All I have 4 molecules in my ASU and I had phenix pick out my NCS operators automatically. Do a round of refinement, load 2fofc maps into coot and ask to calculate NCS Maps (Calculate -> NCS Maps). I have three new maps mapping a single chain onto the other chains (3) and an NCS average map. I look at some of the NCS maps and the question is should the model (all the chains) match to every NCS map? In my set of 3 maps, the model fits one map (independent of chain) but seems offset in the other two maps. Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to). Thanks! FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis,
Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to).
Just something to keep in mind... I always prefer to run two refinements in parallel with and without using NCS. It's resolution (and data-to-parameters ratio) dependent. I've seen a number of cases where using the NCS is very beneficial and similar number of cases where it's better to not use NCS (mostly at resolutions ~2-2.5A). I would also check manually the NCS groups that are found by phenix.refine automatically. I have some cases where automatic detection did not yield a good selection. Pavel.
I was wondering if there a consensus of when it is mandatory to use ncs in refinement. Is is dependent on: 1. resolution? 2. data-to-parameter ratio? 3. difference between Rcryst & Rfree? 4. something else... Or does one just do as Pavel states and try both ways ? Regards, Kate Pavel Afonine wrote:
Hi Francis,
Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to).
Just something to keep in mind... I always prefer to run two refinements in parallel with and without using NCS. It's resolution (and data-to-parameters ratio) dependent. I've seen a number of cases where using the NCS is very beneficial and similar number of cases where it's better to not use NCS (mostly at resolutions ~2-2.5A).
I would also check manually the NCS groups that are found by phenix.refine automatically. I have some cases where automatic detection did not yield a good selection.
Pavel.
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Hi Kate, one can endlessly talk about this matter and there is a number of good papers out there. At some point I spent significant amount of time trying to address the questions you mention below. I selected all structures from PDB for which NCS is available and re-refined them with and without NCS. My goal was to answer this question: given a model and data, can I tell for sure if I need to use NCS or it's better to refine without using NCS. In the end I couldn't derive any reliable formula to be able to decide if I need to use NCS or not. All I re-discovered was the old and well known fact: if have have NCS, then lower the resolution, more likely you want to use NCS -:) Obviously, at ~1.5A resolution the use of NCS was only damaging. And ~2.0A is kind of "gray area". So this is why I wrote in my previous email that it is much easier, quicker and reliable to just try both ways and see which one works better, rather than waste time on speculating -:) Cheers, Pavel. On 8/25/2008 11:33 AM, Kate Kavanagh wrote:
I was wondering if there a consensus of when it is mandatory to use ncs in refinement. Is is dependent on:
1. resolution? 2. data-to-parameter ratio? 3. difference between Rcryst & Rfree? 4. something else...
Or does one just do as Pavel states and try both ways ?
Regards, Kate
Pavel Afonine wrote:
Hi Francis,
Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to).
Just something to keep in mind... I always prefer to run two refinements in parallel with and without using NCS. It's resolution (and data-to-parameters ratio) dependent. I've seen a number of cases where using the NCS is very beneficial and similar number of cases where it's better to not use NCS (mostly at resolutions ~2-2.5A).
I would also check manually the NCS groups that are found by phenix.refine automatically. I have some cases where automatic detection did not yield a good selection.
Pavel.
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Thanks for the reply Pavel However, with regard to the NCS maps issue, which should I be building to?Does the 2fofoc that phenix puts out adjusted for ncs and use that? Thanks FR On Aug 25, 2008, at 11:59 AM, Pavel Afonine wrote:
Hi Francis,
Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to).
Just something to keep in mind... I always prefer to run two refinements in parallel with and without using NCS. It's resolution (and data-to-parameters ratio) dependent. I've seen a number of cases where using the NCS is very beneficial and similar number of cases where it's better to not use NCS (mostly at resolutions ~2-2.5A).
I would also check manually the NCS groups that are found by phenix.refine automatically. I have some cases where automatic detection did not yield a good selection.
Pavel.
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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, If you are using autobuild, then it will by default identify the NCS and build into a NCS-based density-modified map. If you build by hand, I'd recommend the same map anyhow, because this map has automatically adjusted weighting on the NCS, so that regions that do not show the NCS should not be averaged (much) and those that do show NCS are more NCS-averaged in the density modification procedure. I think if you use the 2Fo-Fc map it will not be adjusted for NCS, but rather will show a standard map. This map may also be useful to consult to verify what parts of the structure really are different in different NCS copies. -Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Aug 25, 2008, at 1:37 PM, Francis E Reyes wrote:
Thanks for the reply Pavel
However, with regard to the NCS maps issue, which should I be building to?Does the 2fofoc that phenix puts out adjusted for ncs and use that?
Thanks
FR
On Aug 25, 2008, at 11:59 AM, Pavel Afonine wrote:
Hi Francis,
Also if anyone has a paper/protocol for NCS refinement, I'd love to check it out (to figure out which map to fit to).
Just something to keep in mind... I always prefer to run two refinements in parallel with and without using NCS. It's resolution (and data-to-parameters ratio) dependent. I've seen a number of cases where using the NCS is very beneficial and similar number of cases where it's better to not use NCS (mostly at resolutions ~2-2.5A).
I would also check manually the NCS groups that are found by phenix.refine automatically. I have some cases where automatic detection did not yield a good selection.
Pavel.
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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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participants (4)
-
Francis E Reyes -
Kate Kavanagh -
Pavel Afonine -
Tom Terwilliger