- modeller_usage - salilab.org

model.loops crosses chains
by Shyam Saladi 23 Feb '17

23 Feb '17

Hello -- In the process of using model.loops to identify regions that I will need to model in a multi-chain situation, I have noticed that it returns insertions between chains as a single loop. Furthermore, when specifying insertion_ext > 0, if the loop is at the N- or C-terminus of a chain in the middle of the molecule, the extension crosses to the next chain. Are these two intended behaviors? For the first case, this complicates things for me since I would like to apply restraints to each loop separately (which means I need to split up a couple of the loops returned). For the second case, I feel like this may not be the intended behavior since the C terminus of one chain and the N terminus of the next can be far apart in space. Thanks, Shyam ## Reproducible for the first case (can be modified to show the second) ## wget https://files.rcsb.org/download/5KXI.pdb ## remove residues A 74 and B 1 # contents of alignment file: 5xki_fill.aln >P1;2abx structureX:2abx: 1 :A:+148 :B:MOL_ID 1; MOLECULE ALPHA-BUNGAROTOXIN; CHAIN A, B; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC BUNGARUS MULTICINCTUS; ORGANISM_COMMON MANY-BANDED KRAIT; ORGANISM_TAXID 8616; TISSUE VENOM: 2.50: 0.24 IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQP-/ -VCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* >P1;2abx_fill sequence::::::::: IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG/ IVCHTTATIPSSAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCCSTDKCNHPPKRQPG* # modeller code from modeller import environ, selection from modeller.automodel import automodel class MyModel(automodel): # only refine loop regions def select_atoms(self): aln = self.read_alignment() loops = self.loops(aln, minlength=1, maxlength=100, insertion_ext=0, deletion_ext=0) for i in loops[0]: print(i) raise ValueError("stop here") return selection(loops).only_std_residues() env = environ() env.io.atom_files_directory = ['.'] a = MyModel(env, alnfile = '2abx_fill.aln', # alignment filename knowns = '2abx', # codes of the templates sequence = '2abx_fill') # code of the target a.starting_model = 5 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do the actual comparative modeling

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Excluded volume/Planar spatial restraint
by Shyam Saladi 22 Feb '17

22 Feb '17

Hello, I am trying to model missing residues from a solved structure of a membrane protein to prepare it for MD simulations. Some of these residues (~10) are follow a transmembrane segment at the C-terminus of the protein. After loop refinement, these residues always end up in the "membrane region" that I know from the solved TMs in the structure. However, I know these loop residues are soluble and should not be in this region. I would like to specify some sort of planar spatial restraint to describe where the residues can be, e.g. residues allowed above 10 A in the z direction? Is there a way to specify this? I appreciate any help in advance. Thanks, Shyam

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Modeller 9.18 release
by Modeller Caretaker 22 Feb '17

22 Feb '17

The new version of Modeller, 9.18, 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 8 or 9, there is no need to reregister for Modeller 9.18 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.18 is primarily a bugfix release relative to the last public release (9.17), although it also adds support for Python 3.6. See the Modeller manual for a full change log: https://salilab.org/modeller/9.18/manual/node40.html If you encounter bugs in Modeller 9.18, please see https://salilab.org/modeller/9.18/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 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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Distance restraint violations
by Albers, Thomas 04 Jan '17

04 Jan '17

Hello! I'm trying to model a certain membrane protein. There are two template structures with decent sequence similariry (~ 40 %) and not-so-great resolution (~ 3 angstrom). When building a model against either template nothing in particular sticks out in the logfile, but when building a model model against both templates combined there are lots of distance violations (CA-CA and N-O) in the log, however this model gives the lowest DOPE score. What gives? Thomas

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EXTREME BOND LENGTHS IN OPTIMIZED MODELS
by Mahesh Velusamy 19 Dec '16

19 Dec '16

Dear All, I have tried to do build single point mutant models (n=100) along with separate optimization step on the neighbor residues around the mutated residue.I can able to get 98 models without any issue out of 100 models but in some models, the bond lengths of longer residues(ARG,LYS,TYR) became extreme than original value. For example: IN ARG residue, the distance between (CZ & NH1) or (CZ & NH2) was extreme (3.4Å) than the original value (1.5Å ) which makes the bonds disappear. I really don't understand that what makes these issue and I use the default MD&SA parameters which used in mutate_model.py with Lenard-Jones potential. *I don't get this issue if I change the restraint from Lenard-Jones into soft-sphere potential. So, kindly give me some suggestion about the parameters that I can tune to resolve this issue. Thanking you in advance With Regards Mahesh V

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Difference between dynamic_sphere and lennard-jones potential restraints ?
by Mahesh Velusamy 12 Dec '16

12 Dec '16

Dear All, This might be very basic question and also I have read this from the manual https://salilab.org/modeller/9v8/manual/node102.html but still I am curious to know the answer for the following questions: 1.what is the difference between these two restraints in terms (when to use) usage ? 2.Which one do we need to prefer with respect to mutate_model.py? 3.Why dynamic_sphere kept as False in this script https://salilab.org/modeller/wiki/Mutate%20model ? 4.Is it good idea if I use dynamic_sphere in mutate_model.py ? Thanking you in advance With Regards Mahesh V

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ERROR IN MODELS ASSESSMENT
by Mahesh Velusamy 12 Dec '16

12 Dec '16

Dear All, This is to inform you that I have introduced new residue type called BGC which has a Glycosidic linkage between ASP and Beta-D-GLUCOSE as mentioned in the following protocol https://salilab.org/modeller/6v2/FAQ.html#2. I can access this newly introduced residue successfully throughout the modeling but after the models generation I get the following warning message for the single models assessment. >> Model assessment by DOPE potential iatmcls_286W> MODEL atom not classified: BGC:N BGC iatmcls_286W> MODEL atom not classified: BGC:CA BGC iatmcls_286W> MODEL atom not classified: BGC:CB BGC iatmcls_286W> MODEL atom not classified: BGC:CG BGC iatmcls_286W> MODEL atom not classified: BGC:OD1 BGC iatmcls_286W> MODEL atom not classified: BGC:OD2 BGC iatmcls_286W> MODEL atom not classified: BGC:C BGC iatmcls_286W> MODEL atom not classified: BGC:O BGC iatmcls_286W> MODEL atom not classified: BGC:C1 BGC iatmcls_286W> MODEL atom not classified: BGC:O5 BGC iatmcls_286W> MODEL atom not classified: BGC:C5 BGC iatmcls_286W> MODEL atom not classified: BGC:C2 BGC iatmcls_286W> MODEL atom not classified: BGC:O2 BGC iatmcls_286W> MODEL atom not classified: BGC:C3 BGC iatmcls_286W> MODEL atom not classified: BGC:O3 BGC iatmcls_286W> MODEL atom not classified: BGC:C4 BGC iatmcls_286W> MODEL atom not classified: BGC:O4 BGC iatmcls_286W> MODEL atom not classified: BGC:C6 BGC iatmcls_286W> MODEL atom not classified: BGC:O6 BGC iatmcls_286W> MODEL atom not classified: ALA:OXT ALA preppdf_453W> No fixed restraints selected; there may be some dynamic ones. preppdf_454W> Restraints file was probably not read; use restraints.append(). Here, I just want to know what does these statements implies "No fixed restraints selected; there may be some dynamic ones. Restraints file was probably not read; use restraints.append()" Even, I added all these "BGC" atoms in "/atmcls-mf.lib" file but still I am getting this warning. So, Kindly let me know that is it necessary to worry about this warning ? If not can you guide me how to append this "BGG new residue" restraints? Thanking you

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Is it possible to control atom movements of specific residue during optimization?
by Mahesh Velusamy 07 Dec '16

07 Dec '16

Dear All, I have been doing separate optimization steps on selected region where i experienced that certain residue(ARG,LYS,TYR) atoms get distorted (like bonds between two atoms were distorted). So is their anyway to control the random deviation of certain residues atoms. Thanking you in advance With Regards Mahesh V

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Modeling loop using template from PDB file
by Markus Heller 07 Dec '16

07 Dec '16

Hello, I have a structure (A) which is missing a stretch of a dozen or so residues. I also have the structure of the protein from a different organism which has said stretch of residues resolved (B). Now I'd like to take the coordinates of A and model the missing residues using the relevant coordinates (i.e. for these residues only) from B. How would I go about doing this? Thanks Markus

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using crosslinking information as restrain
by ncuspywangxuedong 07 Dec '16

07 Dec '16

Hey all, I was using modeller in order to obtain a model satisfying crosslink restrains. Now I know the crosslinked sites, but I do not know how to add crosslink restrains. Could you tell me how to do it? It is best If you can give specific examples to me! thanks a lot!!!! Su Mu

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