Re: [ccp4bb] validating ligand density
Hi Srinivasan, I always use edstats from the command line: 'edstats.pl HKLIN 101m_0cyc.mtz XYZIN 101m_0cyc.pdb'. I hadn't noticed it was well-hidden (or the limit case: not present) in CCP4i. I guess a feature request is in order. Cheers, Robbie Date: Wed, 13 Mar 2013 03:42:45 +0800 From: sreera...@yahoo.co.in Subject: Re: [ccp4bb] validating ligand density To: CCP4BB@JISCMAIL.AC.UK Thank you very much to all those who suggested a way out for our situation. We have so far refined the occupancies on phenix and the ligand shows an uniform occupancy of 0.8 post the refinement. The B-factors of the ligand are around 20 (atleast for the regions with a well defined electron density), which is slightly lower than the average B-factors of the whole structure which is 24. We have a few poorly defined regions in our electron density. This was the starting point of our problem and it remains to be a problem. @ Robbie --- we would like to run EDSTAT on CCP4 but we dont find the program in both 6.3.0 and 6.3.1 versions. It would be kind to know if we are doing something wrong to not find it on the ensuite. @ Herman We did add the cryo from the crystallisation condition as another strategy but that also doesnt look too convincing. There is just that enough more to the density to think its our substrate. The density also does not compare well with the apo structures. @ Eleanor We set the occupancies to zero and refined the structure but we did not get any conclusive answers from it. We have a continious density for the best part of the ligand; but as you mentioned a few carbon atoms which are wobbly are poorly defined. We will look carefully into the geometrical restraints as you suggested. Thank you all again for the suggestions!Srinivasan From: Bosch, Juergen jubo...@jhsph.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 12 March 2013 4:32 PM Subject: Re: [ccp4bb] [ccp4bb] validating ligand density Going back to the initial question.I would recommend looking at AFITThttp://www.eyesopen.com/afitt Works like a dream (in certain cases). Jürgen P.S. I wish I had some stocks from them but I don't.. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Mar 12, 2013, at 11:25 AM, herman.schreu...@sanofi.com herman.schreu...@sanofi.com wrote: You are the one who should judge your statement, but it looks plausible to me. Now that I think of it: why do we need referees if every scientist should judge their own hypothesis? Publication will be a lot faster if we no longer need to heed the remarks of some grumpy referees and send in revision after revision. Also the number of publications will increase significantly if every scientist is allowed to judge their own papers! HS From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: Tuesday, March 12, 2013 4:14 PM To: Schreuder, Herman RD/DE Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] validating ligand density Dear Jacob, You are overinterpreting, the statement is about judging, not proving a hypothesis. I am sure Mr. Edwards judged his statement to be ok. I guess there is a good likelihood that you are right, but who am I to judge? JPK Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Tuesday, March 12, 2013 3:44 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] validating ligand density One final quote that is not in the twilight paper summarizes it nicely: The scientist must be the judge of his own hypotheses, not the statistician. A.F.W. Edwards (1992) in Likelihood - An account of the statistical concept of likelihood and its application to scientific inference , p. 34. There must be a lot of thinking behind this statement--while it seems plausible, it seems far from proven prima facie. Also, it assumes that the scientist is not a statistician. Jacob Btw, the book is good reading. Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Tuesday, March 12, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] validating ligand density Dear Srinivasan, Although the Twilight program can only look at deposited PDB entries, the tips about ligand validation in the paper are very useful. I
Re: [ccp4bb] Diffraction data with big rotation angle
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, could you let us know more about what you have already tried? - - use more images, maybe all images for indexing - - try a different program: xds instead of mosflm instead of hkl200 instead of d*trek instead of xds depending what you have tried. - - try to find the unit cell dimensions manually from adxv - - try cell_now with the SPOTS.XDS in XDS I would check the output of IDXREF.LP to figure out if indexing seems possible, i.e. if the input parameters seem stable or if they are just floating around and many more - it depends on the data set, really! Best, Tim On 03/13/2013 09:12 PM, Niu Tou wrote: Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu - -- - -- 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/ iD8DBQFRQZZFUxlJ7aRr7hoRAmr3AKD28Mml3XY2LIWkDknKrkJFToLDvwCgu1DI LDaPuAMfGlEIEObuWcckM7Y= =yuwC -END PGP SIGNATURE-
[ccp4bb] Fwd: RE: [ccp4bb] Diffraction images compression and long-term storage
I forgot to reply to CCP4BB, but this could be interesting not just for Eugene. Dear Eugene, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? -Yes, in Utrecht we do routinely compress images (ncompress). Our data processing software EVAL can read those and decompress on the fly. This works very convient. It depends on the specific image format how efficient the compression is. For a discussion on image compression and data archiving see our paper in Journal of Applied Crystallography, 2013, Volume 46, pages 108-119, http://dx.doi.org/10.1107/__S0021889812044172 http://dx.doi.org/10.1107/S0021889812044172 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ http://bl831.als.lbl.gov/%7Ejamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) -The IUCr has established a Data Depostion Work Group (have a look at http://forums.iucr.org/), that is discussing and trying to establish the possiblities of long-term storage of diffraction images and raw data in general. One of this issues is lossy or lossless data compression. I personally have no experience with lossy data compression. 3)Is there any advice for long-term diffraction image storage? - There is a policy issue to that. How do we get that arranged for diffraction data wordwide? For now, we have to find a way to store our raw data locally. It is certain that every storage system (like USB drives) will fail in the end. So without active conservation on tapes or raid systems, data will eventually get lost. Initiatives to preseve data locally are underway, e.g. example the Manchester University is setting up a data depository for raw scientific data, were all data will be indentified by a DOI. Best wishes, Loes ___ Dr. Loes Kroon-Batenburg Dept. of Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands E-mail : l.m.j.kroon-batenb...@uu.nl phone : +31-30-2532865 fax : +31-30-2533940
[ccp4bb] Diffraction images compression and long-term storage
Many thanks for responses! I will try check and find most convenient for me. 14.03.2013 13:39, Loes Kroon-Batenburg пишет: I forgot to reply to CCP4BB, but this could be interesting not just for Eugene. Dear Eugene, I have a couple of questions about images compression and storage: 1)do someone use it in routine work and does it works well for them? -Yes, in Utrecht we do routinely compress images (ncompress). Our data processing software EVAL can read those and decompress on the fly. This works very convient. It depends on the specific image format how efficient the compression is. For a discussion on image compression and data archiving see our paper in Journal of Applied Crystallography, 2013, Volume 46, pages 108-119, http://dx.doi.org/10.1107/__S0021889812044172 http://dx.doi.org/10.1107/S0021889812044172 2)I found this page by google: http://bl831.als.lbl.gov/~jamesh/lossy_compression/ http://bl831.als.lbl.gov/%7Ejamesh/lossy_compression/ And want to ask about reports of usage of this program (of course if someone already uses it) -The IUCr has established a Data Depostion Work Group (have a look at http://forums.iucr.org/), that is discussing and trying to establish the possiblities of long-term storage of diffraction images and raw data in general. One of this issues is lossy or lossless data compression. I personally have no experience with lossy data compression. 3)Is there any advice for long-term diffraction image storage? - There is a policy issue to that. How do we get that arranged for diffraction data wordwide? For now, we have to find a way to store our raw data locally. It is certain that every storage system (like USB drives) will fail in the end. So without active conservation on tapes or raid systems, data will eventually get lost. Initiatives to preseve data locally are underway, e.g. example the Manchester University is setting up a data depository for raw scientific data, were all data will be indentified by a DOI. Best wishes, Loes ___ Dr. Loes Kroon-Batenburg Dept. of Crystal and Structural Chemistry Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8, 3584 CH Utrecht The Netherlands E-mail : l.m.j.kroon-batenb...@uu.nl phone : +31-30-2532865 fax : +31-30-2533940 -- Eugene Osipov Junior Research Scientist Laboratory of Enzyme Engineering A.N. Bach Institute of Biochemistry Russian Academy of Sciences Leninsky pr. 33, 119071 Moscow, Russia e-mail: e.m.osi...@gmail.com
[ccp4bb] PDBe website update: What's new
Dear all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new and improved tools and services. Our first website update of 2013 features: 1. A new weekly overview of new biology in the PDB 2. Improved searching of EMDB entries with rapid filtering of results 3. New features for visual analysis of EMDB entries 4. Improved pages with chemical-shift-validation information for NMR entries 5. Easy sharing of PDBe pages 1. A new weekly overview of new biology in the PDB. You can now view instances of new biology in the PDB including Pfam families, GO terms and UniProt entries that appear in the archive for the first time. For example, this week's release includes the first structure ever from a member of the Alternative Oxidase Pfam sequence family (http://www.ebi.ac.uk/pdbe/searchResults.html?display=latesttab=xref). Note that two kinds of new biology are shown: cases where an existing Pfam family etc. maps to a newly released structure in the PDB for the first time, and cases where an existing PDB entry maps to a new entry in Pfam, GO, UniProt, CATH or SCOP. 2. Improved searching of EMDB entries with rapid filtering of results. We have made searching the EMDB easier by implementing search filters that enable you to rapidly narrow down the set of search results. Filters based on experimental details, journal, organism etc. can be applied when searching (http://pdbe.org/emsearch) or browsing the contents of the archive (http://pdbe.org/embrowse). 3. New features for visual analysis of EMDB entries. We have introduced several new features to aid visual analysis and validation of EMBD entries, including: * A volume-estimate graph that shows how the enclosed volume of a map varies with the contour level (e.g. http://pdbe.org/emd-5357/analysis). * A Fourier-shell correlation (FSC) curve used to estimate the resolution of single particle maps (e.g. http://pdbe.org/emd-5357/analysis). * A residue-based atom-inclusion chart that can be used to assess the quality of fit of PDB models to an EMDB map (e.g. * http://pdbe.org/emd-2017/analysis). * An image showing the overlay of any deposited masks on a map, that show segmentations or some particular feature of an entry (e.g. http://pdbe.org/emd-1206/analysis). (Note that not all features are available or applicable for all entries.) 4. Improved pages with chemical-shift-validation information for NMR entries. We have improved the presentation of information on the validation of chemical shifts with VASCO. The redesigned webpages now show statistics on the assigned chemical shifts, any referencing corrections and a list of atoms with unusual chemical shifts values (e.g. http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr). 5. Easy sharing of PDBe pages. Regular visitors of the PDBe website may have noticed some small changes to the headers of our pages. The new headers include feedback and sharing buttons on every PDBe webpage. If you want to share what you find on one of our pages with friends or colleagues, use the share button to post the URL on Facebook, Twitter, etc. or to email it. If you have suggestions for improvements, please let us know by using the feedback button. You may also have noticed our new logo. Based on a motif that is found at all levels of structure, we hope that our new logo will quickly become synonymous with the provision of high-quality information about 3D molecular and cellular structure. Our new logo and guidelines for its use are available from our website at http://pdbe.org/logo As always, we welcome your comments and suggestions through the feedback button at the top of every PDBe webpage. Gary. -- Gary Battle Protein Data Bank in Europe (PDBe) http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] PDBe website update: What's new
Ah yes a new logo... But it might be of interest to hear in this forum what has happened to the CCP4 logo that used to appear on the PISA and Fold pages in acknowledgement of the support from the BBSRC on the underlying algorithms for these services. It is only by acknowledgement of the contribution of projects such as CCP4 that we can establish a continuing funding stream for the improvement of scientific software. I distinctly remember that this was acknowledged by the presence of the CCP4 logo on appropriate pages in the old PDBe website. Surely there is still space for that acknowledgement too? Yours perplexedly, Martyn Dr Martyn Symmons Cambridge From: Gary Battle bat...@ebi.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 14 March 2013, 10:27 Subject: [ccp4bb] PDBe website update: What's new Dear all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org) releases new and improved tools and services. Our first website update of 2013 features: 1. A new weekly overview of new biology in the PDB 2. Improved searching of EMDB entries with rapid filtering of results 3. New features for visual analysis of EMDB entries 4. Improved pages with chemical-shift-validation information for NMR entries 5. Easy sharing of PDBe pages 1. A new weekly overview of new biology in the PDB. You can now view instances of new biology in the PDB including Pfam families, GO terms and UniProt entries that appear in the archive for the first time. For example, this week’s release includes the first structure ever from a member of the Alternative Oxidase Pfam sequence family (http://www.ebi.ac.uk/pdbe/searchResults.html?display=latesttab=xref). Note that two kinds of new biology are shown: cases where an existing Pfam family etc. maps to a newly released structure in the PDB for the first time, and cases where an existing PDB entry maps to a new entry in Pfam, GO, UniProt, CATH or SCOP. 2. Improved searching of EMDB entries with rapid filtering of results. We have made searching the EMDB easier by implementing search filters that enable you to rapidly narrow down the set of search results. Filters based on experimental details, journal, organism etc. can be applied when searching (http://pdbe.org/emsearch) or browsing the contents of the archive (http://pdbe.org/embrowse). 3. New features for visual analysis of EMDB entries. We have introduced several new features to aid visual analysis and validation of EMBD entries, including: * A volume-estimate graph that shows how the enclosed volume of a map varies with the contour level (e.g. http://pdbe.org/emd-5357/analysis). * A Fourier-shell correlation (FSC) curve used to estimate the resolution of single particle maps (e.g. http://pdbe.org/emd-5357/analysis). * A residue-based atom-inclusion chart that can be used to assess the quality of fit of PDB models to an EMDB map (e.g. * http://pdbe.org/emd-2017/analysis). * An image showing the overlay of any deposited masks on a map, that show segmentations or some particular feature of an entry (e.g. http://pdbe.org/emd-1206/analysis). (Note that not all features are available or applicable for all entries.) 4. Improved pages with chemical-shift-validation information for NMR entries. We have improved the presentation of information on the validation of chemical shifts with VASCO. The redesigned webpages now show statistics on the assigned chemical shifts, any referencing corrections and a list of atoms with unusual chemical shifts values (e.g. http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr). 5. Easy sharing of PDBe pages. Regular visitors of the PDBe website may have noticed some small changes to the headers of our pages. The new headers include feedback and sharing buttons on every PDBe webpage. If you want to share what you find on one of our pages with friends or colleagues, use the share button to post the URL on Facebook, Twitter, etc. or to email it. If you have suggestions for improvements, please let us know by using the feedback button. You may also have noticed our new logo. Based on a motif that is found at all levels of structure, we hope that our new logo will quickly become synonymous with the provision of high‐quality information about 3D molecular and cellular structure. Our new logo and guidelines for its use are available from our website at http://pdbe.org/logo As always, we welcome your comments and suggestions through the feedback button at the top of every PDBe webpage. Gary. -- Gary Battle Protein Data Bank in Europe (PDBe) http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
Re: [ccp4bb] statistical or systematic? bias or noise?
Ed, no the fact that you don't, can't or won't estimate the precision doesn't change anything (only as you say it becomes a poorly designed experiment). A measurement has a standard deviation regardless of whether you possess an estimate of its value or not. The exact true value of the standard deviation can never be known, just as the true value of any physical quantity can never be known, even after measuring it umpteen times! The measurements are only estimates of the true value, sampled from the error distribution of the true value. The experimental estimate of the standard deviation is called the 'standard uncertainty' (indeed I remember when it was called the 'estimated standard deviation' or e.s.d.), again sampled from the error distribution of the SD. Sometimes I see in the literature the term 'estimated standard uncertainty' but this is a term that does not appear in any literature on statistics (it seems to be peculiar to protein crystallography literature!). Also it would then be the 'estimated estimated standard deviation' which is one more level of estimation that you need (an estimate of an estimate is still an estimate - it just has a bigger uncertainty than the previous estimate!). See http://physics.nist.gov/cgi-bin/cuu/Info/Constants/definitions.html for the terminology approved by NIST. Cheers -- Ian On 13 March 2013 20:36, Ed Pozharski epozh...@umaryland.edu wrote: Ian, On Wed, 2013-03-13 at 19:46 +, Ian Tickle wrote: So I don't see there's a question of wilfully choosing to ignore. or not sampling certain factors: if the experiment is properly calibrated to get the SD estimate you can't ignore it. So perhaps I can explain better by using the same example of protein concentration measurement. It is certainly true that only taking one dilution is poor design. (Although in crystallization practice it may not matter given that it is not imperative to have a protein exactly at 10 mg/ml, 9.7 will do). If I don't bother including pipetting precision in my error estimate either by direct experiment or by using manufacturer's declaration I am willfully ignoring this source of error. That would be wrong. But what if I only have one measurement worth of sample? And pipetting precision cannot be calibrated (I know it can be so this is hypothetical - say pipettor was stolen and company that made it is out of business, their offices burned down by raging mob). Is the pipetting error now systematic because experimental situation (not design) prevents it from being sampled or estimated? I actually like the immutable error type better for my own purposes, but I am trying to see whether some argument might stand that allows some error that can be sampled to be called inaccuracy nonetheless. Cheers and thanks, Ed. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
[ccp4bb] [off-topic] CNS solve profit license
Dear CCP4users biologists, I'm trying to get a CNS solve v1.3 profit license. I don’t know how to contact person who deals with CNS profit license. Could you give the hint for getting the license or authorization for CNS program? Kind regards, Genie Genie 790-784 room 204, Dept of Life Science, POSTECH, san31, Hyoja-dong, Nam-gu, Pohang, Gyungbuk, Korea tel:82-54-279-8627 fax:82-54-279-8111
Re: [ccp4bb] PDBe website update: What's new
Dear Martyn, Numerous external databases, resources and software have contributed significantly to the quality of the PDBe database and its web applications. We gratefully acknowledge all these contributions, including those from CCP4 at: http://www.ebi.ac.uk/pdbe/?tab=aboutussubtab=acknowledgements Note that we also list all current (and past) funders at: http://www.ebi.ac.uk/pdbe/?tab=aboutussubtab=funding Regards, Gary. On 14/03/2013 10:55, MARTYN SYMMONS wrote: Ah yes a new logo... But it might be of interest to hear in this forum what has happened to the CCP4 logo that used to appear on the PISA and Fold pages in acknowledgement of the support from the BBSRC on the underlying algorithms for these services. It is only by acknowledgement of the contribution of projects such as CCP4 that we can establish a continuing funding stream for the improvement of scientific software. I distinctly remember that this was acknowledged by the presence of the CCP4 logo on appropriate pages in the old PDBe website. Surely there is still space for that acknowledgement too? Yours perplexedly, Martyn Dr Martyn Symmons Cambridge *From:* Gary Battle bat...@ebi.ac.uk *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Thursday, 14 March 2013, 10:27 *Subject:* [ccp4bb] PDBe website update: What's new Dear all, Twice a year, the Protein Data Bank in Europe (PDBe; http://pdbe.org http://pdbe.org/) releases new and improved tools and services. Our first website update of 2013 features: 1. A new weekly overview of new biology in the PDB 2. Improved searching of EMDB entries with rapid filtering of results 3. New features for visual analysis of EMDB entries 4. Improved pages with chemical-shift-validation information for NMR entries 5. Easy sharing of PDBe pages 1. A new weekly overview of new biology in the PDB. You can now view instances of new biology in the PDB including Pfam families, GO terms and UniProt entries that appear in the archive for the first time. For example, this week’s release includes the first structure ever from a member of the Alternative Oxidase Pfam sequence family (http://www.ebi.ac.uk/pdbe/searchResults.html?display=latesttab=xref http://www.ebi.ac.uk/pdbe/searchResults.html?display=latesttab=xref). Note that two kinds of new biology are shown: cases where an existing Pfam family etc. maps to a newly released structure in the PDB for the first time, and cases where an existing PDB entry maps to a new entry in Pfam, GO, UniProt, CATH or SCOP. 2. Improved searching of EMDB entries with rapid filtering of results. We have made searching the EMDB easier by implementing search filters that enable you to rapidly narrow down the set of search results. Filters based on experimental details, journal, organism etc. can be applied when searching (http://pdbe.org/emsearch) or browsing the contents of the archive (http://pdbe.org/embrowse). 3. New features for visual analysis of EMDB entries. We have introduced several new features to aid visual analysis and validation of EMBD entries, including: * A volume-estimate graph that shows how the enclosed volume of a map varies with the contour level (e.g. http://pdbe.org/emd-5357/analysis). * A Fourier-shell correlation (FSC) curve used to estimate the resolution of single particle maps (e.g. http://pdbe.org/emd-5357/analysis). * A residue-based atom-inclusion chart that can be used to assess the quality of fit of PDB models to an EMDB map (e.g. * http://pdbe.org/emd-2017/analysis). * An image showing the overlay of any deposited masks on a map, that show segmentations or some particular feature of an entry (e.g. http://pdbe.org/emd-1206/analysis). (Note that not all features are available or applicable for all entries.) 4. Improved pages with chemical-shift-validation information for NMR entries. We have improved the presentation of information on the validation of chemical shifts with VASCO. The redesigned webpages now show statistics on the assigned chemical shifts, any referencing corrections and a list of atoms with unusual chemical shifts values (e.g. http://www.ebi.ac.uk/pdbe-apps/nmr/vasco/searchEntry?pdbCode=2knr). 5. Easy sharing of PDBe pages. Regular visitors of the PDBe website may have noticed some small changes to the headers of our pages. The new headers include feedback and sharing buttons on every PDBe webpage. If you want to share what you find on one of our pages with friends or colleagues, use the share button to post the URL on Facebook, Twitter, etc. or to email it. If you have suggestions for improvements, please let us know by using the feedback button. You may also have noticed our new logo. Based on a motif that is found at all levels of structure, we hope that our new logo will quickly become synonymous with the
[ccp4bb] Last chance - ESS Science Symposium on Neutron Protein Crystallography
Dear All Tomorrow friday the 15th of march is the deadline for registration to ESS Science Symposium on Neutron Protein Crystallography to be held at Aarhus University, Denmark 21-22 March 2013 For more info and registration go to http://www.bioxray.au.dk/essprotein Looking forward to see you in Aarhus. The organisers Ditlev Brodersen, Poul Nissen, Søren Thirup __ Søren Skou Thirup Asc. Professor, Ph.D Centre for Structural Biology Dept. of Molecular Biology, Aarhus University Gustav Wiedsvej 10C, DK 8000 Aarhus C s...@mb.au.dk phone: +45 8715 5464 mob. : +45 2058 5981 fax: +45 8612 3178
Re: [ccp4bb] Diffraction data with big rotation angle
I had a similar situation once where I intentionally collected 5-degree images from a salt crystal. I found this page: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Small_molecules most helpful. Particularly the DELPHI keyword. Thanks to Kay Diederichs for pointing this out to me. -James Holton MAD Scientist On 3/13/2013 1:12 PM, Niu Tou wrote: Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu
[ccp4bb] 4th Edition of the ISBC2013
4th Edition of the ISBC2013 Dear Colleague, The Laboratory of Crystallographic Studies is pleased to announce the 4th International School on Biological Crystallization (ISBC2013), to be held in Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for postgraduate/postdoctoral students and research scientists from industrial and academic backgrounds. The International School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization from solution and their applications to the field of crystallization of biological materials, including biological macromolecules, biominerals and biomimetic materials. One day will be fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes. For more information, please visit http://www.isbcgranada.org/. Best regards, ISBC2103 Organizing Committee
[ccp4bb] indexing/data reduction
Dear colleagues, we have collected 200 degrees worth of oscillation data on a selenomethionine derivative (1 non-terminal methionyl per 120 residues) to 2A resolution. XDS provides the following output: COLLECT.LP LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM DEGREES) CHARACTER LATTICE OF FIT a b c alpha beta gamma * 44aP 0.0 47.9 47.9 171.2 90.1 90.0 119.9 * 31aP 0.4 47.9 47.9 171.2 89.9 90.0 60.1 * 39mC 0.8 83.0 47.9 171.2 90.0 90.1 89.9 * 14mC 2.2 47.9 82.9 171.2 90.0 90.1 90.0 * 34mP 2.3 47.9 171.2 47.9 90.1 119.9 90.0 * 29mC 2.6 47.9 82.9 171.2 90.0 90.1 90.0 * 38oC 2.8 47.9 83.0 171.2 89.9 90.0 90.1 * 10mC 2.8 83.0 47.9 171.2 90.0 90.1 89.9 * 13oC 2.9 47.9 82.9 171.2 90.0 90.1 90.0 * 12hP 3.4 47.9 47.9 171.2 90.1 90.0 119.9 35mP249.9 47.9 47.9 171.2 90.0 90.1 119.9 33mP250.4 47.9 47.9 171.2 90.0 90.1 119.9 32oP251.8 47.9 47.9 171.2 90.1 90.0 119.9 . . . SPACE-GROUP UNIT CELL CONSTANTSUNIQUE Rmeas COMPARED LATTICE- NUMBER a b c alpha beta gamma CHARACTER 5 82.9 48.0 171.3 90.0 90.0 90.0 1303315.336401 10 mC 143 47.9 47.9 171.3 90.0 90.0 120.0837117.441063 12 hP 149 47.9 47.9 171.3 90.0 90.0 120.0449617.044938 12 hP 150 47.9 47.9 171.3 90.0 90.0 120.0472016.844714 12 hP 168 47.9 47.9 171.3 90.0 90.0 120.0425516.945179 12 hP * 177 47.9 47.9 171.3 90.0 90.0 120.0254916.746885 12 hP 21 48.0 82.9 171.3 90.0 90.0 90.0675815.142676 13 oC 5 48.0 82.9 171.3 90.0 90.1 90.0 1275115.836683 14 mC 5 48.0 82.9 171.3 90.0 90.1 90.0 1275115.836683 29 mC 1 47.9 47.9 171.3 89.9 90.0 60.1 24755 9.424679 31 aP 21 47.9 83.0 171.3 90.0 90.0 90.06765 9.242669 38 oC 3 47.9 171.3 47.9 90.0 119.9 90.0 12671 9.636763 34 mP 5 83.0 47.9 171.3 90.0 90.1 90.0 13029 8.936405 39 mC 1 47.9 47.9 171.3 90.1 90.0 119.9 24755 9.424679 44 aP /COLLECT.LP We scaled reflections, with reasonable residuals, assuming space group P622 and have a reasonable solution in P6122. Refinement does not take us past an Rfree of aprrox. 0.4. The apparent quality of the model-phased map varies across the asymmetric unit. The L-test does not indicate merohedral twinning. Translational pseudosymmetry was not detected. Merohedral twinning has been tentatively ruled out. Before considering Order-Disorder-type crystal defects (as reviewed by Andrey Lebedev here: http://www.ysbl.york.ac.uk/mxstat/andrey/ecm2010.pdf), we would like to rule out that we might have erroneously applied too many symmetry constraints. To that end, we have scaled data in C2. We observed anomalous difference fourier peaks corresponding to positions of 6 selenium atoms in the current model, but refinement still does not proceed, and maps look similar to P6122 treatment. To cover all bases we would like to extend the asymmetric unit to P1. And here is the question: Does it suffice to pursue any one of the P1-associated lattices in the XDS table or do both need to be tested? Many thanks as always, Wolfram Tempel
[ccp4bb] RNA 3D structure alignment
Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single aligned structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
Re: [ccp4bb] RNA 3D structure alignment
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Chen, lsqman, lsqkab, and most likely coot should be able to do this. Best, Tim On 03/14/2013 09:53 PM, Chen Zhao wrote: Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single aligned structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen - -- 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/ iD8DBQFRQjrYUxlJ7aRr7hoRArxwAJ4wNRFJWiJ5V4Vfn10yMAS9UrVC7ACfcC8+ Uciknls+q1i8vHKKkYeoDw8= =8Eg+ -END PGP SIGNATURE-
Re: [ccp4bb] RNA 3D structure alignment
Dear Chen, you can find lsqkab and Topp in ccp4 : coordinates utility and superpose molecule (if you use the GUI). Hope to help you. Nicolas Le 14/03/13 21:53, Chen Zhao a écrit : Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single aligned structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
Re: [ccp4bb] indexing/data reduction
I would keep the hexagonal lattice, assuming your integration was OK - no missed spots and then index the data as P1. If the anom Pattersons should then show the correct symmetry - if the Patterson shows P6/mmm symmetry you should be safe in either assigning P6122 or P6522 to the structure SG. Eleanor But actually it should be enough to index and merge as P3 then let the Patterson symmetry suggest the SG. Cant you run pointless on the unmerged data? That gives a useful indication of what symmetry operators are present. Eleanor On 14 Mar 2013, at 20:31, wtempel wrote: Dear colleagues, we have collected 200 degrees worth of oscillation data on a selenomethionine derivative (1 non-terminal methionyl per 120 residues) to 2A resolution. XDS provides the following output: COLLECT.LP LATTICE- BRAVAIS- QUALITY UNIT CELL CONSTANTS (ANGSTROEM DEGREES) CHARACTER LATTICE OF FIT a b c alpha beta gamma * 44aP 0.0 47.9 47.9 171.2 90.1 90.0 119.9 * 31aP 0.4 47.9 47.9 171.2 89.9 90.0 60.1 * 39mC 0.8 83.0 47.9 171.2 90.0 90.1 89.9 * 14mC 2.2 47.9 82.9 171.2 90.0 90.1 90.0 * 34mP 2.3 47.9 171.2 47.9 90.1 119.9 90.0 * 29mC 2.6 47.9 82.9 171.2 90.0 90.1 90.0 * 38oC 2.8 47.9 83.0 171.2 89.9 90.0 90.1 * 10mC 2.8 83.0 47.9 171.2 90.0 90.1 89.9 * 13oC 2.9 47.9 82.9 171.2 90.0 90.1 90.0 * 12hP 3.4 47.9 47.9 171.2 90.1 90.0 119.9 35mP249.9 47.9 47.9 171.2 90.0 90.1 119.9 33mP250.4 47.9 47.9 171.2 90.0 90.1 119.9 32oP251.8 47.9 47.9 171.2 90.1 90.0 119.9 . . . SPACE-GROUP UNIT CELL CONSTANTSUNIQUE Rmeas COMPARED LATTICE- NUMBER a b c alpha beta gamma CHARACTER 5 82.9 48.0 171.3 90.0 90.0 90.0 1303315.336401 10 mC 143 47.9 47.9 171.3 90.0 90.0 120.0837117.441063 12 hP 149 47.9 47.9 171.3 90.0 90.0 120.0449617.044938 12 hP 150 47.9 47.9 171.3 90.0 90.0 120.0472016.844714 12 hP 168 47.9 47.9 171.3 90.0 90.0 120.0425516.945179 12 hP * 177 47.9 47.9 171.3 90.0 90.0 120.0254916.746885 12 hP 21 48.0 82.9 171.3 90.0 90.0 90.0675815.142676 13 oC 5 48.0 82.9 171.3 90.0 90.1 90.0 1275115.836683 14 mC 5 48.0 82.9 171.3 90.0 90.1 90.0 1275115.836683 29 mC 1 47.9 47.9 171.3 89.9 90.0 60.1 24755 9.424679 31 aP 21 47.9 83.0 171.3 90.0 90.0 90.06765 9.242669 38 oC 3 47.9 171.3 47.9 90.0 119.9 90.0 12671 9.636763 34 mP 5 83.0 47.9 171.3 90.0 90.1 90.0 13029 8.936405 39 mC 1 47.9 47.9 171.3 90.1 90.0 119.9 24755 9.424679 44 aP /COLLECT.LP We scaled reflections, with reasonable residuals, assuming space group P622 and have a reasonable solution in P6122. Refinement does not take us past an Rfree of aprrox. 0.4. The apparent quality of the model-phased map varies across the asymmetric unit. The L-test does not indicate merohedral twinning. Translational pseudosymmetry was not detected. Merohedral twinning has been tentatively ruled out. Before considering Order-Disorder-type crystal defects (as reviewed by Andrey Lebedev here: http://www.ysbl.york.ac.uk/mxstat/andrey/ecm2010.pdf), we would like to rule out that we might have erroneously applied too many symmetry constraints. To that end, we have scaled data in C2. We observed anomalous difference fourier peaks corresponding to positions of 6 selenium atoms in the current model, but refinement still does not proceed, and maps look similar to P6122 treatment. To cover all bases we would like to extend the asymmetric unit to P1. And here is the question: Does it suffice to pursue any one of the P1-associated lattices in the XDS table or do both need to be tested? Many thanks as always, Wolfram Tempel
Re: [ccp4bb] Diffraction data with big rotation angle
Hi Tim, I only tried HKL2000, and index with different resolution and different number of images. I am not quite familiar with XDS or d*trek. One thing I am not sure is if this large oscillation angle will cause problem in indexing? If this is true, any method to overcome it? The situation I met was when I chose different settings to do index, HKL2000 would give different cell dimensions while most of them were not small enough for a peptide crystal. The unit cell should be pretty small since even collecting data with 5 degree oscillation angle, the spots in one image were still fewer than a normal protein crystal case, so there is no spots overlap. Best, Yang On Thu, Mar 14, 2013 at 5:20 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, could you let us know more about what you have already tried? - - use more images, maybe all images for indexing - - try a different program: xds instead of mosflm instead of hkl200 instead of d*trek instead of xds depending what you have tried. - - try to find the unit cell dimensions manually from adxv - - try cell_now with the SPOTS.XDS in XDS I would check the output of IDXREF.LP to figure out if indexing seems possible, i.e. if the input parameters seem stable or if they are just floating around and many more - it depends on the data set, really! Best, Tim On 03/13/2013 09:12 PM, Niu Tou wrote: Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu - -- - -- 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/ iD8DBQFRQZZFUxlJ7aRr7hoRAmr3AKD28Mml3XY2LIWkDknKrkJFToLDvwCgu1DI LDaPuAMfGlEIEObuWcckM7Y= =yuwC -END PGP SIGNATURE-
Re: [ccp4bb] Diffraction data with big rotation angle
5 degrees per image may be problematic for some algorithms since the diffraction spots have uncertain positions in three dimensions. Two dimensions will come from the position of the spot on the detector and the position of the detector. The third dimension will come from the rotation angle value of the image which will have a large uncertainty. There are ways around this and d*TREK uses some of them. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Niu Tou [niutou2...@gmail.com] Sent: Thursday, March 14, 2013 6:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Diffraction data with big rotation angle Hi Tim, I only tried HKL2000, and index with different resolution and different number of images. I am not quite familiar with XDS or d*trek. One thing I am not sure is if this large oscillation angle will cause problem in indexing? If this is true, any method to overcome it? The situation I met was when I chose different settings to do index, HKL2000 would give different cell dimensions while most of them were not small enough for a peptide crystal. The unit cell should be pretty small since even collecting data with 5 degree oscillation angle, the spots in one image were still fewer than a normal protein crystal case, so there is no spots overlap. Best, Yang On Thu, Mar 14, 2013 at 5:20 AM, Tim Gruene t...@shelx.uni-ac.gwdg.demailto:t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Niu, could you let us know more about what you have already tried? - - use more images, maybe all images for indexing - - try a different program: xds instead of mosflm instead of hkl200 instead of d*trek instead of xds depending what you have tried. - - try to find the unit cell dimensions manually from adxv - - try cell_now with the SPOTS.XDS in XDS I would check the output of IDXREF.LP to figure out if indexing seems possible, i.e. if the input parameters seem stable or if they are just floating around and many more - it depends on the data set, really! Best, Tim On 03/13/2013 09:12 PM, Niu Tou wrote: Dear colleagues, We have some diffraction data from small peptide crystals, the shape of diffraction spots looks normal, and resolution is beyond 2A. The data were collected with 5 degree rotation per image. Later on we found it is hard to do index. Does anybody know some skills to figure this problem? Best wishes, Niu - -- - -- 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/ iD8DBQFRQZZFUxlJ7aRr7hoRAmr3AKD28Mml3XY2LIWkDknKrkJFToLDvwCgu1DI LDaPuAMfGlEIEObuWcckM7Y= =yuwC -END PGP SIGNATURE-
[ccp4bb] Resolution and data/parameter ratio, which one is more important?
I have this question. For exmaple, a protein could be crystallized in two crystal forms. Two crystal form have same space group, and 1 molecule/asymm. One crystal form diffracts to 3A with 50% solvent; and the other diffracts to 3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=2.5 times larger because of higher solvent content. If both data collecte to same completeness (say 100%), 3.6A data actually have higher data/parameter ratio, 5/2/(3.6/3)**3= 1.45 times to 3A data. For refinement, better data/parameter should give more accurate structure, ie. 3.6A data is better. But higher resolution should give a better resolved electron density map. So which crystal form really give a better (more reliable and accurate) protein structure?
Re: [ccp4bb] [off-topic] CNS solve profit license
Hi Genie, I'll ask someone from our Korea office to get in touch with you regarding your request. CNS for profit licenses do have to be licensed through Accelrys. Thanks, Francisco Francisco Hernandez-Guzman, PhD Sr. Product Manager Accelrys Software, Inc From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of JinSoo.Bae Sent: Thursday, March 14, 2013 4:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] [off-topic] CNS solve profit license Dear CCP4users biologists, I'm trying to get a CNS solve v1.3 profit license. I don't know how to contact person who deals with CNS profit license. Could you give the hint for getting the license or authorization for CNS program? Kind regards, Genie Genie 790-784 room 204, Dept of Life Science, POSTECH, san31, Hyoja-dong, Nam-gu, Pohang, Gyungbuk, Korea tel:82-54-279-8627 fax:82-54-279-8111
Re: [ccp4bb] RNA 3D structure alignment
I find that least-squares fitting of RNA in coot is fairly painless, robust and straightforward. It will move all of the contents of one pdb file, not just the RNA residues you select to align. On Mar 14, 2013, at 1:53 PM, Chen Zhao chenzhaoh...@gmail.com wrote: Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single aligned structure, or they left the ligand out. Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
