September 2016 - modeller_usage

Re: [modeller_usage] (no subject)
by Markus Heller 28 Sep '16

28 Sep '16

Ah, ok, makes sense.. Thanks for the exmplanation! Markus -----Original Message----- From: Modeller Caretaker [mailto:modeller-care@salilab.org] Sent: Wednesday, September 28, 2016 12:05 PM To: Markus Heller Subject: Re: [modeller_usage] (no subject) On 9/28/16 10:43 AM, Markus Heller wrote: > 3. $ python calc_model.py > console_output.txt Modeller numbers residues starting from 1; it doesn't reset the counter to 1 at the start of a new chain, so your residues are numbered 1:A through 470:A and 471:B through 940:B (see the .ini file). If you want to also renumber the residues, use the renumber_residues argument to rename_segments(): https://salilab.org/modeller/9.17/manual/node191.html 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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(no subject)
by Markus Heller 27 Sep '16

27 Sep '16

Hi, I'm trying to model two missing loops in a homo-dimeric protein, following the example on the web: https://salilab.org/modeller/wiki/Missing%20residues I have saved chains A and C (forming the dimer) as pdb, and then extracted the sequence using get_seq.py (see below). Then I created an alignment file and inserted the missing residues to give the alignment file shown below. When I try to do the modeling, I get a "KeyError: 'No such residue: 346:B'" (see calc_model.py below). I've tried to rename the chains in my script. What's my mistake? Thanks and Cheers Markus %%%%%%%%%%%%%%%%%%%%%% calc_model.py %%%%%%%%%%%%%%%%% from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def special_patches(self, aln): # Rename both chains self.rename_segments(segment_ids=['A', 'B']) def select_atoms(self): return selection(self.residue_range('346:A', '350:A'), self.residue_range('346:B', '348:B')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '4yng_AC', sequence = '4yng_AC_fill') a.starting_model= 1 a.ending_model = 5 a.make() %%%%%%%%%%%%%%%%%%%%%% end of calc_model.py %%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%% alignment.ali %%%%%%%%%%%%%%%%% >P1;4yng_AC structureX:4yng_AC: 1 :A:+932 :C:MOL_ID 1; MOLECULE PYRUVATE KINASE I; CHAIN A, B, C, D, E, F, G, H; SYNONYM PK-1; EC 2.7.1.40; ENGINEERED YES:MOL_ID 1; ORGANISM_SCIENTIFIC ESCHERICHIA COLI; ORGANISM_TAXID 562; GENE PYKF, Z2704, ECS2383; EXPRESSION_SYSTEM ESCHERICHIA COLI BL21(DE3); EXPRESSION_SYSTEM_TAXID 469008: 2.28: 0.22 MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTM KLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNG DLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQE GLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVAN AILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEF-----KLRITEAVCRGAVETAEKLDAPLIV VATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVV MVSGALVPSGTTNTASVHVL/MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVM SKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGL IGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIR EHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQ MLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEF---NRKLRI TEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDF YRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL* >P1;4yng_AC_fill sequence::::::::: MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTM KLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNG DLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQE GLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVAN AILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRITEAVCRGAVETAEKLDAPLIV VATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVV MVSGALVPSGTTNTASVHVL/MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVM SKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGL IGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIR EHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQ MLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRI TEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDF YRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL* %%%%%%%%%%%%%%%%%%%%%% end of alignment.ali %%%%%%%%%%%%%%%%%

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Conda package not working on windows (32 bit?) and python 3.5
by Ajasja Ljubetič 16 Sep '16

16 Sep '16

Hi! If I install modeller via conda: export KEY_MODELLER=XXXX conda install -c salilab modeller Then I get an error when importing modeller Python 3.5.2 |Anaconda 4.1.1 (32-bit)| (default, Jul 5 2016, 11:45:57) [MSC v.1900 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import modeller Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Anaconda3\Library\modeller\modlib\modeller\__init__.py", line 93, in <module> import _modeller ImportError: DLL load failed: The specified module could not be found. >>> I tried copying around the file _modeller.pyd to folders in the PATH, but that did not solve the problem. The installed version is modeller 9.17 py35_1 salilab But if I install from the stand-alone installer everything works fine. Best, Ajasja

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