[ccp4bb] MR question
Dear ccp4 members I have something that surprises me with molecular replacement. I have obtained a solution for a single point mutation using Phaser, the solution seems ok. I do one round of refinement with refmac and I check the structure using molprobity before I even start really to refine it. The structure looks very good. MolProbity gives all green lights. Then I start to fix the structure, I add waters, I check fit to density, rotamers, geometry etc, I do some more refinements. I check with MolProbity and it looks a lot worse... many clashes, many bad ramachandran and rotamers, many red lights. I do not understand. How can each successive round of refinement make the structure worse and worst? Is there a fundamental problem, perhaps, like undiagnosed NCS or incorrect space group or incorrect MR solution? Could they be giving these strange result do you think? Thanks Careina
Re: [ccp4bb] MR question
Hi Careina, I can think of two possibilities: - your restraints are not strong enough. - if your mutant dataset is of significantly lower resolution than the native, almost any refinement will make the model worse. If this is your case, just change the mutated residue and very, very obvious things in the difference map. Then refine with strict restraints, perhaps only refining overall B and only refining the position of the mutated residue and any other obviously changed residues. If possible refine restraining to the native structure (I only did this a long time ago with TNT with a script Jan Pieter Abrahams wrote, I don't know if refmac has this possibility). greetings, Mark Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/content/research/macromolecular/mvraaij On 22 Jun 2011, at 08:25, Careina Edgooms wrote: Dear ccp4 members I have something that surprises me with molecular replacement. I have obtained a solution for a single point mutation using Phaser, the solution seems ok. I do one round of refinement with refmac and I check the structure using molprobity before I even start really to refine it. The structure looks very good. MolProbity gives all green lights. Then I start to fix the structure, I add waters, I check fit to density, rotamers, geometry etc, I do some more refinements. I check with MolProbity and it looks a lot worse... many clashes, many bad ramachandran and rotamers, many red lights. I do not understand. How can each successive round of refinement make the structure worse and worst? Is there a fundamental problem, perhaps, like undiagnosed NCS or incorrect space group or incorrect MR solution? Could they be giving these strange result do you think? Thanks Careina
[ccp4bb] hello
Dear all, Could any one help me regarding my serious problem actually i have collected data at 3.0 and cut off 3.1 where the data statics showed the good values for the further processing. According to the methew coefficient there would be two molecule in the asymmetric unit but after running the molrep its provide only one monomer instead of two, for this reason R values is very high 50%. Actually homologous model having P6322 space group where as my one is F4132. I had tried to run phaser as well phenix but both were failed to process further. i really do not know how can i get the second chain in my structure. Please if you have some ideas i will appreciate and would be many thankful to you. Hope to hearing you soon Best Regards AFSHAN
Re: [ccp4bb] MR question
If possible refine restraining to the native structure (I only did this a long time ago with TNT with a script Jan Pieter Abrahams wrote, I don't know if refmac has this possibility). Prosmart generates restraints for use in refmac: http://www.ysbl.york.ac.uk/mxstat/Rob/index.html It worked well for me.
Re: [ccp4bb] hello
Hi, The R-factor you mention, is it an R-factor before any refinement of the model ? Like an R-factor at the very beginning of the entire modeling procedure, right after molecular replacement ? If this is so: you should always compare such initial R-factors to the R-factors for the atoms placed randomly in the asymmetric unit (in the crystal thus, see X-ray Structure Determination by Stout and Jensen, pp 246 in the edition I have here - 1968, 1st edition?). R for centric reflections = 0.83, R for acentric reflections = 0.59. In space group F4132 there are many centric reflections. The random R-factor may be around 0.65 or higher... (I didn't count), and if the value you quote (0.5) is indeed a starting R-factor it is well below that for a random distribution of atoms in the asymmetric unit. Matthews coefficient only gives a probability of the number of molecules in the asymmetric unit, but it does not provide you with that figure. You may well have plenty of solvent in your asymmetric unit. The most important thing are the electron density maps: do these provide indications of where the search model has to be modified in order to fit the target molecule ? Also, if you have a component missing from your molecular replacement calculations (as in the case you locate only one molecule instead of two), very often there is some additional proteinacious density appearing in the crystal contact regions between your correctly placed molecule and the ghost molecule (which you haven't positioned yet). So if R=0.5 is the starting R-factor just after molecular replacement, I think it is an appropriate R-factor for molecular replacement calculations. HTH, Fred. Afshan Begum wrote: Dear all, Could any one help me regarding my serious problem actually i have collected data at 3.0 and cut off 3.1 where the data statics showed the good values for the further processing. According to the methew coefficient there would be two molecule in the asymmetric unit but after running the molrep its provide only one monomer instead of two, for this reason R values is very high 50%. Actually homologous model having P6322 space group where as my one is F4132. I had tried to run phaser as well phenix but both were failed to process further. i really do not know how can i get the second chain in my structure. Please if you have some ideas i will appreciate and would be many thankful to you. Hope to hearing you soon Best Regards AFSHAN **
Re: [ccp4bb] Refmac for windows
Rex, I think the problem is that the latest version of the dictionary which contains LBT (and many other new ligands) only works with Refmac 5.6 (but check with Garib on that!), but that version hasn't yet been compiled for Windows. Unfortunately Windows versions tend to lag a bit behind Linux Mac/OSX versions for historical reasons. Have you looked here: http://ligand-depot.rutgers.edu/ld-search.html You could download the ideal PDB coords and use Garib's JLIGAND to make the library entry. Cheers -- Ian PS Can someone explain to me why alpha-lactose is LBT and beta-lactose is LAT? On Tue, Jun 21, 2011 at 9:58 PM, REX PALMER rex.pal...@btinternet.comwrote: Dear protein crystallographers We tried downloading the latest version of Refmac for Windows, Refmac 5.5.0071 from the prerelease page on ccp4. However it does not seem to have alpha lactose in the monomer library. Does anyone know if it is possible to obtain the latest Refmac version complete with both alpha and beta forms of lactose in the dictionary? Rex Palmer Birkbeck College Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://rexpalmer2010.homestead.com
[ccp4bb] Waters in ADIT
Dear colleagues, I want to deposit one structure, but ADIT reports tens more waters that are further than 3.5 AA away from macromolecule atoms. I inspected about half of them manually, but all of them are OK. I have observed this incorrect behavior of ADIT also in one previous structure for deposition, but just ignored three or four reports, because I knew, I was doing the right thing. Does anyone know how to solve this problem? I have already tried: - changing HETATM to ATOM - assigning different chain ID for waters to have same ID as protein chain - renumbering of residues (not in this case, but the previous one) I do not have to solve this problem, but I do not want to have so strange Validation Report from ADIT. Many thanks for any idea. Petr PS: Not important, but refined with REFMAC5 at medium resolution. -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
Re: [ccp4bb] Waters in ADIT
No. Some of them have 2.7 AA contacts to main chain!, some of them are in second, or third solvatation shell. And they are not distributed around some special area. It is somehow random. Thanks anyway! Petr 2011/6/22 Charles Allerston charles.allers...@sgc.ox.ac.uk: Are they bound to the symmetry-related molecule? cheers, charlie Dr. Charles Allerston Genome Integrity Group Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.sgc.ox.ac.uk/ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Kolenko Sent: 22 June 2011 12:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Waters in ADIT Dear colleagues, I want to deposit one structure, but ADIT reports tens more waters that are further than 3.5 AA away from macromolecule atoms. I inspected about half of them manually, but all of them are OK. I have observed this incorrect behavior of ADIT also in one previous structure for deposition, but just ignored three or four reports, because I knew, I was doing the right thing. Does anyone know how to solve this problem? I have already tried: - changing HETATM to ATOM - assigning different chain ID for waters to have same ID as protein chain - renumbering of residues (not in this case, but the previous one) I do not have to solve this problem, but I do not want to have so strange Validation Report from ADIT. Many thanks for any idea. Petr PS: Not important, but refined with REFMAC5 at medium resolution. -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
[ccp4bb] How to create a link-record
Hello All, I have a covalent link in my structure model that I created using JLigand. I manually typed the link record in the header information of the pdb file, however when I refine the structure using this pdb, the output pdb does not show the link record. Please can anyone help me with establishing a link record in the pdb? Thank you very much, Subhangi
Re: [ccp4bb] Waters in ADIT
On Wed, 2011-06-22 at 14:10 +0200, Petr Kolenko wrote: Some of them have 2.7 AA contacts to main chain! it may be a good idea to report this to the PDB, this seems like a bug. -- Hurry up before we all come back to our senses! Julian, King of Lemurs
Re: [ccp4bb] hello
In addition to Fred's suggestion, are you certain about your space group ? I assume you tried phaser with different space groups turned on ? Another thing to look at maybe the model you are using for MR has some extensions that lead to clashes in your crystal packing and therefore the second molecule can not be placed. You can trim your model to a core and try searching with that. Or if your one molecule is correctly placed do some rigid body refinement, then use this solution as fixed input model for molrep and try placing the second one. How does your selfrotation function look like ? 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/ On Jun 22, 2011, at 5:08, Afshan Begum afshan...@yahoo.com wrote: Dear all, Could any one help me regarding my serious problem actually i have collected data at 3.0 and cut off 3.1 where the data statics showed the good values for the further processing. According to the methew coefficient there would be two molecule in the asymmetric unit but after running the molrep its provide only one monomer instead of two, for this reason R values is very high 50%. Actually homologous model having P6322 space group where as my one is F4132. I had tried to run phaser as well phenix but both were failed to process further. i really do not know how can i get the second chain in my structure. Please if you have some ideas i will appreciate and would be many thankful to you. Hope to hearing you soon Best Regards AFSHAN
Re: [ccp4bb] How to create a link-record
dear Subhangi, have a look at http://www.ysbl.york.ac.uk/mxstat/JLigand/tutorial_link.html#link cheers Stefan On Wed, 22 Jun 2011 14:04:31 +0100 Subhangi Ghosh subhang...@gmail.com wrote: Hello All, I have a covalent link in my structure model that I created using JLigand. I manually typed the link record in the header information of the pdb file, however when I refine the structure using this pdb, the output pdb does not show the link record. Please can anyone help me with establishing a link record in the pdb? Thank you very much, Subhangi Dr Stefan Gerhardt Albert-Ludwigs-Universität Freiburg Inst.f.Org.Chem.u.Biochem Albertstrasse 21 79104 Freiburg Tel. +49 761 2035970 Fax. +49 761 2036161
Re: [ccp4bb] Waters in ADIT
In my experience ADIT (or ADIT2) is aware of symmetry mates, and gives a different message for waters related to them- something about these waters will be moved for you if you don't do it yourself. I would go ahead and deposit, and when you are given the final file to OK for release, if it erroneously indicates isolated waters point out the error to your helpful annotator. (actually someone from pdb or pdbe will probably post a reply shortly). eab Petr Kolenko wrote: No. Some of them have 2.7 AA contacts to main chain!, some of them are in second, or third solvatation shell. And they are not distributed around some special area. It is somehow random. Thanks anyway! Petr 2011/6/22 Charles Allerstoncharles.allers...@sgc.ox.ac.uk: Are they bound to the symmetry-related molecule? cheers, charlie Dr. Charles Allerston Genome Integrity Group Structural Genomics Consortium Nuffield Department of Medicine Old Road Campus University of Oxford OX3 7DQ http://www.sgc.ox.ac.uk/ -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr Kolenko Sent: 22 June 2011 12:18 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Waters in ADIT Dear colleagues, I want to deposit one structure, but ADIT reports tens more waters that are further than 3.5 AA away from macromolecule atoms. I inspected about half of them manually, but all of them are OK. I have observed this incorrect behavior of ADIT also in one previous structure for deposition, but just ignored three or four reports, because I knew, I was doing the right thing. Does anyone know how to solve this problem? I have already tried: - changing HETATM to ATOM - assigning different chain ID for waters to have same ID as protein chain - renumbering of residues (not in this case, but the previous one) I do not have to solve this problem, but I do not want to have so strange Validation Report from ADIT. Many thanks for any idea. Petr PS: Not important, but refined with REFMAC5 at medium resolution. -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
Re: [ccp4bb] Waters in ADIT
Dear Petr, I guess ADIT only looks for interaction between water molecules and the protein and does not take into account the interactions between water molecules. So if a water molecule interacts with another water molecule but not with the protein, ADIT will give you these error report even though the water is well coordinated. On Jun 22, 2011, at 1:18 PM, Petr Kolenko wrote: Dear colleagues, I want to deposit one structure, but ADIT reports tens more waters that are further than 3.5 AA away from macromolecule atoms. I inspected about half of them manually, but all of them are OK. I have observed this incorrect behavior of ADIT also in one previous structure for deposition, but just ignored three or four reports, because I knew, I was doing the right thing. Does anyone know how to solve this problem? I have already tried: - changing HETATM to ATOM - assigning different chain ID for waters to have same ID as protein chain - renumbering of residues (not in this case, but the previous one) I do not have to solve this problem, but I do not want to have so strange Validation Report from ADIT. Many thanks for any idea. Petr PS: Not important, but refined with REFMAC5 at medium resolution. -- Petr Kolenko kole...@imc.cas.cz http://kolda.webz.cz
[ccp4bb] Y-Chi2 running out of chart
Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing attachment: Chi1.gif
Re: [ccp4bb] Y-Chi2 running out of chart
What is your cold stream - phi axis relative and absolute orientation? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jun 22, 2011, at 19:22 , bie gao wrote: Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing Chi1.gif
[ccp4bb] How to feed local structures to BALBES?
I would like to provide BALBES a set of locally-generated models to use as MR probes. These files contain SEQRES records and an arbitrary CRYST1 record CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 followed by the usual ATOM records. I created a subdirectory ./myprobes containing the models, and invoked BALBES using balbes -o `pwd` -f 182-3-h32.mtz -s Lm3759.pir -l myprobes/ However, balbes apparently could not interpret the PDB files. In the top level output it says #---# # Model Database Analysis # #---# number of amino acids in the input sequence file is 113 4 structures found to be above 15% identity with the given sequence, Error message : no structure was found In process_details/get_structure*log it gave messages like: -- monomers start === == structure 1 INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 === -- monomers -- ==:U__1___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file === == structure 2 INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 === -- monomers -- ==:U__5___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file Do I need to pre-process the PDB files somehow before giving them to BALBES? I notice that its own database is not really in PDB format. I used BALBES_1.1.4 (Linux) Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Y-Chi2 running out of chart
The two most likely possibilities are: 1. Beam position changed somewhat after the repair and the site file was not updated with the new position. This could result in misindexing of the diffraction pattern with poor positional agreement (Chi2) as a consequence. The diagnosis of misindexing is very simple, as it will not produce acceptable merging statistics even in P1 space group. The correction is also simple: by updating the site file with the correct beam position. 2. A non-ideal crystal with a complex spot shape in its diffraction pattern. This could result, for example, from uneven cooling rates and variability in the crystal lattice. Merging statistics should be acceptable, however they may not be perfect. Better cryo-cooling is likely to help. Zbyszek Otwinowski Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353 Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] Y-Chi2 running out of chart
If you make your images available via ftp, I can take a closer look and come up with plausible explanations and fixes. Did you lock down the phi-axis? _ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of bie gao Sent: Wednesday, June 22, 2011 11:23 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Y-Chi2 running out of chart Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing
Re: [ccp4bb] How to feed local structures to BALBES?
Hi Ethan, You need to put the files of PDB format in your own database or library. The error message in get_structure*log shows that BALBES encountered problems when it started to read your files to prepare the template models. Thanks, Fei On Wed, 22 Jun 2011 10:26:26 -0700, Ethan Merritt merr...@u.washington.edu wrote: I would like to provide BALBES a set of locally-generated models to use as MR probes. These files contain SEQRES records and an arbitrary CRYST1 record CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 followed by the usual ATOM records. I created a subdirectory ./myprobes containing the models, and invoked BALBES using balbes -o `pwd` -f 182-3-h32.mtz -s Lm3759.pir -l myprobes/ However, balbes apparently could not interpret the PDB files. In the top level output it says #---# # Model Database Analysis # #---# number of amino acids in the input sequence file is 113 4 structures found to be above 15% identity with the given sequence, Error message : no structure was found In process_details/get_structure*log it gave messages like: -- monomers start === == structure 1 INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 === -- monomers -- ==:U__1___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file === == structure 2 INFO: Nmod= 3 Percent of volume: 25.7 Limit: 0.80 === -- monomers -- ==:U__5___u ERR: Number of atoms = 0 ERROR: in READPDB read user pdb file Do I need to pre-process the PDB files somehow before giving them to BALBES? I notice that its own database is not really in PDB format. I used BALBES_1.1.4 (Linux) Ethan
Re: [ccp4bb] Problem running shelxC/D/E
Thanks, Boaz, That was the problem. Once programs were moved to $CBIN directory they worked fine through either ccp4i or hkl2map GUI. Thanks also George and Tim for useful hints. Huiying On Tue, 21 Jun 2011, Boaz Shaanan wrote: They should reside in the $CBIN directory for the gui to see them, is that where you have them installed? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Huiying Li [h...@crystal.bio.uci.edu] Sent: Tuesday, June 21, 2011 9:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problem running shelxC/D/E We had trouble running shelxC/D/E through ccp4i (CCP4 Suite 6.1.13 CCP4Interface 2.0.6). The log file gave the following error: shelxC: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory We do have the shelx programs installed in the system. Any help to trouble shoot this problem is appreciated. Huiying Li, Ph. D Department of Molecular Biology and Biochemistry Natural Sciences I, Rm 2443 University of California at Irvine Irvine, CA 92697, USA Tel: 949-824-4322(or -1953); Fax: 949-824-3280 email: h...@uci.edu
[ccp4bb] Call for paper International Interdisciplinary Science Conference 2011
Dear colleagues I am pleased to inform that we are organizing an international conference entitled, “International Interdisciplinary Science Conference (I-ISC, 2011) On Bioinformatics: An interface between Computer Science and Biology” on 15-17, November 2011. The purpose of this conference is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of life science. Bioinformatics conference aims at providing a unique platform to both academia as well as medical industry to meet and share the cutting-edge development in the field. The conference provides varied opportunities for the scientists to exchange new ideas and application experiences face to face, to establish business, research and other professional relations and to find global partners for future collaboration. For more detail please visit our web page www.i-isc.com Looking for your active participation! = Md. Imtiyaz Hassan, Ph.D. Assistant Professor (Biophysics) Centre for Interdisciplinary Research In Basic Saciences Jamia Millia Islamia New Delhi 10025, INDIA TeleFax: +91 11 26983409 Mob-9311323414 9990323217 E-mail: mihas...@jmi.ac.in http://www.jmi.nic.in/cirbs/cirbs.htm
Re: [ccp4bb] Y-Chi2 running out of chart
As a follow up to the excellent suggestions made by others I would suggest that a close examination of x-file headers may reveal abnormalities in e.g. crystal orientation -- suspecting an unlocked or drifting goniostat. It may also indicate a precession around the phi, which should also manifest itself in a systematic deviation of average intensities (i.e. scale factors) in a similar pattern (assuming uneven illumination of the crystal). Sometimes the precession is caused by a bubble or a tiny chunk of ice trapped under the pin, it can melt unevenly and re-align the pin a few minutes into the run (something similar used to happen a lot at one or two beam lines and it drove me nuts until I figured out the need to re-align the crystal after the initial screening). Artem On Wed, Jun 22, 2011 at 11:22 AM, bie gao gao...@gmail.com wrote: Dear Colleagues, I'm collecting a dataset on our recently repaired Rigaku home source. Crystal diffracts to 2.2A. Indexing seems to be all fine. However, during integration, I realize Y-Chi2 is increasing constantly (from 2 to 4.5, almost linear) within 60 degree collection, whereas X-Chi2 stays the same. An image is attached. There are still another 60 degree to go. Although the prediction fits the images well so far, I'm afraid the Y-Chi2 will eventually run out of the chart. My question is could it be related to any hardware malfunctioning, i.e., goniometer, image plates, etc, which may be a side effect of the recent major repair? Or what else it can be? Thanks, Bing
