Dear all, I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program. However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it? Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Almudena, it would be better to go back one step to the scaling and scale the two data sets together. The program you used for scaling each of the two data sets will be able to do so. In XSCALE you would simply declare to INPUT_FILEs and it would do everything right. Merging the anomalous data with the native one would make sense if this would improve the native data set (which has better resolution), i.e. by improving the completeness. Unless you are desperate there is probably not much reason to do so. If you still insist, again you should go back to the scaling step, e.g. with XSCALE as mentioned above. with regards, Tim On 04/14/2015 11:29 AM, Almudena Ponce Salvatierra wrote:
Dear all,
I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program.
However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it?
Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data.
Best,
Almudena
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- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iD8DBQFVLO+WUxlJ7aRr7hoRArujAJwMmSPnE67ND76s6KwDA+JKxdoKFwCggCKE oDz0VF3W2EkbOO+gkOIUE90= =ZDC5 -----END PGP SIGNATURE-----
Hi Almudena, You could use phenix.scale_and_merge for this and give it both datasets. Its purpose is to scale anomalous datasets but it will work with a mixture of datasets as well. (If you wait for tomorrow's nightly build it will work a little more nicely than the current version which crashes after writing out the scaled data to scaled_data.mtz because it expected anomalous data). Note: It may be useful to set the keyword: minimum_datafile_fraction=0.01 so that datasets with few reflections are included (i.e., your low-res data), so your command might look like: phenix.scale_and_merge data=lowres.sca data=native.sca minimum_datafile_fraction=0.01 and this will write out scaled_data.mtz with all the data merged (and scaled). All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Almudena Ponce Salvatierra [[email protected]] Sent: Tuesday, April 14, 2015 3:29 AM To: [email protected] Subject: [phenixbb] reflections file editor Dear all, I would like to merge two datasets containing anomalous signal. If have done so earlier for native data within phenix in the reflections editor by selecting the arrays corresponding to FP and SIGFP and then running the program. However when I try to do so for the anomalous datasets it writes FP SIGFP and FP2 SIGFP2 instead or merging them, so it does with the anomalous signal... so I guess I have basically only one file containing two datasets but not a merged dataset. How can I solve it? Would it be possible, on the other hand, to merge a dataset with anomalous signal with a native one? The intention behind is to extend the resolution to the one of the native data. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany
participants (3)
-
Almudena Ponce Salvatierra -
Terwilliger, Thomas Charles -
Tim Gruene