Re: [ccp4bb] Help needed in solving a MAD dataset
Crank is a good tool for doing this automatically. Follow the instructions here: http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=Automated_experimental_phasing_with_Crank Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu
Re: [ccp4bb] Help needed in solving a MAD dataset
Minor correction: SHELX software are not part of CCP4 but if you have them installed as part of your crystallograhic software, you can call them from the CCP4 GUI. You can obtain the SHELX suite free to academic labs from Ggeorge Sheldrickbe Email George Sheldrick. George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de Jürgen Bosch wrote: CCP4 way: locate the Se sites with SHELX (if you use the CCP4I gui it's technically a ccp4 program :-) ) Try using only your peak data set first. If you can't locate your sites with the single wavelength then add remote (DAD) and if that doesn't work go MAD. non-ccp4 way run hkl2map as frontend to SHELX, do the same thing. After 10 minutes go and open a bottle of your favourite sparkling cider* and start tracing the structure. Jürgen * can be replaced by other sparkling product containing trace amounts of EtOH supplemented with flavours On May 19, 2010, at 12:01 PM, Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] translational NCS
pdbset xyzin mol1.pdb xyzout mol1-tran1.pdb SHIFT frac x,y,z (where x,y,z is the patterson peak) end OR pdbset xyzin mol1.pdb xyzout mol1-tran2.pdb SHIFT frac -x,-y,-z (since -x,-y,-z is also a the patterson peak) end Nicolas Soler wrote: Dear CCP4bbs, I am dealing with a case involving pseudo-translational symmetry. I wanted to know what was the simplest way to draw NCS copies of a molecule deduced from the positions I observed in native Patterson. Is there a translate option where on can give fractional coordinates in Coot or Pymol? Thanks for your help! Nicolas
Re: [ccp4bb] Translational pseudosymmetry?
This looks a bit strange.. If you have a hexamer in the asymmetric unit, in P3, then that means all symmetry copies lie in the same plane. To generate the Patterson peak, 2/3,1/3,0 the hexamer must be centred at 1/3,1/3, z (with symmetry equivalents 0,-1/3,z and -1/3,0,z ) I would expect ypu to have a pseudo higher symmetry SG - does pointless make any suggestions? Eleanor Jürgen Bosch wrote: Hi Owen, you should also make the following plot with your data: y-axis relative intensity of off-origin peak versus x-axis resolution cutoff used for calculation (30 Å - 4 Å in 2 Å steps). You can have multiple cases of shifts and I would start with a perfect hexamer first, take some random monomer and apply a perfect sixfold, move it along the axis where it should be in your crystal lattice (things get more complicated if you have a top/down hexamer, so keep it simple). Now if you shift your hexamer to 2/3,1/3,0 your plot should yield a straight line and be independent of resolution. Now start rotating the second hexamer relative to the first clockwise with your sixfold, I would use increments of 3 degrees, which will result in 19 models, then recalculate the off-origin peak heights and see if they match up with your data. I should note here, if your real data does not show a strong drop in peak height of the off-origin peak, then you most likely don't have a slight rotational translation in your second hexamer. One other important thing you should look at is the relative orientation of your sixfold axis, is it truly perfectly aligned with one of the cell axis ? If not fix this in your model, otherwise your calculations will be of academic nature. For this particular case the use of GLRF is more helpful than MOLREP (sorry Garib, but maybe Garib can come up with a solution to zoom into certain peaks like you can do in GLRF). When the tilt is fixed you should be able to figure out the rotational translation in your second hexamer. Enjoy your puzzle, Jürgen P.S. P3 is certain ? Check with pointless or by human brain visual inspection (HBVI) On May 15, 2010, at 11:53 PM, Owen Pornillos wrote: Dear ccp4bb – I have questions with regards to crystal disorder that gives rise to translational pseudosymmetry. We have a rotationally hexameric protein that crystallized in P3, with one hexamer in the asu. The local 6-fold axis of the hexamer is non- crystallographic, and is essentially parallel to the crystallographic 3-fold, which gave rise to translational pseudosymmetry. Intensities for the (h,h+/-3n,l) reflections were on average about 8 times stronger than the weak reflections, and the native patterson gave an off-origin peak about 70-80% of origin (depending on the crystal) at fractional coordinates (2/3,1/3,0). We are hypothesizing that the break in local 6-fold symmetry is caused by small rigid-body displacements of each subunit (as opposed to conformational changes in the protein), and we are trying to estimate the magnitude of the displacements in the crystal. To do this, a perfectly symmetric hexamer with the local 6-fold axis parallel to the crystallographic 3-fold was generated, and then shifts were introduced to the atomic coordinates. The direction of the shift was chosen randomly for each atom, and a single magnitude applied to all atoms, which was then changed incrementally. Structure factors were calculated from these models, and their pattersons were examined. The magnitude of the off-origin peak could be reproduced with an atomic shift of say, 1 Å. Because all of these calculations were made with synthetic structure factors, this is not necessarily a reliable estimate. The questions are, how far off are we, and in what direction (i.e., are these shifts underestimates or overestimates)? Is there a way to obtain a reliable estimate? Thanks in advance, Owen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Help needed in solving a MAD dataset
Dear Qing Lu, Now that several suggestions, both ccp4 and non-ccp4, have been made, may I suggest that you (also) try autoSHARP, available free of charge at http://www.globalphasing.com/sharp/ It includes the invocation of SHELXD to solve the substructure, and takes you all the way to autobuilding with ARP/wARP if you have it installed and your data resolution is sufficient. It has been around for quite a while and has many happy users. With best wishes, Gerard. -- On Wed, May 19, 2010 at 09:06:54AM -0700, Qing Lu wrote: Hi All, I am new to protein crystallography. I would like to know the steps involved in solving a MAD dataset by using the program in CCP4 where you determine the phases and then obtain the trace. The dataset is collected at 3 different wavelengths (peak, inflection and remote) using Se-Met as the scatterer. The crystals diffracted to resolution of 2 Angstrsoms and has a good anomalous signal. Thanks, Qing Lu -- === * * * 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] electron microscopy: where open access fails
sent on behalf of the EMDATABANK.org team: The EM Databank (EMDB, http://www.emdatabank.org/) is a resource for the archival deposition and retrieval of EM maps and associated metadata. It was established in 2002 by the European Bioinformatics Institute (EMBL-EBI, UK), and is now run jointly by EBI, the Research Collaboratory for Structural Bioinformatics (RCSB, USA), and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine. Following the model of the wwPDB, development of EMDB policies and procedures is community-driven. The resource is advised by a panel of leading experts. This fall, an Electron Microscopy Validation Task Force (EM VTF) will be convened to make recommendations as to how best to assess the quality of both maps and models that have been obtained from cryo-EM data. Its recommendations will form the basis for a validation suite that will be used for maps and models deposited in the appropriate databases (EMDB and PDB). As seen by the history of the PDB, journal requirements can greatly influence data deposition. For articles reporting the results of electron microscopy studies, the rate of EM map deposition is higher for journals that have well-defined and consistently-enforced policies than for journals without deposition requirements. We have recently contacted journals that publish EM studies to encourage them to include a deposition policy for EM structural data in the instructions to Authors, and we are continuing to follow up with them. Currently, depositors may choose to release deposited data immediately, upon publication (selected by the majority), after 1 year, or after 2 years. The 1 and 2 year holds are intended to encourage EM scientists to deposit maps by providing a time period in which they can perform additional studies/analyses before the map is made public. Based upon community feedback, the option to hold a map for 4 years was retired in 2008. Questions about the EMDB may be sent to h...@emdatabank.org.
Re: [ccp4bb] Translational pseudosymmetry?
Dear Eleanor - That is correct. The pseudo-sg is P6, and the structure has been refined in this sg. The intensity difference between the strong and weak subsets is quite significant that for most data sets, auto- indexing routines will miss the weak spots and pick the pseudo-sg instead. The pseudo-sg is a'=b'=90, c'=56, the true sg is a=b=156, c=56. Note that a = a' * sqrt(3). So, the sg assignment is certain. Owen On May 20, 2010, at 6:33 AM, Eleanor Dodson wrote: This looks a bit strange.. If you have a hexamer in the asymmetric unit, in P3, then that means all symmetry copies lie in the same plane. To generate the Patterson peak, 2/3,1/3,0 the hexamer must be centred at 1/3,1/3, z (with symmetry equivalents 0,-1/3,z and -1/3,0,z ) I would expect ypu to have a pseudo higher symmetry SG - does pointless make any suggestions? Eleanor Jürgen Bosch wrote: Hi Owen, you should also make the following plot with your data: y-axis relative intensity of off-origin peak versus x-axis resolution cutoff used for calculation (30 Å - 4 Å in 2 Å steps). You can have multiple cases of shifts and I would start with a perfect hexamer first, take some random monomer and apply a perfect sixfold, move it along the axis where it should be in your crystal lattice (things get more complicated if you have a top/down hexamer, so keep it simple). Now if you shift your hexamer to 2/3,1/3,0 your plot should yield a straight line and be independent of resolution. Now start rotating the second hexamer relative to the first clockwise with your sixfold, I would use increments of 3 degrees, which will result in 19 models, then recalculate the off- origin peak heights and see if they match up with your data. I should note here, if your real data does not show a strong drop in peak height of the off-origin peak, then you most likely don't have a slight rotational translation in your second hexamer. One other important thing you should look at is the relative orientation of your sixfold axis, is it truly perfectly aligned with one of the cell axis ? If not fix this in your model, otherwise your calculations will be of academic nature. For this particular case the use of GLRF is more helpful than MOLREP (sorry Garib, but maybe Garib can come up with a solution to zoom into certain peaks like you can do in GLRF). When the tilt is fixed you should be able to figure out the rotational translation in your second hexamer. Enjoy your puzzle, Jürgen P.S. P3 is certain ? Check with pointless or by human brain visual inspection (HBVI) On May 15, 2010, at 11:53 PM, Owen Pornillos wrote: Dear ccp4bb – I have questions with regards to crystal disorder that gives rise to translational pseudosymmetry. We have a rotationally hexameric protein that crystallized in P3, with one hexamer in the asu. The local 6-fold axis of the hexamer is non- crystallographic, and is essentially parallel to the crystallographic 3-fold, which gave rise to translational pseudosymmetry. Intensities for the (h,h+/-3n,l) reflections were on average about 8 times stronger than the weak reflections, and the native patterson gave an off-origin peak about 70-80% of origin (depending on the crystal) at fractional coordinates (2/3,1/3,0). We are hypothesizing that the break in local 6-fold symmetry is caused by small rigid-body displacements of each subunit (as opposed to conformational changes in the protein), and we are trying to estimate the magnitude of the displacements in the crystal. To do this, a perfectly symmetric hexamer with the local 6-fold axis parallel to the crystallographic 3-fold was generated, and then shifts were introduced to the atomic coordinates. The direction of the shift was chosen randomly for each atom, and a single magnitude applied to all atoms, which was then changed incrementally. Structure factors were calculated from these models, and their pattersons were examined. The magnitude of the off-origin peak could be reproduced with an atomic shift of say, 1 Å. Because all of these calculations were made with synthetic structure factors, this is not necessarily a reliable estimate. The questions are, how far off are we, and in what direction (i.e., are these shifts underestimates or overestimates)? Is there a way to obtain a reliable estimate? Thanks in advance, Owen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] Grenoble: PhD fellowship in kinetic crystallography
A PhD studentship (3 years) is available at the Institut de Biologie Structurale (http://www.ibs.fr) in Grenoble, France. The project is to explore the structural dynamics of the medically important enzyme acetylcholinesterase by a panoply of complementary biophysical methods, including kinetic crystallography. During past decades, research in macromolecular biology focused mainly on structure-function relationships. Yet, only by taking into account the dynamic personality of macromolecules and by studying structure-dynamics-function relationships can we understand biological systems on the molecular level and in their cellular context. Acetylcholinesterase, being one of Nature's fastest enzymes, represents a major challenge concerning the study of its structural dynamics in the context of the enzyme's crucial role in cholinergic synapses. A particular focus will be on changes in the structural dynamics of acetylcholinesterase upon inhibitor binding. The results obtained will be exploited in a collaborative effort to improve existing anti-Alzheimer drugs that target acetylcholinesterase and to develop molecules capable of reactivating poisoned acetylcholinesterase. Biophysical methods applied include kinetic crystallography that films proteins in action, in crystallo spectrophotometry, and molecular dynamics simulations. The multidisciplinary project at the interface of biology, physics and chemistry will be conducted in an international environment. It will make extensive use of the nearby European Synchrotron Radiation Facility (http://www.esrf.eu) and its Cryobench laboratory (http://www.esrf.eu/UsersAndScience/Experiments/MX/Cryobench) dedicated to in crystallo spectroscopic studies complementary to X-ray crystallography. Candidates should preferably have a biophysical education. Applications, including two letters of reference, should be sent to Dr. Martin Weik (w...@ibs.fr). Representative publications • Colletier, Fournier, Greenblatt, Stojan, Sussman, Zaccai, Silman Weik (2006) Structural insights into substrate traffic and inhibition in acetylcholinesterase. EMBO J. 25, 2746. • Colletier, Bourgeois, Sanson, Fournier, Sussman, Silman Weik (2008) Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography. PNAS 105, 11742. • Xu, Colletier, Jiang, Silman, Sussman Weik (2008) Induced-fit or preexisting equilibrium dynamics? Lessons from protein crystallography and MD simulations on acetylcholinesterase and implications for structure-based drug design. Protein Sci., 17, 601. • Weik Colletier (2010) Temperature-dependent macromolecular X-ray crystallography. Acta D 66, 437. Press release related to the group's research on acetylcholienesterase • Observing a target enzyme of Alzheimer’s disease drugs in action. http://www.esrf.eu/news/spotlight/spotlight70/spotlight70/ • La cible de médicaments anti-Alzheimer observée en pleine action. http://www2.cnrs.fr/presse/communique/1392.htm?debut=64
Re: [ccp4bb] electron microscopy: where open access fails
Dear Cathy/EMDATABANK team: It is hard to comprehend the option for keeping maps on hold for up to 2 years. It seems any depositor would do this for pure selfish reasons: keep the data to themselves, don't allow anybody to verify the data for a long time, and have the exclusive right to do experiments with the maps. For example, this would allow the depositor to be the only one perform docking experiments with any partial crystal structure for 2 years, and also these experiments wouldn't be falsifiable for a period of 2 years (!). Comparing this with crystallography: one would keep a crystal structure of a good drug target 'on hold' for 2 years, thus not allowing anybody to use it to start rationally designing new drugs (the success rate aside for this matter). In scientific terms, two years is 'huge'. It is in this time frame that a new theory can be postulated by one, and then shot down by ten other papers. It is 40% of the time frame of an NIH ROI1 grant, and 66% of a typical Canadian CIHR grant. When it comes to cryoEM and crystal structures of important therapeutic targets, delaying the field for 2 years will ultimate cost lives. In the end, journal editors should create firmer and waterproof policies like those implemented for crystal structures, such as not allowing publication until the data are in the 'hold for publication' status. Some journals already have the clear policy of requiring deposition of the cryoEM maps, but the 2 year hold is currently a big loophole. Many more journals, however, don't require the deposition of maps at all. Of course it would help if the EMDB didn't allow for these loopholes... Sincerely, Filip Van Petegem On Thu, May 20, 2010 at 7:16 AM, Cathy Lawson cathy.law...@rutgers.eduwrote: sent on behalf of the EMDATABANK.org team: The EM Databank (EMDB, http://www.emdatabank.org/) is a resource for the archival deposition and retrieval of EM maps and associated metadata. It was established in 2002 by the European Bioinformatics Institute (EMBL-EBI, UK), and is now run jointly by EBI, the Research Collaboratory for Structural Bioinformatics (RCSB, USA), and the National Center for Macromolecular Imaging (NCMI) at Baylor College of Medicine. Following the model of the wwPDB, development of EMDB policies and procedures is community-driven. The resource is advised by a panel of leading experts. This fall, an Electron Microscopy Validation Task Force (EM VTF) will be convened to make recommendations as to how best to assess the quality of both maps and models that have been obtained from cryo-EM data. Its recommendations will form the basis for a validation suite that will be used for maps and models deposited in the appropriate databases (EMDB and PDB). As seen by the history of the PDB, journal requirements can greatly influence data deposition. For articles reporting the results of electron microscopy studies, the rate of EM map deposition is higher for journals that have well-defined and consistently-enforced policies than for journals without deposition requirements. We have recently contacted journals that publish EM studies to encourage them to include a deposition policy for EM structural data in the instructions to Authors, and we are continuing to follow up with them. Currently, depositors may choose to release deposited data immediately, upon publication (selected by the majority), after 1 year, or after 2 years. The 1 and 2 year holds are intended to encourage EM scientists to deposit maps by providing a time period in which they can perform additional studies/analyses before the map is made public. Based upon community feedback, the option to hold a map for 4 years was retired in 2008. Questions about the EMDB may be sent to h...@emdatabank.org. -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
[ccp4bb] Ion identification in crystal structures
What is a good resource for identifying what seem to be ions (Na+, Cl-, CO3-, NH4-) and not simply water molecules in a crystal structure? James W. Murphy, Ph.D. Associate Research Scientist; Dept. of Pharmacology Facility Manager; Macromolecular Crystallography Facility Yale University School of Medicine 333 Cedar Street, SHMB345 New Haven, CT 06510 Office: 203-737-1526 Cell: 203-906-5759 Fax: 203-737-2027
[ccp4bb] The organizers: Frontiers in Automated Crystal Handling and Visualization invite you to participate
The Organizers of the workshop: Frontiers in Automated Crystal Handling and Visualization May 26-27, 2010 National Synchrotron Light Source, Brookhaven National Laboratorty Hamilton Conference Room Bldg 555 Chemistry Department would like to invite you to participate in this exciting workshop which will discuss the latest happenings at the 'Frontier in Automated Crystal Handling and Visualization'. A panel of distinguished speakers will discuss new methods in crystal handling, crystal harvesting, and trends in automatic crystal screening, exploring challenges in micro crystal visualization and handling. A detailed agenda can be viewed at: http://www.nsls.bnl.gov/users/meeting/workshops/workshop.aspx?id=13 . These trends will influence the concepts for your new MX beam lines at NSLS-II (http://www.bnl.gov/nsls2/), the ultra-bright new light source now under construction at BNL. In fact, you may also be interested to help shape the beam line proposals by expressing your views in a MX planning group meeting that will take place immediately after the workshop in the afternoon of May 27. For further information please contact one of the organizers, We are looking forward to seeing you. Dieter Schneider (schnei...@bnl.gov), Alexei Soares (soa...@bnl.gov), and Vivian Stojanoff (stoja...@bnl.gov)
Re: [ccp4bb] electron microscopy: where open access fails
Dear crystallographers, For those of you who have shared personal frustration with cryoEM map availability, or for those of you who would simply like to see science proceed as it should, here's your opportunity to sign an on-line petitition. Please feel free to send the link below to any of your colleagues. More signatures = more pressure. http://www.petitiononline.com/cryoEM/petition.html Sincerely, Filip Van Petegem -- Filip Van Petegem, PhD Assistant Professor The University of British Columbia Dept. of Biochemistry and Molecular Biology 2350 Health Sciences Mall - Rm 2.356 Vancouver, V6T 1Z3 phone: +1 604 827 4267 email: filip.vanpete...@gmail.com http://crg.ubc.ca/VanPetegem/
Re: [ccp4bb] ncsfind
Hello, If you have Phenix, try phenix.find_ncs (sorry for the non-CCP4 answer). The example run in the PHENIX documentation is: phenix.find_ncs anb.pdb mlt.mtz This will then write out the NCS operators in various flavours. Basically if you have a list of Se sites it calls RESOLVE, but has a simpler, command-line interface. http://www.phenix-online.org/documentation/find_ncs.htm#anch20 Good luck, Mark On 20 May 2010 23:47, Karin van Straaten kev...@mail.usask.ca wrote: Dear all, Does anyone know if NCSFIND is still available or how I can get it. If not is there another program that I can use to determine noncrystallographic symmetry between Se-sites. Thanks in advance, Karin -- Skype: markabrooks
Re: [ccp4bb] Help needed in solving a MAD dataset
I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it.
Re: [ccp4bb] Help needed in solving a MAD dataset
I don't like the site finding option in autosharp, takes too long in most of my cases. So my approach is locate sites via SHELX, then feed them into Sharp. Sorry Gerard :-) Jürgen On May 20, 2010, at 10:02 PM, Jeremiah Farelli wrote: I second autoSHARP/SHARP. It makes great initial maps, and once you get it running, it is totally worth it. - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] Hope for breakthroughs
http://www.ebi.ac.uk/chemblntd And the related publication Thousands of chemical starting points for antimalarial lead identification http://www.nature.com/nature/journal/v465/n7296/pdf/nature09107.pdf Good luck with the goldmine ! Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
[ccp4bb] TLSANL total B factor question
Dear Crystallographers I am trying to print out my total B factors using TLSANL (version: 6.1) in CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version: 5.5.0072) using the TLS restraint refinement option and isotropic B factors. The TLSANL’s output file.pdb contains the following ATOM and ANISOU records as an example. REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS ATOM 88 C ASN A 14 0.748 -5.841 -6.258 1.00 35.84 C ANISOU 88 C ASN A 14 5335 4549 3734 0 0 0 C ATOM 89 O ASN A 14 0.807 -6.941 -6.845 1.00 35.04 O ANISOU 89 O ASN A 14 5229 4375 3709 0 0 0 O I am not able to understand why my ANISOU record contains ‘0 0 0’ for the anisotropic component. Something is not correct and I'm not sure why I am not able to print out my total B factors. I would appreciate it if someone could tell me what is going wrong and how can I print my total B factors. Thanks Regards Shiva Kumar
Re: [ccp4bb] TLSANL total B factor question
On Thursday 20 May 2010, Shiva Kumar wrote: Dear Crystallographers I am trying to print out my total B factors using TLSANL (version: 6.1) in CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version: 5.5.0072) using the TLS restraint refinement option and isotropic B factors. The TLSANL’s output file.pdb contains the following ATOM and ANISOU records as an example. REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS ATOM 88 C ASN A 14 0.748 -5.841 -6.258 1.00 35.84 C ANISOU 88 C ASN A 14 5335 4549 3734 0 0 0 C ATOM 89 O ASN A 14 0.807 -6.941 -6.845 1.00 35.04 O ANISOU 89 O ASN A 14 5229 4375 3709 0 0 0 O I am not able to understand why my ANISOU record contains ‘0 0 0’ for the anisotropic component. Something is not correct and I'm not sure why I am not able to print out my total B factors. The simplest explanation would be that those particular atoms are not in any TLS group, and therefore they have only an isotropic ADP component. If that is not the case, please show the contents of the header records that describe these 2 TLS groups. Ethan I would appreciate it if someone could tell me what is going wrong and how can I print my total B factors. Thanks Regards Shiva Kumar
Re: [ccp4bb] TLSANL total B factor question
The simplest explanation would be that those particular atoms are not in any TLS group, and therefore they have only an isotropic ADP component. Unfortunately, the '0 0 0' for the anisotropic component in ANISOU record is for all of my protein atoms. If that is not the case, please show the contents of the header records that describe these 2 TLS groups. The header records are: REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS :2 REMARK 3 ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS REMARK 3 ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3NUMBER OF COMPONENTS GROUP :1 REMARK 3COMPONENTSC SSSEQI TO C SSSEQI REMARK 3RESIDUE RANGE : A4A 372 REMARK 3ORIGIN FOR THE GROUP (A): 5.8065 -0.6242 -14.8498 REMARK 3T TENSOR REMARK 3 T11: 0.0568 T22: 0.0595 REMARK 3 T33: 0.0153 T12: -0.0103 REMARK 3 T13: 0.0065 T23: 0.0022 REMARK 3L TENSOR REMARK 3 L11: 1.1685 L22: 1.8292 REMARK 3 L33: 0.8417 L12: 0.0945 REMARK 3 L13: 0.2145 L23: 0.5509 REMARK 3S TENSOR REMARK 3 S11: 0.0110 S12: -0.1328 S13: -0.1118 REMARK 3 S21: 0.2334 S22: 0.0025 S23: -0.0249 REMARK 3 S31: 0.1311 S32: 0.0150 S33: -0.0134 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3NUMBER OF COMPONENTS GROUP :1 REMARK 3COMPONENTSC SSSEQI TO C SSSEQI REMARK 3RESIDUE RANGE : A 373A 469 REMARK 3ORIGIN FOR THE GROUP (A): 1.9633 16.6927 8.0263 REMARK 3T TENSOR REMARK 3 T11: 0.0322 T22: 0.0531 REMARK 3 T33: 0.0250 T12: -0.0032 REMARK 3 T13: 0.0021 T23: -0.0070 REMARK 3L TENSOR REMARK 3 L11: 1.7358 L22: 0.5530 REMARK 3 L33: 2.3849 L12: 0.2397 REMARK 3 L13: -0.5610 L23: -0.8025 REMARK 3S TENSOR REMARK 3 S11: 0.0490 S12: -0.0959 S13: -0.0548 REMARK 3 S21: 0.0573 S22: -0.0352 S23: -0.0473 REMARK 3 S31: -0.0729 S32: 0.1153 S33: -0.0139 REMARK 3 Thanks Regards Shiva
