Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Yuri et al., I like the fact that one must not use the output mtz-file from refmac as input to the next round of refinement. It encourages to think about why this is and then makes you realise what your data really are: the result of data processing and that the coordinate file is only a model which one tries to make as consistent as possible with the data. Tim On 12/11/2011 06:28 AM, Yuri Pompeu wrote: > PHENIX has an otpion under the reflection editor program that will create R > flags that are compatible with ccp4 programs. > Another point worth mentioning is in phenix.refine it is appropriate to use > the data.mtz files generated each round of refinement, as these are the raw > data plus the Rfree flags. In refmac however the newly generated refmacX.mtz > file contains phase info as PHIC calculated from your model. Using this for > subsequent rounds of refinement results in terrific looking maps as they are > now biased (even more so) by the input model. > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFO5MbDUxlJ7aRr7hoRAqPtAJ97ftne0fQXVPoCMOXZl1fK/AcL9wCfdVvF I3bJWTQdMoPUTyZ4y6idMaQ= =qysO -END PGP SIGNATURE-
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
On Sun, 2011-12-11 at 05:28 +, Yuri Pompeu wrote: > In refmac however the newly generated refmacX.mtz file contains phase > info as PHIC calculated from your model. Using this for subsequent > rounds of refinement results in terrific looking maps as they are now > biased (even more so) by the input model. PHIC won't be used in refinement unless you specify it, so this can't happen if you just use the refmac output mtz. AFAIU, the reason the output mtz should never be used in subsequent refinement is because the Fo's are modified. I never understood why one would even have an idea of using the output mtz as a new input. Maybe you can explain this to me at last. Cheers, Ed. -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] PHENIX vs REFMAC refinement had me fooled
Precisely, one should not use it! I have seen people do it either because they dont fully understand what is going on or are not at all familiar with the documentation. In phenix the output .mtz contains Fo plus x% Rfree flag=1, so one may try and do this for refmac because of one of the two above mentioned reasons (or both) On Sun, 11 Dec 2011 20:41:48 -0500, Ed Pozharski wrote: On Sun, 2011-12-11 at 05:28 +, Yuri Pompeu wrote: In refmac however the newly generated refmacX.mtz file contains phase info as PHIC calculated from your model. Using this for subsequent rounds of refinement results in terrific looking maps as they are now biased (even more so) by the input model. PHIC won't be used in refinement unless you specify it, so this can't happen if you just use the refmac output mtz. AFAIU, the reason the output mtz should never be used in subsequent refinement is because the Fo's are modified. I never understood why one would even have an idea of using the output mtz as a new input. Maybe you can explain this to me at last. Cheers, Ed. -- Yuri Pompeu
