Looking at omit maps in coot

newer
geometry_restraints between sym...

xaravich ivan

15 May 2010 15 May '10

12:40 a.m.

Hi, Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless. Thanks, Ivan

Attachments:

attachment.html (text/html — 495 bytes)

Show replies by date

Nathaniel Echols

15 May 15 May

12:52 a.m.

On Fri, May 14, 2010 at 5:40 PM, xaravich ivan wrote:

...

Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless.

Some clarification: 1. Which version of Phenix, and which platform? 2. GUI or command-line? 3. If you're really making a composite omit map (as opposed to a simple omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and stick to the original. One common problem is that on Mac, if you try to open the MTZ file in Coot (using the "Open MTZ", not auto-open), it will open a window to choose column labels in the file, but it opens *behind* the main window, which you need to move to the side temporarily. -Nat

xaravich ivan

1:45 a.m.

Thanks Nat, Its the latest version I downloaded less than a week back. It is in Mac OS X. I am using GUI. Basically I have made most of the model and as it was from Molecular Replacement it still has that high R free and I am sure that parts of the model has that bias and does not fit niceley. I deleted those regions and used SA_omit map in phenix GUI. It made a composite omit map by default. and it has made those number of regions of pdb and mtz files. The coot is distinctly indicating that it could not open the map/mtz. even when I try to open from phenix or separately from command line. Thanks, Ivan On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols wrote:

...

On Fri, May 14, 2010 at 5:40 PM, xaravich ivan wrote:

...
Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless.

Some clarification:

1. Which version of Phenix, and which platform? 2. GUI or command-line? 3. If you're really making a composite omit map (as opposed to a simple omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and stick to the original.

One common problem is that on Mac, if you try to open the MTZ file in Coot (using the "Open MTZ", not auto-open), it will open a window to choose column labels in the file, but it opens *behind* the main window, which you need to move to the side temporarily.

-Nat

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nathaniel Echols

17 May 17 May

7:11 p.m.

On Fri, May 14, 2010 at 6:45 PM, xaravich ivan wrote:

...

Its the latest version I downloaded less than a week back. It is in Mac OS X. I am using GUI. Basically I have made most of the model and as it was from Molecular Replacement it still has that high R free and I am sure that parts of the model has that bias and does not fit niceley. I deleted those regions and used SA_omit map in phenix GUI. It made a composite omit map by default. and it has made those number of regions of pdb and mtz files.

FYI, if you are generating a composite omit map, you do not need to delete anything first. If you just want to look at a specific region, there are much faster ways to do this: 1. Specify the region to omit "Omit map options->Omit region specification", either using a PDB file containing the atoms to leave out, or an atom selection. or 2. delete the region manually, then run phenix.refine with simulated annealing for a couple of macrocycles, and look at those maps. As long as you have simulated annealing turned on (always a good idea for omit maps), these are approximately equivalent. The composite omit procedure basically does (2) for every region of the model, then stitches the maps around those regions back together, so it will take ~20x longer to run. The coot is distinctly indicating that it could not open the map/mtz. even

...

when I try to open from phenix or separately from command line.

That sounds bad. Could you please send me (not the list!) the final MTZ file? thanks, Nat

5338

Age (days ago)

5340

Last active (days ago)

List overview

Download

3 comments

2 participants

participants (2)

Nathaniel Echols
xaravich ivan