may have (which I think is better or more appropriate) involves using non-ccp4 programs, I do it off-list. By replying privately to the person who asked the question. Fred. Dirk Kostrewa wrote: Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk.
Re: [ccp4bb] anomalous difference fourier maps
I am inclined to agree with Gerard. Of course if there is a specific question to CCP4bb about SHELX, I try to answer it. Since I am too lazy to maintain my own bb, this is very convenient. However I have stopped 'poaching', for example for the thread in question I resisted the temptation to point out that SHELXE has a convenient way of making such anomalous maps, because that would not have been a direct answer to the question and CCP4 provides similar facilities (and SHARP would be even better). We use the CCP4 programs (especially REFMAC and COOT) extensively and are very grateful for all the support we get. In particular, we should not underestimate the unique role CCP4bb plays in crystallographic education. 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 On Fri, 19 Feb 2010, Gerard Bricogne wrote: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * *
Re: [ccp4bb] anomalous difference fourier maps
The guidelines for the CCP4BB are extremely broad and certainly include discussion of other software packages. Since the original poster's question had to do with a specific problem with CCP4, it would have been appropriate for Pavel to prefix his reply with something like I hope you receive an answer to your question shortly, but in the meantime here is an alternative. But this is a nicety I would be glad to forgo for the sake of getting the extra information. The problem is not that the phenix team was so quick to promote their software, but rather that now 14 hours after the original post, no one has answered the CCP4 question. It is too easy to say yes, I think I could help this guy, but half the readers of this BB could probably give a better answer. Maybe someone at CCP4 should be assigned to answer all reasonable queries that go unanswered for more than 8 hours. The phenomenal rise in popularity of the phenix package is probably due as much to the incredible responsiveness of the phenix team, not only in support but in adding requested features, as it is to the power and ease of use of the programs. Vellieux Frederic wrote: Hi Dirk, When it happens that I reply to a ccp4bb message and that the answer, or solution I may have (which I think is better or more appropriate) involves using non-ccp4 programs, I do it off-list. By replying privately to the person who asked the question. Fred. Dirk Kostrewa wrote: Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk.
Re: [ccp4bb] anomalous difference fourier maps
On Fri, 2010-02-19 at 10:37 -0500, Edward A. Berry wrote: The problem is not that the phenix team was so quick to promote their software, but rather that now 14 hours after the original post, no one has answered the CCP4 question. The original poster returned to indicate that he had received multiple responses. I gather that he received them off-board. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] anomalous difference fourier maps, or how to keep chastity of CCP4BB
I guess Phenix people are just trying to help. After all they are not selling us Zinger sewing machines (zin...@sewing CO, my apology) nor they are trying to push us Kirby (http://www.consumeraffairs.com/in_home/kirby.htm, no apology) vacuum cleaners using naive chastity of CCP4BB site. They are a bunch of young dynamic people, all of them excellent crystallographers, who are participate in evolution of the alternative tool for crystallographic calculations with already possess visible nice features. They trespass borders of CCP4BB quite frequently, but for that they don't have to be prosecuted. However CCP4BB subscribers can start discussion about implementation of chastity belt (see Wiki site http://en.wikipedia.org/wiki/Chastity_belt for explanation of chastity belt metaphor) for prevention of CCP4BB abuse. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972 3640 8723 Fax: ++972 3640 9407 Cellular: ++972 547 459 608 On Feb 19, 2010, at 16:04 , Gerard Bricogne wrote: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan -- === * * * Gerard Bricogne
Re: [ccp4bb] anomalous difference fourier maps
ok I think I should say something here.For some reason I was unable to find REPLY-ALL button and my reply did not go to everyone first so I had to write another message.I got the answer to my original query and I used CCP4 (CAD) and coot as suggested by Jan. Having said that I did not know that you could do it in so many ways. and that is perhaps the most valuable thing!!! Thanks all of you for your replies and I think the best thing of this forum is to be able to get answers when you do not have anyone in the lab to guide you. People like us need you guys the most. Irrespective of whether it is ccp4bb or phenix or any other program, the goal is to share the knowledge and help the less experienced (less fortunate) with your vast expertise, so that people can enjoy doing exciting crystallography related research. Thanks to everyone, Ivan On Fri, Feb 19, 2010 at 7:37 AM, Edward A. Berry ber...@upstate.edu wrote: The guidelines for the CCP4BB are extremely broad and certainly include discussion of other software packages. Since the original poster's question had to do with a specific problem with CCP4, it would have been appropriate for Pavel to prefix his reply with something like I hope you receive an answer to your question shortly, but in the meantime here is an alternative. But this is a nicety I would be glad to forgo for the sake of getting the extra information. The problem is not that the phenix team was so quick to promote their software, but rather that now 14 hours after the original post, no one has answered the CCP4 question. It is too easy to say yes, I think I could help this guy, but half the readers of this BB could probably give a better answer. Maybe someone at CCP4 should be assigned to answer all reasonable queries that go unanswered for more than 8 hours. The phenomenal rise in popularity of the phenix package is probably due as much to the incredible responsiveness of the phenix team, not only in support but in adding requested features, as it is to the power and ease of use of the programs. Vellieux Frederic wrote: Hi Dirk, When it happens that I reply to a ccp4bb message and that the answer, or solution I may have (which I think is better or more appropriate) involves using non-ccp4 programs, I do it off-list. By replying privately to the person who asked the question. Fred. Dirk Kostrewa wrote: Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk.
Re: [ccp4bb] anomalous difference fourier maps
I guess it is a BB hosted by CCP4, but I think it serves a much wider community of structural biologists, and it is valuable for that community that there are suggestions about how to solve problems using SHELX, or BUSTER or PHENIX software.. Certainly I learn new tricks. So speaking as a CCP4 contributer lets keep it as broad based as possible. Maybe we should subscribe to the PHENIX BB and suggest alternative solutions there! Eleanor Dodson George M. Sheldrick wrote: I am inclined to agree with Gerard. Of course if there is a specific question to CCP4bb about SHELX, I try to answer it. Since I am too lazy to maintain my own bb, this is very convenient. However I have stopped 'poaching', for example for the thread in question I resisted the temptation to point out that SHELXE has a convenient way of making such anomalous maps, because that would not have been a direct answer to the question and CCP4 provides similar facilities (and SHARP would be even better). We use the CCP4 programs (especially REFMAC and COOT) extensively and are very grateful for all the support we get. In particular, we should not underestimate the unique role CCP4bb plays in crystallographic education. 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 On Fri, 19 Feb 2010, Gerard Bricogne wrote: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan --
Re: [ccp4bb] anomalous difference fourier maps
Dear Ivan, It is great to have confirmation that you got answers to your initial question that enabled you to solve your problem. The idea of the BB is that, in exchange for the gift of other people's contribution to solving your problem, you are expected to share the solution with the other subscribers. If you look through the archives, you will see numerous cases when people who received contributions, either as replies to the BB or in messages sent to them off-board, then took the trouble to collect them into a message to the BB as a whole, so that everyone learned something. It would be really good if you could do the same with the answers you got. I think I will bow out of this thread by retracting any churlish content in my previous posting. I felt it was not quite satisfactory that a question asked in terms of CCP4 programs should only leave a Phenix-based solution as a written trace - but avoiding this takes some work from the beneficiaries of the answers and not just a modicum of tact from the repliers in answering the questions that are actually being asked. Of course, any broadening of subject matter beyond the initial specific question asked is a wonderful thing to see happen in any scientific forum; but this was not at all the case in this particular instance. With best wishes, Gerard. -- On Fri, Feb 19, 2010 at 08:13:26AM -0800, xaravich ivan wrote: ok I think I should say something here.For some reason I was unable to find REPLY-ALL button and my reply did not go to everyone first so I had to write another message.I got the answer to my original query and I used CCP4 (CAD) and coot as suggested by Jan. Having said that I did not know that you could do it in so many ways. and that is perhaps the most valuable thing!!! Thanks all of you for your replies and I think the best thing of this forum is to be able to get answers when you do not have anyone in the lab to guide you. People like us need you guys the most. Irrespective of whether it is ccp4bb or phenix or any other program, the goal is to share the knowledge and help the less experienced (less fortunate) with your vast expertise, so that people can enjoy doing exciting crystallography related research. Thanks to everyone, Ivan On Fri, Feb 19, 2010 at 7:37 AM, Edward A. Berry ber...@upstate.edu wrote: The guidelines for the CCP4BB are extremely broad and certainly include discussion of other software packages. Since the original poster's question had to do with a specific problem with CCP4, it would have been appropriate for Pavel to prefix his reply with something like I hope you receive an answer to your question shortly, but in the meantime here is an alternative. But this is a nicety I would be glad to forgo for the sake of getting the extra information. The problem is not that the phenix team was so quick to promote their software, but rather that now 14 hours after the original post, no one has answered the CCP4 question. It is too easy to say yes, I think I could help this guy, but half the readers of this BB could probably give a better answer. Maybe someone at CCP4 should be assigned to answer all reasonable queries that go unanswered for more than 8 hours. The phenomenal rise in popularity of the phenix package is probably due as much to the incredible responsiveness of the phenix team, not only in support but in adding requested features, as it is to the power and ease of use of the programs. Vellieux Frederic wrote: Hi Dirk, When it happens that I reply to a ccp4bb message and that the answer, or solution I may have (which I think is better or more appropriate) involves using non-ccp4 programs, I do it off-list. By replying privately to the person who asked the question. Fred. Dirk Kostrewa wrote: Dear Gerard, I can only agree with you - I've also noticed a growing and sometimes irritating cross-advertisement of non-CCP4 programs on the CCP4BB over the last months (mainly Phenix). Unless, the specific task that was asked for, can only be (reasonably) solved with non-CCP4 programs, such replies leave a somewhat bad aftertaste. Personally, I think, it would be perfectly acceptable if both solutions with CCP4 programs and other programs would be given, so that the user may choose, or try them all. Best wishes, Dirk.
[ccp4bb] Fwd: [ccp4bb] anomalous difference fourier maps
Begin forwarded message: From: Charles W. Carter, Jr car...@med.unc.edu Date: February 19, 2010 10:28:55 AM EST To: George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de Subject: Re: [ccp4bb] anomalous difference fourier maps I'm also inclined to join this discussion. I agree with both Gérard and George. I also sympathize with Ivan. Over the years, I've used Bijvoet Difference Fouriers for many purposes, and every time I attempt to calculate one with CCP4 programs, I must spend an inordinate amount of time experimenting to find the commands that give the result I expect. Often I've kept a toy problem to ensure that I was doing it right. It has always been extremely aggravating, and several times I've had to resort to personal appeals to Eleanor to help me out. It should not have been so obscure, and if it remains so, then shame on CCP4! I also share Gérard's nostalgia for the days when virtually all crystallographers had first-hand experience with such questions. The enterprise has grown exponentially since then by the inclusion of increasing numbers of people from other fields who can take advantage of the institutionalization of computing software, pioneered by the CCP4, to extend structural biology into realms that were only dreams two decades ago. Both Gérard and George played pivotal roles in that transformation while I did not. Nonetheless, I sympathize with their explicit and implicit sentiments and remind others of two excellent papers describing this important method: Blow, DM (2003) How Bijvoet Made the Difference. Methods in Enzymology 374, Chapter 1. 3-22. Roach, Jeffrey (2003) The Bijvoet Difference Fourier Synthesis. Methods in Enzymology 374, Chapter 6. 137-145. Charlie On Feb 19, 2010, at 9:57 AM, George M. Sheldrick wrote: I am inclined to agree with Gerard. Of course if there is a specific question to CCP4bb about SHELX, I try to answer it. Since I am too lazy to maintain my own bb, this is very convenient. However I have stopped 'poaching', for example for the thread in question I resisted the temptation to point out that SHELXE has a convenient way of making such anomalous maps, because that would not have been a direct answer to the question and CCP4 provides similar facilities (and SHARP would be even better). We use the CCP4 programs (especially REFMAC and COOT) extensively and are very grateful for all the support we get. In particular, we should not underestimate the unique role CCP4bb plays in crystallographic education. 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 On Fri, 19 Feb 2010, Gerard Bricogne wrote: Dear all, This is a remark I have wanted to make for a long time but managed so far to repress. However, this case is absolutely clear: Ivan was not asking for general advice on how to carry out a general task, but how to perform a specific task with the CCP4 software. In response we get (surprise, surprise, ...) another instance of the relentless touting for Phenix on the CCP4BB, which has long been an expected (or tolerated?) feature of this BB. Contributions from Phenix developers are of course much appreciated when questions are about general crystallographic matters where their expertise and experience is valuable; but when people ask specifically how to do something with CCP4 programs, could they please not be grabbed by the sleeve and enticed to buy their sweets from the shop next door? In this case, for instance, Ivan thanks guys (plural) for the answers he got (All of your suggestions were great). Perhaps one of those was a CCP4-based answer, but if so it has not even been communicated to the rest of the CCP4BB subscribers - so not only is this touting in bad taste after a while: it even interferes with the sharing of expertise in using the CCP4 software, which after all must be one of the main missions of this BB. I have long wondered whether anyone on the CCP4 side been assigned the task of answering every question to the Phenix BB by describing how to do it with CCP4 programs ... . With best wishes, Gerard. -- On Thu, Feb 18, 2010 at 03:53:02PM -0800, Pavel Afonine wrote: Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM
Re: [ccp4bb] anomalous difference fourier maps
Hi Everyone, I hope everyone gets this email. Below are the two answers I got on how to solve my problem using ccp4.I actually emailed another person who wanted to know how I did it. So I got to transfer what I learned immediately. But his email was offline not through the forum. The answers to my queries on how to make an anomalous difference fourier map using CCP4. The first answer is the one that I used, but I am attaching all the answers that I got. 1) Hi Ivan, coot can do that quite nicely. Make sure you have the DANOs in the same file as the phases, else use CAD to merge files. Then 'load mtz', go to 'Expert mode', select DANO as amplitudes, PHWT as phases, unselect 'difference map' and contour at somewhere between 3-5 sigma. 2) Xaravich, Just to clarify you are using: PHI=PHIC (SFALL), DANO=DANO (data), Sigma=SIGDANO (data) and WEIGHT=FOM (SFALL)..to my recollection, you shouldn't be using FCalc.. I've never used SFALL to generate phases. I would use the PHIC from the output mtz of refmac..but I think this is the same thing. All the other steps look correct to me. thanks, Ivan
[ccp4bb] anomalous difference fourier maps
Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan
Re: [ccp4bb] anomalous difference fourier maps
Hi Ivan, two ways (at least) to do it in PHENIX: - phenix.refine always computes anomalous difference Fourier map (provided that your input data file contains Fobs(+) and Fobs(-)). The command below will do it: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=0 output.prefix=maps_only - you can use phenix.maps that is a general tool to compute a broad variety of maps. Type phenix.maps from the command line for usage instructions. You need to have the latest development (or one of) PHENIX nightly build for this. All this is available from the GUI too. Pavel. On 2/18/10 3:34 PM, xaravich ivan wrote: Hello, I wanted to make an anomalous difference fourier map of a structure with zinc bound to it. However I have not been successful in making the map and I would really appreciate your help if anyone could suggest me where I am going wrong. I solved this zinc bound structure, by molecular replacement from a calcium bound structure (1.4 angstrom) that I solved. I want to show that the zinc binds to the identical site by the anomalous difference fourier map. I am using CCP4i and the steps that I have been taking are, (names of the files are arbitrary) 1) generating structure factors and phases from the solved coordinates by SFALL Input files zinc bound pdb original zinc .mtz data from synchrotron output file sfall.mtz 2)merging the sfall.mtz containing the PHICalc and FCalc columns with the original synchrotron .mtz file containing DANO and SIGDANO by running CAD. input files sfall.mtz and zinc synchrtron .mtz output file CAD.mtz 3) Running FFT to make anomalous map, selecting labels from CAD.mtz as input files. There is an output map file but nothing in it. all the values are 0 and the map is not recognized by coot. There is no error message in the log file. I must be missing something or doing something wrong/stupid. Thanks, Ivan
