Dear Modeller users,
I have generated some models using Modeller, and I wonder if you could recommend the best way to evaluate them. My sequence homology between modeled protein and the templates is about 30%, so the confidence in some regions of the sequence alignments is low.
I have generated several plots for energy versus residue number using ProsaII, and these show quite nicely which regions have poorer structure. These correlate to regions of low sequence conservation in the alignments.
My question to you is how valid the more specific analyses of atomic-level contacts in the models would be. I have run Procheck and Whatif analyses as well, and the quality check scores are within acceptable ranges. In cases with 30% homology I would expect many errors in atom placements, so should I even consider these stereochemical and packing constraints?
Can you recommend a good reference that discusses these issues?
Thanks very much for your help.
Sincerely,
Giselle Knudsen graduate student, CCB Program University of California San Francisco knudsen@cgl.ucsf.edu
Hi-
Will modeller perform a calculation of RMSD (Ca, etc) between the target and template and output the RMSD? I'm looking to have a semi-automated (or automatable) method for doing this (to compare 50+ models at once quickly).
Many thanks, Doug Kojetin
Hi,
Look at MODELLER commands: SUPERPOSE and COMPARE.
Good luck, Bozidar
On Monday May 20 2002 01:49 pm, Douglas Kojetin wrote: > Hi- > > Will modeller perform a calculation of RMSD (Ca, etc) between the target > and template and output the RMSD? I'm looking to have a semi-automated > (or automatable) method for doing this (to compare 50+ models at once > quickly). > > Many thanks, > Doug Kojetin
Hi-
I figured out how to get an RMSD fit using the following script (look correct?):
######################################## # RMSD script ######################################## SET OUTPUT_CONTROL = 1 1 1 1 1
READ_MODEL FILE = 'B99990100' SEQUENCE_TO_ALI ATOM_FILES = 'B99990100', ALIGN_CODES = 'B99990100' READ_MODEL FILE = '../../atom_files/template' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'template', ; ALIGN_CODES = ALIGN_CODES 'template' ALIGN GAP_PENALTIES_1D = -600 -400 ALIGN3D GAP_PENALTIES_3D = 0 2.0 WRITE_ALIGNMENT FILE = 'B99990100.ali'
READ_MODEL FILE = 'sB99990100' PICK_ATOMS ATOM_TYPES = 'CA' READ_MODEL2 FILE = '../../atom_files/template' SUPERPOSE FIT_ATOMS = 'CA' ########################################
This is my output from the .log file
######################################## # output ######################################## Least-squares superposition:
PICKed MODEL atoms are used for superposition if they have equivalent atoms in MODEL2
Superposition done : T Numb of residues in MODEL : 120 Numb of atoms/sel atoms in MODEL : 959 120 Numb of residues in MODEL2 : 122 Numb of atoms in MODEL2 : 980 Equivalences refinement : F Numb of aligned equiv positions : 113 Numb of aligned equiv distances : 6328 RMS before superposition : 44.1902 RMS after superposition : 1.3978 DRMS : 1.1250
Distance cutoff : 3.5000 Numb of equiv cutoff positions : 112 Numb of equiv cutoff distances : 6304 Cutoff RMS after superposition : 1.3642 Cutoff DRMS : 1.1009 ########################################
My question is -- what exactly do all the categories/listings mean? I looked (briefly) in the manual for an explanation for each but could not find one.
I guess in a round-about way -- which value should I use for my alpha carbon value RMSD when comparing models?
Many thanks, Doug Kojetin
Bozidar Yerkovich wrote:
>Hi, > >Look at MODELLER commands: SUPERPOSE and COMPARE. > >Good luck, >Bozidar > > > >On Monday May 20 2002 01:49 pm, Douglas Kojetin wrote: > >>Hi- >> >>Will modeller perform a calculation of RMSD (Ca, etc) between the target >>and template and output the RMSD? I'm looking to have a semi-automated >>(or automatable) method for doing this (to compare 50+ models at once >>quickly). >> >>Many thanks, >>Doug Kojetin >>
Hi,
The log file says that you have 112 CA positions which are superposable to better than 4.0A and the RMSD over the equivalent positions is 1.3642.
Eashwar.
Douglas Kojetin wrote: > > Hi- > > I figured out how to get an RMSD fit using the following script (look > correct?): > > ######################################## > # RMSD script > ######################################## > SET OUTPUT_CONTROL = 1 1 1 1 1 > > READ_MODEL FILE = 'B99990100' > SEQUENCE_TO_ALI ATOM_FILES = 'B99990100', ALIGN_CODES = 'B99990100' > READ_MODEL FILE = '../../atom_files/template' > SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'template', ; > ALIGN_CODES = ALIGN_CODES 'template' > ALIGN GAP_PENALTIES_1D = -600 -400 > ALIGN3D GAP_PENALTIES_3D = 0 2.0 > WRITE_ALIGNMENT FILE = 'B99990100.ali' > > READ_MODEL FILE = 'sB99990100' > PICK_ATOMS ATOM_TYPES = 'CA' > READ_MODEL2 FILE = '../../atom_files/template' > SUPERPOSE FIT_ATOMS = 'CA' > ######################################## > > This is my output from the .log file > > ######################################## > # output > ######################################## > Least-squares superposition: > > PICKed MODEL atoms are used for superposition if > they have equivalent atoms in MODEL2 > > Superposition done : T > Numb of residues in MODEL : 120 > Numb of atoms/sel atoms in MODEL : 959 120 > Numb of residues in MODEL2 : 122 > Numb of atoms in MODEL2 : 980 > Equivalences refinement : F > Numb of aligned equiv positions : 113 > Numb of aligned equiv distances : 6328 > RMS before superposition : 44.1902 > RMS after superposition : 1.3978 > DRMS : 1.1250 > > Distance cutoff : 3.5000 > Numb of equiv cutoff positions : 112 > Numb of equiv cutoff distances : 6304 > Cutoff RMS after superposition : 1.3642 > Cutoff DRMS : 1.1009 > ######################################## > > My question is -- what exactly do all the categories/listings mean? I > looked (briefly) in the manual for an explanation for each but could not > find one. > > I guess in a round-about way -- which value should I use for my alpha > carbon value RMSD when comparing models? > > Many thanks, > Doug Kojetin > > Bozidar Yerkovich wrote: > > >Hi, > > > >Look at MODELLER commands: SUPERPOSE and COMPARE. > > > >Good luck, > >Bozidar > > > > > > > >On Monday May 20 2002 01:49 pm, Douglas Kojetin wrote: > > > >>Hi- > >> > >>Will modeller perform a calculation of RMSD (Ca, etc) between the target > >>and template and output the RMSD? I'm looking to have a semi-automated > >>(or automatable) method for doing this (to compare 50+ models at once > >>quickly). > >> > >>Many thanks, > >>Doug Kojetin > >>
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Bozidar Yerkovich -
Douglas Kojetin -
Eashwar Narayanan -
Giselle Knudsen