Re: [phenixbb] On Mac two separate installations?
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Also, following the protocol as outlined by Andy Karplus in his Science paper on data processing using data extending to CC1/2's near 0.2. Both together seem to really extend the resolution of my datasets and also improve refinement! ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________
On Tue, Jul 23, 2013 at 10:29 AM, Joseph Noel
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps!
Okay, that definitely isn't included in the GUI yet - I was waiting to hear from Pavel before I added it. I am sure Pavel would be interested in seeing any cases where this helps. In general, although we obviously test new methods against existing datasets, it is always more impressive to demonstrate that they help solve new problems. -Nat
Hi Joseph,
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Okay, that definitely isn't included in the GUI yet - I was waiting to hear from Pavel before I added it.
I am sure Pavel would be interested in seeing any cases where this helps. In general, although we obviously test new methods against existing datasets, it is always more impressive to demonstrate that they help solve new problems.
I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major. The only documentation at present is this set of slides: http://www.phenix-online.org/presentations/fem.pdf which also provides usage instructions (using command line). Nat: yes, it would great to have GUI for this! Thanks! Pavel
Hi Pavel, I just used the FEM maps for the first time today. 3A dataset, marginal maps, some broken density of the main chain in disordered regions. The FEM maps are very impressive and pull out quite some features and waters from the noise, which were not visible before. The broken main chain density cleared up, some disordered side-chains were better defined as well as the inhibitor. It cannot do wonders in case of really disordered regions, as one of my colleagues found out on a pretty tough case, but it is certainly worth a try. Also real space refinement in coot against the FEM maps worked well. In general the maps do not look like a 3A map, but rather 2.5'ish or better, which makes correcting tracing mistakes much easier. Again this is an N of one, so the feedback should be taken with a grain a salt for now, but I think this is a very good tool and worthwhile checking out. Thanks for the development Cheers Carsten -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Pavel Afonine Sent: Tuesday, July 23, 2013 2:08 PM To: PHENIX user mailing list Subject: Re: [phenixbb] feature enhanced maps Hi Joseph,
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Okay, that definitely isn't included in the GUI yet - I was waiting to hear from Pavel before I added it.
I am sure Pavel would be interested in seeing any cases where this helps. In general, although we obviously test new methods against existing datasets, it is always more impressive to demonstrate that they help solve new problems.
I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major. The only documentation at present is this set of slides: http://www.phenix-online.org/presentations/fem.pdf which also provides usage instructions (using command line). Nat: yes, it would great to have GUI for this! Thanks! Pavel _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Dear Pavel, I had a try today for feature enhaced maps on 3.7 and4 A resolution datasets. The maps look great and I feel especially at low resolution this new tool helps a lot to interpret the maps. I would be very much interested to test the fem for e-densities calculated from experimental phases. Is it possible in the future to use heavy atom derived phase information instead of a model to calculate FEMs? Best wishes, Guenter
Hi Joseph,
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Okay, that definitely isn't included in the GUI yet - I was waiting to hear from Pavel before I added it.
I am sure Pavel would be interested in seeing any cases where this helps. In general, although we obviously test new methods against existing datasets, it is always more impressive to demonstrate that they help solve new problems.
I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major.
The only documentation at present is this set of slides: http://www.phenix-online.org/presentations/fem.pdf which also provides usage instructions (using command line).
Nat: yes, it would great to have GUI for this! Thanks!
Pavel
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- PD Dr. Günter Fritz Fachbereich Biologie Universität Konstanz
Hi Guenter, thanks for feedback - very much appreciated! Yes, there is no excuse for not using experimental phases. The only reason it's not there yet is because I did not have a chance to implement it. I'll add to todo list. Pavel On 7/24/13 10:25 AM, Guenter Fritz wrote:
Dear Pavel, I had a try today for feature enhaced maps on 3.7 and4 A resolution datasets. The maps look great and I feel especially at low resolution this new tool helps a lot to interpret the maps. I would be very much interested to test the fem for e-densities calculated from experimental phases. Is it possible in the future to use heavy atom derived phase information instead of a model to calculate FEMs? Best wishes, Guenter
Dear Pavel,
I've been using the feature enhanced maps for a 2.1Å dataset, and it really helped for building those tricky loop-regions.
I also experience the waters to stand out clear in this type of map.
And btw., does it make any sense to calculate a FEM based on a composite omit map?
Best rgds.,
Mads
********************************
Mads Beich-Frandsen, PhD
Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10
08028 Barcelona - Spain
Tel: +34-9340-37188 | Fax: +34-9340-39960
E-mail: [email protected]
On Jul 24, 2013, at 7:25 PM, Guenter Fritz
Dear Pavel, I had a try today for feature enhaced maps on 3.7 and4 A resolution datasets. The maps look great and I feel especially at low resolution this new tool helps a lot to interpret the maps. I would be very much interested to test the fem for e-densities calculated from experimental phases. Is it possible in the future to use heavy atom derived phase information instead of a model to calculate FEMs? Best wishes, Guenter
Hi Joseph,
Thanks Nat! I am trying out the new "Featured Enhanced Map" option. Preliminary analysis says it really helps! Okay, that definitely isn't included in the GUI yet - I was waiting to hear from Pavel before I added it.
I am sure Pavel would be interested in seeing any cases where this helps. In general, although we obviously test new methods against existing datasets, it is always more impressive to demonstrate that they help solve new problems.
I'm glad it worked for you, and I'm very interested to hear any feedback or answer questions. This is still considered under development, though current implementation is stable and ready to use. There might be some changes to the algorithm in future (mostly to make it faster, so it can be routinely run after refinement, for example), but I don't think these changes will be major.
The only documentation at present is this set of slides: http://www.phenix-online.org/presentations/fem.pdf which also provides usage instructions (using command line).
Nat: yes, it would great to have GUI for this! Thanks!
Pavel
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- PD Dr. Günter Fritz Fachbereich Biologie Universität Konstanz
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Mads,
I've been using the feature enhanced maps for a 2.1Å dataset, and it really helped for building those tricky loop-regions.
oh good!
I also experience the waters to stand out clear in this type of map.
Yes, they should (especially those that are real, as opposed to noise!).
And btw., does it make any sense to calculate a FEM based on a composite omit map?
Conceptually yes, though currently the procedure requires model and Fobs data and it computes the 2mFo-DFc map internally and then applies FEM protocol. I may extent it to other map types in future. Pavel
participants (6)
-
Guenter Fritz -
Joseph Noel -
Mads Beich-Frandsen -
Nathaniel Echols -
Pavel Afonine -
Schubert, Carsten [JRDUS]