Dear all, how do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run? Thanks, D. B.
Hello D.B. The restraints are specified in the (output) target model residue numbering, not in any of the templates. You are not restraining the templates, only the model that comes out, so there is no need to specify individual templates in the restraints file. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative> "Distance restraints file (optional) - Specify an input file containing distance restraints (see example file distres.txt). Each line in the file should be of the format: res1 res2 dist stdev where res1 and res2 are residue numbers or ranges of residue numbers in the target sequence, dist is the distance in Å, and stdev is the standard deviation. If a single residue is specified, its Cα will be used to anchor the restraint. If a residue range (e.g. 233-275) is specified, the range's center of mass will be used to anchor the restraint.” See also the Modeller manual <https://salilab.org/modeller/manual/node28.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 14, 2019, at 5:12 PM, Danilo Boškovic <a01406823@unet.univie.ac.at> wrote:
Dear all, how do i add restraints specific to my templates that i use for comparative modelling in chimera? Specifically what are the names assigned to those templates? Do i need the names to specify the template residues that i want to restrain? Are the names same as in the tab when i choose the templates for the run? Thanks, D. B.
Dear all, I have just made a model according to the tutorial for missing residues for Modeller. I wanted all atoms not to move so i used the script at the bottom of the tutorial. It seems to work but when i do match align i can still see a very very slight misalignment in certain areas that are not supposed to be touched. I used residue ranges from the alignment window by just clicking on residues and reading their positions at the bottom of the alignment window (might be an issue with numbering?). As a starting structure i used the structure i wanted to take the loops from and as a template structure i used the structure in which i wanted to fill the loops (100% same, difference is in states). I edited the script in chimera as follows: from modeller import * from modeller.automodel import * namelist = open( 'namelist.dat', 'r' ).read().split('\n') tarSeq = namelist[0] template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] ) log.verbose() env = environ() env.io.atom_files_directory = ['.', './template_struc'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('312', '315'), self.residue_range('630', '642'), self.residue_range('668', '674')) #code overrides the special_restraints method #def special_restraints(self, aln): #code overrides the special_patches method. # e.g. to include the addtional disulfides. #def special_patches(self, aln): a = MyModel(env, sequence = tarSeq, # alignment file with template codes and target sequence alnfile = 'alignment.ali', # PDB codes of the templates knowns = template) a.starting_model = 1 a.ending_model = 1 loopRefinement = False a.assess_methods = (assess.GA341, assess.normalized_dope) a.make() Link to tutorial: https://salilab.org/modeller/wiki/Missing%20residues
Hi Danilo, We aren’t the Modeller group… this is the UCSF Chimera mailing list, and I don’t know the answer to your question. Instead, you may want to look at the Modeller FAQ or wiki, or ask a question on the Modeller forum: <https://salilab.org/modeller/discussion_forum.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 19, 2019, at 3:34 AM, Danilo Boškovic <a01406823@unet.univie.ac.at> wrote:
Dear all,
I have just made a model according to the tutorial for missing residues for Modeller. I wanted all atoms not to move so i used the script at the bottom of the tutorial. It seems to work but when i do match align i can still see a very very slight misalignment in certain areas that are not supposed to be touched. I used residue ranges from the alignment window by just clicking on residues and reading their positions at the bottom of the alignment window (might be an issue with numbering?). As a starting structure i used the structure i wanted to take the loops from and as a template structure i used the structure in which i wanted to fill the loops (100% same, difference is in states). I edited the script in chimera as follows:
from modeller import * from modeller.automodel import *
namelist = open( 'namelist.dat', 'r' ).read().split('\n') tarSeq = namelist[0] template = tuple( [ x.strip() for x in namelist[1:] if x != '' ] )
log.verbose()
env = environ()
env.io.atom_files_directory = ['.', './template_struc']
class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('312', '315'), self.residue_range('630', '642'), self.residue_range('668', '674')) #code overrides the special_restraints method
#def special_restraints(self, aln):
#code overrides the special_patches method. # e.g. to include the addtional disulfides. #def special_patches(self, aln):
a = MyModel(env, sequence = tarSeq, # alignment file with template codes and target sequence alnfile = 'alignment.ali', # PDB codes of the templates knowns = template)
a.starting_model = 1 a.ending_model = 1 loopRefinement = False
a.assess_methods = (assess.GA341, assess.normalized_dope)
a.make()
Link to tutorial: https://salilab.org/modeller/wiki/Missing%20residues
Dear all, I combined a PDB file from three chains to single chain format. In between those chains are TER. Now i need to add missing residues as SEQRES. I added them all properly, all atoms are named properly but chimera detects a missing residue at last position instead of the first position of chain B making the whole sequence shift for 1 nucleic acid residue to the left. Pymol, which does not read SEQRES, registers all missing residues as blanks and their positions are 100% correct (checked 3 times). SEQRES was copied from the three-chain PDB file and edited to resemble a single chain file (C and E were renamed to A, SEQRES numbering was continued uninterrupted). How does chimera read SEQRES? Here is the full pdb file in gist: https://gist.github.com/danilob2929/34c303a5b1981f0a60942bc322052672 Thanks in forwards, D.B.
Is there some reason you’re trying to put several distinct chains into the same chain A? Unfortunately, Chimera is too “smart” for this. It looks at both of the residues you’ve numbered 1218 (with a TER card in between) and sees they are too far apart physically to be consecutive in sequence and inserts a sequence gap between them rather than the start of the chain. I don’t think there is anything you can do about this other than assign distinct chain IDs to the sequences that are in fact different physical chains. Well, if there are in fact missing residues there, you could update the SEQRES records to reflect that, then things would probably work. You should also renumber things to avoid having residues with the same sequence number and chain ID. —Eric
On Jul 24, 2019, at 5:04 AM, Danilo Boškovic <a01406823@unet.univie.ac.at> wrote:
Dear all,
I combined a PDB file from three chains to single chain format. In between those chains are TER. Now i need to add missing residues as SEQRES. I added them all properly, all atoms are named properly but chimera detects a missing residue at last position instead of the first position of chain B making the whole sequence shift for 1 nucleic acid residue to the left. Pymol, which does not read SEQRES, registers all missing residues as blanks and their positions are 100% correct (checked 3 times). SEQRES was copied from the three-chain PDB file and edited to resemble a single chain file (C and E were renamed to A, SEQRES numbering was continued uninterrupted). How does chimera read SEQRES? Here is the full pdb file in gist:
https://gist.github.com/danilob2929/34c303a5b1981f0a60942bc322052672
Thanks in forwards,
D.B. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Danilo Boškovic -
Elaine Meng -
Eric Pettersen