Structure Comparison questions
Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather [email protected]
Hi Heather, I think phenix.superpose_pdbs (http://www.phenix-online.org/documentation/superpose_pdbs.htm) might do what you want. You can specify atom selections to identify which chains you want to compare. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Heather Condurso [[email protected]] Sent: Wednesday, May 29, 2013 11:11 AM To: [email protected] Subject: [phenixbb] Structure Comparison questions Dear all, I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies? I will try a few things but any advice would be greatly appreciated. Heather [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Wed, May 29, 2013 at 10:11 AM, Heather Condurso
I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies?
Have you tried this yet? http://phenix-online.org/documentation/structure_comparison.htm Note that the superposition is very simplistic - but it will let you compare active site density in the same frame of reference. And it works for both multiple structures and NCS-related chains. -Nat
I can get it to work with different completely different structures but I can't figure out how to compare NCS related chains.
| On Wed, 29 May 2013 10:21:01 -0700
| Nathaniel Echols
On Wed, May 29, 2013 at 10:24 AM, Heather Condurso
I can get it to work with different completely different structures but I can't figure out how to compare NCS related chains.
It's no different than comparing related structures - if it finds multiple copies of the chain of interest in an input PDB file, it will treat each separately. But you probably want to check the box labeled "Superpose processed structures with reference model" (which by default will be the first chain it finds). -Nat
OH! I get it now. I only needed to input the single pdb and mtz and it superimposes each chain! I knew there had to be an easy way! Thank you so much! I feel like I should have been able to figure that out but I guess I haven't had enough coffee today.
~Heather
| On Wed, 29 May 2013 10:28:08 -0700
| Nathaniel Echols
Does PHENIX have a utility that aligns the principal axes of an atom selection along the laboratory orthogonal x,y,z axes? I have done this previously with cns using coord orient sele=(...) end Thanks. Jack -- John J. Tanner Professor of Chemistry and Biochemistry University of Missouri-Columbia 125 Chemistry Building Columbia, MO 65211 Phone: 573-884-1280 Fax: 573-882-2754 Email: [email protected] http://www.chem.missouri.edu/TannerGroup/tanner.html
Are your structures different MR solutions based on the same dataset? If so, then you could use phenix.find_alt_orig_sym_mate to transform one structure to the same ASU and origin as the other. For the transformed pdb file you could then generate a corresponding mtz file using phenix.maps. Regards, Rob On May 29 2013, Heather Condurso wrote:
Dear all,
I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies?
I will try a few things but any advice would be greatly appreciated. Heather [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
On Wed, 2013-05-29 at 13:11 -0400, Heather Condurso wrote:
Dear all,
I have a few related structures that I would like to compare to make figures for publication but I have a few issues. The biggest issue is that my structures are large (12- 422aa chains) and any attempt at simple alignment in pymol results in a crash. I would like to first compare entire structures, but also compare the differences between related chains in the same structure. I want to look at the small differences in the active site density. What is the best way to do this? Is there a simple way to do this or do I need to make separate pdb files for each chain? Can I use the same mtz or should I rename copies?
I will try a few things but any advice would be greatly appreciated. Heather
From what you describe, you need coot - you can show "NCS ghosts" as well as transform maps by NCS.
-- Coot verendus est
participants (6)
-
Ed Pozharski -
Heather Condurso -
Nathaniel Echols -
R.D. Oeffner -
Tanner, John J. -
Terwilliger, Thomas C