How do I turn off sidechain rotamer fitting?
I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature? Many thanks, Owen
Hi Owen, you can disable it by turning of real-space refinement off. I'm interested to know what exactly is not going well: could you please explain this to me off list and send files so I can reproduce the problem? Pavel On 7/15/13 10:46 AM, Owen Pornillos wrote:
I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature?
Many thanks,
Owen
Hi Pavel - Thanks for the reply. I have a 2.6 A data set that has a dimer in the asymmetric unit, and so I'm using NCS. Some of the big sidechain densities (LYS, ARG, etc.) are not well-defined so I'd like to just restrain them to the other chain. The auto rotamer fitting of course tries to fit them, and the result is a list of half a dozen or so rotamer violations. I'm going through the list to see if the density truly defines different conformations. I think this is just a general run of the mill problem with fitting/refinement with NCS. Thanks, Owen On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote:
Hi Owen,
you can disable it by turning of real-space refinement off.
I'm interested to know what exactly is not going well: could you please explain this to me off list and send files so I can reproduce the problem?
Pavel
On 7/15/13 10:46 AM, Owen Pornillos wrote:
I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature?
Many thanks,
Owen
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Owen, local real-space refinement will not fit a side-chain into a rotamer outlier: it uses both, map and rotamer library, and also it uses a quite complex logic that aims to find best density fit and at the same time keep good geometry (no outliers of any sort). That's why I wanted to look at the files because to me what you described is an indicator of a problem somewhere else or a bug.. Pavel On 7/15/13 11:56 AM, Owen Pornillos wrote:
Hi Pavel -
Thanks for the reply.
I have a 2.6 A data set that has a dimer in the asymmetric unit, and so I'm using NCS. Some of the big sidechain densities (LYS, ARG, etc.) are not well-defined so I'd like to just restrain them to the other chain. The auto rotamer fitting of course tries to fit them, and the result is a list of half a dozen or so rotamer violations. I'm going through the list to see if the density truly defines different conformations. I think this is just a general run of the mill problem with fitting/refinement with NCS.
Thanks,
Owen
On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote:
Hi Owen,
you can disable it by turning of real-space refinement off.
I'm interested to know what exactly is not going well: could you please explain this to me off list and send files so I can reproduce the problem?
Pavel
On 7/15/13 10:46 AM, Owen Pornillos wrote:
I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature?
Many thanks,
Owen
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
I'm now doing paired refinement with and without real space refinement and will send you the files when they are done. Thanks, Owen On Jul 15, 2013, at 3:03 PM, Pavel Afonine wrote:
Hi Owen,
local real-space refinement will not fit a side-chain into a rotamer outlier: it uses both, map and rotamer library, and also it uses a quite complex logic that aims to find best density fit and at the same time keep good geometry (no outliers of any sort). That's why I wanted to look at the files because to me what you described is an indicator of a problem somewhere else or a bug..
Pavel
On 7/15/13 11:56 AM, Owen Pornillos wrote:
Hi Pavel -
Thanks for the reply.
I have a 2.6 A data set that has a dimer in the asymmetric unit, and so I'm using NCS. Some of the big sidechain densities (LYS, ARG, etc.) are not well-defined so I'd like to just restrain them to the other chain. The auto rotamer fitting of course tries to fit them, and the result is a list of half a dozen or so rotamer violations. I'm going through the list to see if the density truly defines different conformations. I think this is just a general run of the mill problem with fitting/refinement with NCS.
Thanks,
Owen
On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote:
Hi Owen,
you can disable it by turning of real-space refinement off.
I'm interested to know what exactly is not going well: could you please explain this to me off list and send files so I can reproduce the problem?
Pavel
On 7/15/13 10:46 AM, Owen Pornillos wrote:
I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature?
Many thanks,
Owen
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Owen Pornillos -
Pavel Afonine