Anomalous difference map calcluation
Dear All, I'm looking at my anomalous difference map from phenix.refine and it seems more or less random distributions of electron density peaks. I know that the signal is there since I solved it with SAD. I'm using I(+/-) for refinement and everything seems to work fine except the map generation. The only thing that worries me is that during the creation of _data file for refinement DANO column was not preserved. Is it necessary for phenix.refine in order to generate the anomalous difference map? How can I make sure that the DANO column is preserved (if necessary)? And by the way why is anomalous map file not generated just coefficients in the mtz? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[@]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940
Hi Andrzej,
there is a bug there that we have to fix. Sorry about this.
Pavel.
----- Original Message -----
From: Jendrek
Dear All,
I'm looking at my anomalous difference map from phenix.refine and it seems more or less random distributions of electron density peaks. I know that the signal is there since I solved it with SAD. I'm using I(+/-) for refinement and everything seems to work fine except the map generation. The only thing that worries me is that during the creation of _data file for refinement DANO column was not preserved.
Is it necessary for phenix.refine in order to generate the anomalous difference map? How can I make sure that the DANO column is preserved (if necessary)?
And by the way why is anomalous map file not generated just coefficients in the mtz?
Regards, Andrzej
--
Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[@]helsinki[.]fi)
Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND
TEL.: 358 9 191 58955 FAX : 358 9 191 59940 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi everyone, I would like to use REEL, but get the following error message and only parts of the gui are displayed. (python:7745): Gtk-Warning **: GModule initialization check failed: Gtk+ version too old (micro mismatch) I looked through repositories, but am not entirely sure what I need to update. I am using Suse10.3 (x86_64) Thanks a lot for your help in advance! Sabine ------------------------------------------ Dr. Sabine Schneider Ludwig-Maximilians-University Department of Chemistry and Pharmacy Butenandtstrasse 5-13, Building F 81377 Munich Germany Phone: +49 (0)89 2180 77846 Fax: +49 (0)89 2180 77756 http://www.carellgroup.de/
Hi, If what you're trying to do is to verify which atoms are anomalous scatterers, then you might want to use Phaser for this. In our experience, this gives us much better results than conventional model- phased anomalous difference Fouriers. (I don't know how this would compare with the map that phenix.refine will produce when Pavel fixes the bug, so we'll have to check that later. In any case, phenix.refine will be using functions from Phaser in the not-too- distant future, so the two approaches should converge.) At the moment, you have to run Phaser from a shell script, but we'll be making a Python-based command (something like "phenix.find_anomalous_scatterers_from_model", or perhaps something less wordy). If you want to run a test job, you can do this with the data distributed as example 5b from the Phenix examples (http://www.phenix-online.org/documentation/refinement_examples.htm ). Just give the command: phenix.run_refinement_example 5b This will create a data subdirectory and an example_5b subdirectory with some refinement results. Give the command "cd example_5b" to get into the results directory. In the MTZ file for this example, the Friedel pairs are given separate indices hkl and -h-k-l, like in CNS, instead of being put in F+ and F- columns for a single hkl, as Phaser expects. It turns out you can pair them up with the command: phenix.reflection_file_converter --label="FOBS,SIGFOBS" ../data/ mdg.mtz --mtz=mdg_paired.mtz Phaser wants some idea of the composition of the crystal to put the data on absolute scale, so you can make a file called mdg.seq with the line "UGAGGU" to represent the nucleic acid sequence. Now use Phaser to make an initial SAD log-likelihood-gradient (LLG) map, using the refined structure as a partial model containing only real scatterers. For the LLG map, Phaser needs to know what atom type it is looking for. Because we want to find the imaginary scattering that is missing from the model of real scatterers, we compute an LLG map looking just for imaginary scatterers. The following script will run this job: phenix.phaser << eof > SAD_LLG_initial.log TITLE initial SAD LLG map MODE EP_AUTO HKLIN mdg_paired.mtz LLGCOMPLETE CRYSTAL mdg COMPLETE OFF LLGCOMPLETE CRYSTAL mdg SCATTERING ANOMALOUS PARTIAL PDB 5b_001.pdb IDENT 1.0 CRYSTAL mdg DATASET peak LABIN F+=FOBS(+) SIGF+=SIGFOBS(+) F-=FOBS(-) SIGF-=SIGFOBS(-) COMPOSITION NUCLEIC SEQUENCE mdg.seq NUMBER 1 ROOT SAD_LLG_initial eof You can look at the map from this in coot (columns FLLG/PHLLG in SAD_LLG_initial.mtz) and see that there is a 28-sigma peak at the position of the Br atom. However, Phaser can do better than that (at least in the version that will appear in the upcoming rc3 release of Phenix; unfortunately there's a bug in completing the substructure for purely imaginary scatterers in the version distributed with the rc2 release). If the imaginary scattering from this peak is included in the model and its position, occupancy and B-factor are refined, then the next LLG map will show (with better signal to noise) where there are other anomalous scatterers that would improve the SAD likelihood target. So, when the rc3 version of Phenix is released, you will be able to run this job: #! /bin/csh phenix.phaser << eof > SAD_LLG_complete.log TITLE SAD LLG completion with imaginary scatterers MODE EP_AUTO HKLIN mdg_paired.mtz LLGCOMPLETE CRYSTAL mdg COMPLETE ON LLGCOMPLETE CRYSTAL mdg SCATTERING ANOMALOUS PARTIAL PDB 5b_001.pdb IDENT 1.0 CRYSTAL mdg DATASET peak LABIN F+=FOBS(+) SIGF+=SIGFOBS(+) F-=FOBS(-) SIGF-=SIGFOBS(-) COMPOSITION NUCLEIC SEQUENCE mdg.seq NUMBER 1 ROOT SAD_LLG_complete eof This carries on after the first cycle to find a second site (Co at 19- sigma) and a third site (one of the Na+ ions at 7-sigma). This carries on iteratively, and Phaser finds an additional two anomalous scatterers at the positions of two more of the Na+ ions. Now, note that the LLG map produced by this job is relatively featureless, because the most significant anomalous scatterers have been found, and the map is just looking for sites with missing anomalous scatterers. With the version of Phaser in the rc2 release, however, you can carry out completion looking for a particular anomalous scatterer type, say Br atoms. In this case, when it finds and adds an anomalous scatterer, it deletes clashing atoms from the real (partial) structure before carrying out the next cycle of refinement. Because we're picking a particular anomalous scatterer type, Phaser needs an estimate of the f" value for this atom, which we can provide by guessing that the data were collected with a wavelength around 0.9A. (For the purely imaginary scatterer, the initial f" is set to 1, so the wavelength doesn't matter.) Here is the job: #! /bin/csh phenix.phaser << eof > SAD_LLG_complete_Br.log TITLE SAD LLG completion with Br MODE EP_AUTO HKLIN mdg_paired.mtz LLGCOMPLETE CRYSTAL mdg COMPLETE ON LLGCOMPLETE CRYSTAL mdg SCATTERING ELEMENT Br CRYSTAL mdg DATASET peak SCATTERING WAVELENGTH 0.9 PARTIAL PDB 5b_001.pdb IDENT 1.0 CRYSTAL mdg DATASET peak LABIN F+=FOBS(+) SIGF+=SIGFOBS(+) F-=FOBS(-) SIGF-=SIGFOBS(-) COMPOSITION NUCLEIC SEQUENCE mdg.seq NUMBER 1 ROOT SAD_LLG_complete_Br eof In this case, even though the peak height in the LLG map that finds the Br atom isn't as high, the completion goes a bit further, identifying one more Na+ ion and one of the P atoms from the backbone. However, normally I would expect the completion with a purely imaginary scatterer to be better, when starting from a final refined model. I hope this helps and does not confuse the issue too much! Randy Read On 15 Jul 2008, at 14:03, Jendrek wrote:
Dear All,
I'm looking at my anomalous difference map from phenix.refine and it seems more or less random distributions of electron density peaks. I know that the signal is there since I solved it with SAD. I'm using I(+/-) for refinement and everything seems to work fine except the map generation.
The only thing that worries me is that during the creation of _data file for refinement DANO column was not preserved.
Is it necessary for phenix.refine in order to generate the anomalous difference map? How can I make sure that the DANO column is preserved (if necessary)?
And by the way why is anomalous map file not generated just coefficients in the mtz?
Regards, Andrzej
--
Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[@]helsinki[.]fi)
Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND
TEL.: 358 9 191 58955 FAX : 358 9 191 59940 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk
participants (4)
-
Jendrek -
Pavel Afonine -
Randy Read -
Sabine Schneider