September 2020 - modeller_usage

Sequence difference between alignment and pdb:
by Arnau PC 05 Oct '20

05 Oct '20

Hello, I have been using Modeller a few times for simple approaches but, currently, I have to face a more complex problem. I have the crystal structure of my template (740 residues, PDB: 4J0M) and I want to model three putative homolog sequences coming from a different organism. In that sense, the putative protein sequences are 1100 residues long, so I can only model the region that it locally matches with my template. For this reason, I have to use a local alignment (Smith-Waterman algorithm) between the target and the template and you may imagine which kind of problems I have to face when trying to run Modeller with this alignment: as it is a local alignment, there are multiple positions in the pdb file that have been skipped in the alignment so I have to remove those atoms from the pdb file one by one. Additionally, there are missing positions in the crystal template so I have to remake the alignment (deleting from the template fasta file these residues) each time I find missing atoms in the pdb, plus removing the atoms in the pdb file that do not match with the local alignment. I am pretty sure there is a more intelligent and practical solution to this problem since I have to do this for more than 700 residues and it can take hours for only one model. Since I am a new Modeller user and I have only used it for simple purposes, any help you can provide it would be very appreciated. Thank you very much for your attention and sorry for the inconvenience.

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External Source Sequence Alignment
by Li,Haoxi 05 Oct '20

05 Oct '20

Dear Modeller Users, Hope this email finds you well! I have a question about building homology models with sequence alignments coming from external sources (BLAST, PROMALS3D, etc). Since PIR format alignment files are usually not provided by these sources, do I need to manually construct the file based on the alignment I have? Are there any other ways? Thank you so much! Best wishes, Haoxi

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loop.py
by Jeff Reneker 24 Sep '20

24 Sep '20

Following the example in “Refining an existing PDB file” I want to “refine a region of an existing PDB file without comparative modeling.” The first thing I want to do is to get the loop.py script in the examples to work for any other structure. The only change I made is in this block of code from loop.py where I substitute 6aa0 for 1fdx as follows: m = MyLoop(env, inimodel='1fdx.B99990001.pdb', # initial model of the target sequence='1fdx', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop m = MyLoop(env, inimodel=‘6aa0.pdb', # initial model of the target sequence=‘6aa0', # code of the target loop_assess_methods=assess.DOPE) # assess loops with DOPE # loop_assess_methods=soap_loop.Scorer()) # assess with SOAP-Loop Then, I copy the 6aa0.pdb file to the appropriate directory. This is the error message at the tail end of the output: Traceback (most recent call last): File "loop.py", line 35, in <module> m.make() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 37, in make self.build_seq(self.inimodel, 1) File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 169, in build_seq atmsel = self._check_select_loop_atoms() File "/usr/lib/python3.6/dist-packages/modeller/automodel/loopmodel.py", line 398, in _check_select_loop_atoms atmsel = self.select_loop_atoms() File "loop.py", line 18, in select_loop_atoms return selection(self.residue_range('19:', '28:')) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 329, in residue_range start = self.residues[start]._num File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 259, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/python3.6/dist-packages/modeller/util/modutil.py", line 23, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/python3.6/dist-packages/modeller/coordinates.py", line 323, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19:' So, I’m not sure what the deal is because that’s how new I am to Modeller. Thanks, JR.

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Modeller 9.25 release
by Modeller Caretaker 09 Sep '20

09 Sep '20

A new version of Modeller, 9.25, 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 9.25 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.25 adds binaries and installation packages for Linux on both 32-bit and 64-bit ARM (e.g. on Raspberry Pi), allows overriding the prefix for automodel output file names, and fixes a number of bugs. See the Modeller manual for a full change log: https://salilab.org/modeller/9.25/manual/node40.html If you encounter bugs in Modeller 9.25, please see https://salilab.org/modeller/9.25/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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problem in anaconda
by Anas Jamshed 01 Sep '20

01 Sep '20

I successfully installed modeller through conda install modeller and also change the license key in config.py but when I try to run : from modeller import * it shows the following error : ModuleNotFoundError Traceback (most recent call last)<ipython-input-1-80c5cec1a705> in <module>()----> 1 from modeller import * ModuleNotFoundError: No module named 'modeller' plz help me

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