May 2025 - modeller_usage

Modeller 10.7 release
by Modeller Caretaker 29 May '25

29 May '25

A new version of Modeller, 10.7, is now available for download! Please see the download page at https://salilab.org/modeller/ for more information. If you have a license key for Modeller 9 or 10, there is no need to reregister for Modeller 10.7 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 10.7 is a minor update that improves mmCIF output, adds read support for the BinaryCIF format, better handles the new 5-character PDB residue names, and includes a number of bug fixes. If you encounter bugs in Modeller 10.7, please see https://salilab.org/modeller/10.7/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license and you ticked the "notify me of new releases" box. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply unsubscribe from the modeller_announce mailing list, or reply to this email and let us know. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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Specification of restraints
by Fred Pontes 23 May '25

23 May '25

Hi I'm trying to apply a restraint to keep fixed the CA of a specific residue using a Gaussian form. This mathematical form of restraints accept four arguments: forms.Gaussian(group, feature, mean, stdev) mean and stdev are defined by me according to my system. In the `feature` I could use features.ZCoordinate(*atom_ids). But I`m struggling with the group argument. I think the group is a physical restraints type and I have defined the type `z_coord_type', but I always get an error from MODELLER/10.4. * rsr.add(forms.Gaussian(group=physical.z_coordinate,AttributeError: 'module' object has no attribute 'z_coordinate'* Am I doing this right? Below I include my script file. Thank you in advance. *from modeller import *from modeller.automodel import *from modeller.physical import PhysicalTypez_coord_type = PhysicalType(99, 'z_coordinate')import syslog.verbose()env = Environ()class MyModel(AutoModel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.add(forms.Gaussian(group=physical.z_coordinate, feature=features.ZCoordinate(at['CA:25:A']), mean=193.8, stdev=0.1)) a = MyModel(env, alnfile='multi-co.ali', knowns=('HPI1_fit'), sequence='multi', assess_methods=(assess.DOPE,assess.GA341))a.starting_model = 1a.ending_model = 10a.make()* -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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restraint distance between template and model
by Fred Pontes 22 May '25

22 May '25

Hi! I asked MODELLER to create a protein model using two templates. I think, my model is quite good, but I see a place to improve in relation to the relative position between some helices. In the template, the helices are close to each other and have a shift in the z-coordinates, but it's not appear in my model. How can I apply a restraint between template and model, in order to have the same relative position between the helices? I tried to draw a scheme below, in order to be more clear about what I'm speaking: Z-axis Relative position that I have in model Relative position that I want and see in template ^ H H H | H H H H | H H H H | H H H H H Kind regards, Fred -- Frederico José de S. Pontes PDRA at LICAMM University of Leeds

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