polder vs fem vs composite omit map vs maximum entropy
So I got a MR solution and maybe a dozen residues are not clearly defined (most of them in the surface) I used to compute the feature enhanced map but now I can see there are a lot of options in phenix->maps. Which one is better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) Probably I should try them all, and compare them visually in coot with appropiate sigmas (taken from maps-> map comparison) (is that a good workflow? what you guys do?) ...but some of the maps take a lot of time to compute. So any help will be appreciated. Thanks
Hi,
I recommend polder maps for final stages of model building.
But they are computed quickly, so you can nonetheless try and see what
appears in the map.
Best wishes,
Dorothee
On Thu, Jan 19, 2017 at 2:04 PM, Murpholino Peligro
So I got a MR solution and maybe a dozen residues are not clearly defined (most of them in the surface) I used to compute the feature enhanced map but now I can see there are a lot of options in phenix->maps. Which one is better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) Probably I should try them all, and compare them visually in coot with appropiate sigmas (taken from maps-> map comparison) (is that a good workflow? what you guys do?) ...but some of the maps take a lot of time to compute. So any help will be appreciated.
Thanks
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So I got a MR solution and maybe a dozen residues are not clearly defined (most of them in the surface)
Sounds like you are in the beginning of structure solution/refinement.
I used to compute the feature enhanced map but now I can see there are a lot of options in phenix->maps. Which one is better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) Probably I should try them all, and compare them visually in coot with appropiate sigmas (taken from maps-> map comparison) (is that a good workflow? what you guys do?) ...but some of the maps take a lot of time to compute. So any help will be appreciated.
"(Rebuild->Refine) * N_times" until you are done fixing gross errors; maps will be supplied to you be refinement engine each time cycle is over; no need to use "phenix->maps". Then towards the end focus on smaller details. This is when FEM and Polder maps will be most helpful. Make sure you fully understand what each map calculation option does and when it is best to use it. Ask specific questions if not sure. The strategy "try them all and see what happens" is certainly good in some cases (like when trying plausible refinement choices) by does not sound particularity great in your case. Pavel
Dear, at 1.5A resolution you should be fine with the default options, and your maps should be of high quality showing anything you are interested in. Are you looking into anything specific that makes you believe you should try any special features? Best, Tim On Thursday 19 January 2017 04:04:12 PM Murpholino Peligro wrote: > So I got a MR solution and maybe a dozen residues are not clearly defined > (most of them in the surface) I used to compute the feature enhanced map > but now I can see there are a lot of options in phenix->maps. Which one is > better for me? (~130 residues, 1.5 A resolution, ~ 90% complete) > Probably I should try them all, and compare them visually in coot with > appropiate sigmas (taken from maps-> map comparison) (is that a good > workflow? what you guys do?) ...but some of the maps take a lot of time to > compute. So any help will be appreciated. > > Thanks -- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - Principal Investigator Biology and Chemistry OFLC/102 CH-5232 Villigen PSI Phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A
participants (4)
-
Dorothee Liebschner -
Murpholino Peligro -
Pavel Afonine -
Tim Gruene