[ccp4bb] remove
Please, remove my address from the list. Thank you, Marat Yusupov, PhD Department of Integrated Structural Biology Institute of Genetics and Molecular and Cellular Biology (IGBMC) 1 rue Laurent Fries / BP 10142 / 67404 Illkirch CEDEX / France Tel. : +33 (0)3 88 65 33 01 marat.yusu...@igbmc.frmailto:marat.yusu...@igbmc.fr http://www.igbmc.fr/research/department/3/team/40/
[ccp4bb] AW: [ccp4bb] definitions of unique reflections
Dear Kenneth, You should be able to find the information you are looking for in the logfiles of your dataprocessing at the scaling/merging step. E.g. in the logfiles of scala you will find Total number of observations and Total number unique. I am sure Scalepack will produce similar output. Unique Reflections is the number of measured unique reflections, not the number of theoretically possible unique reflections. As you mentioned, the number of measured unique reflections is usually less than the number of theoretically possible unique reflections. Total reflections is the total number of reflections measured, e.g. the reflections that passed your resolution cutoff and rejection criteria that may be hidden in the data processing software. This is the number of reflections you have before merging. Again, you do not need to look for references but in your logfiles. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Kenneth A. Satyshur Gesendet: Montag, 14. Juli 2014 17:12 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] definitions of unique reflections There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. Unique Reflections My definition is all the possible reflections out to the high resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for both the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207
[ccp4bb] AW: [ccp4bb] Weired Crystal packing
Dear Appu, What is your problem? To me this crystal packing looks completely normal. If you look for tetramers in space groups with 422 symmetry I am sure you will find examples with a similar packing. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Appu kumar Gesendet: Dienstag, 15. Juli 2014 00:57 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Weired Crystal packing Dear All, I need your valuable suggestion in defining the arrangement of tetrameric protein in crystal upon symmetry mates information. I have attached a ppt for your evaluation. The monomer protein is composed of two domain (Domain 1 and Domain 2). In space group I422, the arrangement of tetramer upon symmetry mate information look weired because there are two kind of crystal contacts. The tetramer1 form crystal contact with tetramer2 through domain1 but on other side tetramer1 form crystal contact with tetramer3 through domain 2. Things will be clear if you will have look at the attached ppt. Therefore I request you to please look at the attached ppt. I have looked at the crystal packing in many tetrameric proteins which are either arranged in head to head or tail to tail in crystal but not in both head to head and tail to tail contacts in same crystal. Is this kind of crystal packing is possible? I need your valuable suggestion. Crystal is solved as monomer which upon symmetry mate information gives correct tetramer.
[ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?
Hi, There is a problem about modified DNA refinement. I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. However I found the modified DNA could not be linked to the downstream DNA when I refined it in the COOT. Then I generated another CIF file using sketcher of CCP4, but the problem still existed. Is there any expert to help me? Thanks!! Best Wei
Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?
You may need to 1) modify _chem_comp.group to be DNA in the cif-file 2) import the resulting cif-file in coot Cheers Sent on a Sprint Samsung Galaxy S® III div Original message /divdivFrom: Wang, Wei wew...@ucsd.edu /divdivDate:07/15/2014 5:14 AM (GMT-05:00) /divdivTo: CCP4BB@JISCMAIL.AC.UK /divdivSubject: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT? /divdiv /divHi, There is a problem about modified DNA refinement. I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. However I found the modified DNA could not be linked to the downstream DNA when I refined it in the COOT. Then I generated another CIF file using sketcher of CCP4, but the problem still existed. Is there any expert to help me? Thanks!! Best Wei
Re: [ccp4bb] The modified DNA could not be linked to the downstream DNA in the COOT?
Hello Wei, is the modified base defined as DNA in the cif? (see below) Is the O3* or O3'? You need the latter. And check whether there are three hydrogens on the O3. You need to either remove one from the cif file manually, or name them according to a normal DNA base. (In the latter case, by making the phosphodiester bond, one should be removed, if coot/refmac/phenix know that this is DNA...) Hope that helps! Sabine # --- LIST OF MONOMERS --- # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level GdX G 'Guanosine ' DNA 35 23 . # On 15/07/14 11:14, Wang, Wei wrote: Hi, There is a problem about modified DNA refinement. I generated one CIF file of a modified DNA base using eLBOW software of PHENIX. However I found the modified DNA could not be linked to the downstream DNA when I refined it in the COOT. Then I generated another CIF file using sketcher of CCP4, but the problem still existed. Is there any expert to help me? Thanks!! Best Wei
Re: [ccp4bb] AW: [ccp4bb] Weired Crystal packing
I suggest submitting your coordinates to the PDBe (EBI) web site to run PISA or using it via tthe CCP4I interface. This analysing contacts, and suggests the most favoured packing. It is not fool proof but worth checking. Eleanor On 15 July 2014 09:53, herman.schreu...@sanofi.com wrote: Dear Appu, What is your problem? To me this crystal packing looks completely normal. If you look for tetramers in space groups with 422 symmetry I am sure you will find examples with a similar packing. Best, Herman *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Appu kumar *Gesendet:* Dienstag, 15. Juli 2014 00:57 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* [ccp4bb] Weired Crystal packing Dear All, I need your valuable suggestion in defining the arrangement of tetrameric protein in crystal upon symmetry mates information. I have attached a ppt for your evaluation. The monomer protein is composed of two domain (Domain 1 and Domain 2). In space group I422, the arrangement of tetramer upon symmetry mate information look weired because there are two kind of crystal contacts. The tetramer1 form crystal contact with tetramer2 through domain1 but on other side tetramer1 form crystal contact with tetramer3 through domain 2. Things will be clear if you will have look at the attached ppt. Therefore I request you to please look at the attached ppt. I have looked at the crystal packing in many tetrameric proteins which are either arranged in head to head or tail to tail in crystal but not in both head to head and tail to tail contacts in same crystal. Is this kind of crystal packing is possible? I need your valuable suggestion. Crystal is solved as monomer which upon symmetry mate information gives correct tetramer.
[ccp4bb] LCP lipids
If you were going to start with 4 different LCP lipids what would they be? 9:9, 9:7 etc? why- channel size, temp range?
Re: [ccp4bb] [phenixbb] So what is unique?
So on second thought, practically speaking I guess observed is all, since we never see the ones that are rejected by the -3 sigma observed criterion On 07/15/2014 12:44 PM, Edward A. Berry wrote: I don't think observed means all the reflections that were integrated, becasue one of the other parameters is the criterion for a reflection to be considered observed, so that observed is a subset of all. Here are some lines I saved from an adit2 session (some years back, but I believe it was the same in a recent deposition) I don't think the questions fit very well the way we collect and process data today, but I think most of these are optional. What I called Rsym should probably be called Rmerge, from merging frames not merging crystals. Observed criterion sigma(F) null Observed criterion sigma(I) -3 Resolution (high) 3.000 Resolution (low) 42.68 Number unique reflections (all) ? Number unique reflections (observed) 141782 Percent possible (observed) 91.8 R-merge I (observed) ? R-sym I (observed) 0.124 On 07/15/2014 11:26 AM, Kenneth A. Satyshur wrote: There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. Unique Reflections My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 ___ phenixbb mailing list pheni...@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb
[ccp4bb] Translational NCS and molecular replacement.
Dear Community, I have some doubts to clarify. In a way to solve a structure by Phaser-MR, I found phaser ended up with a potentially good MR solution (with good statistics, packing and electron density, and as we know the homolog structure so in a reasonable biological assembly also). However, the space group where phaser found the potential solution (P22121) is different what we got in pointless (P212121), and phaser also indicated the presence of translational NCS (NCS translation vector = 0.500, 0.494 0.391). Now when we try to refine the structure with its original scala.mtz file (which is indexed and sclaled in P212121) and phaser generated pdb file, the R/Rfree is very high (around 0.5) but when I tried refining with mtz file generated by phaser, it was reasonable, at least for first cycle of refinement (R/Rfree, 0.41/0.46). Now my question is, can I use the phaser generated mtz file instead of the original scala.mtz for further refinement? Or I have to reindex my original data into phaser suggested spacegroup and run the MR again? Translational NCS are generally associated with high R values, is there any way to get rid of that problem? Best regards, Sudipta.
[ccp4bb] Postdoctoral Research Associate available - Structural biology-Computational modeling - University of Minnesota
Dear All, I would like to draw your attention to the postdoctoral vacancy in the research group of Prof. Larry Wackett at the University of Minnesota (USA): A postdoctoral position is available immediately at the University of Minnesota to conduct research with a team of biochemists and engineers studying the structure and substrate specificity of enzymes involved in microbial biodegradation. The ideal candidate will have a background in computational enzyme ligand docking, molecular dynamics simulations, X-ray-crystallography and have some knowledge of database development. The person should have a PhD in Biochemistry, Chemistry or a related field. The project involves the study of diverse biodegradative enzymes and developing predictive tools for assessing substrate specificity that determines metabolic potential for organismal engineering. Working as part of a multi-disciplinary team is an important requirement for this position. For additional information, or to apply (cover letter, CV, and contact information for three referees), contact Professor Larry Wackett ( mailto:wacke...@umn.edu wacke...@umn.edu; http://www.cbs.umn.edu/research/research-cbs/faculty-labs/wackett ). The position is open immediately. The University of Minnesota shall provide equal access to and opportunity in its programs, facilities, and employment without regard to race, color, creed, religion, national origin, gender, age, marital status, disability, public assistance status, veteran status, sexual orientation, gender identity, or gender expression. Best regards, Mikael
Re: [ccp4bb] [phenixbb] So what is unique?
I think that 'observed' goes back to whether it was possible to see a reflection (and estimate its intensity by eye) on the photographic FILM. In small molecule crystallography it is usually understood to mean F4sigma(F) (or I2sigma(I)). George On 07/15/2014 07:02 PM, Edward A. Berry wrote: So on second thought, practically speaking I guess observed is all, since we never see the ones that are rejected by the -3 sigma observed criterion On 07/15/2014 12:44 PM, Edward A. Berry wrote: I don't think observed means all the reflections that were integrated, becasue one of the other parameters is the criterion for a reflection to be considered observed, so that observed is a subset of all. Here are some lines I saved from an adit2 session (some years back, but I believe it was the same in a recent deposition) I don't think the questions fit very well the way we collect and process data today, but I think most of these are optional. What I called Rsym should probably be called Rmerge, from merging frames not merging crystals. Observed criterion sigma(F) null Observed criterion sigma(I) -3 Resolution (high) 3.000 Resolution (low) 42.68 Number unique reflections (all) ? Number unique reflections (observed) 141782 Percent possible (observed) 91.8 R-merge I (observed) ? R-sym I (observed) 0.124 On 07/15/2014 11:26 AM, Kenneth A. Satyshur wrote: There is some disagreement on terms used to deposit data. We need a definition and an algorithm for each definition. Unique Reflections My definition is all the possible reflections out to the highest resolution reported not related by symmetry. Where can I find this? The .mtz contains a list of all HKL calculated to the highest resolution. Usually, we are not able to measure all these diffraction spots due to limits of the detector, mechanical limits, crystal orientation, etc. 'Total reflections' The depositions server asks for total reflections. I assume it wants only those unique reflections we were able to collect, regardless of the sigma cut off. These are called 'observed'. The total we use in refinement will be a subset of the 'unique observed' that are cut on sigma. However, some crystallographers believe that we should not cut on sigma since some of the intensities may in fact be zero. Is this a question for the Refmac and Phenix people? Please give us some guidance and maybe a reference or two that we can use. thanks -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 ___ phenixbb mailing list pheni...@phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
[ccp4bb] AMoRe
Hi, Has anyone tried the tutorial on the CCP4 website for AMoRe? http://www.ccp4.ac.uk/examples/tutorial/html/mr-tutorial-amore.html I am trying to learn how to use the package in CCP4 and it fails and I am wondering if the tutorial has become outdated? Thank you, George
