- modeller_usage - salilab.org

update
by leuven 06 Dec '09

06 Dec '09

Dear all, I found the solution to include disulfide bonds, while the later problem is how to combine multiple cpu caculation and including disulfide bridges together? they can be performed indenpendently but not together, could you please give me some suggestion? model.py # Example of changing the default optmization schedule from modeller import * from modeller.automodel import * from modeller.parallel import * j = job(modeller_path="/usr/lib/modeller9v7/bin/modslave.py") j.append(local_slave()) # 1 Processor j.append(local_slave()) # 2 Processors j.append(local_slave()) # 3 Processors j.append(local_slave()) # 4 Processors class Mymodel(automodel): def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181'])) self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448'])) self.patch(residue_type='DISU', residues=(self.residues['420'],self.residues['482'])) log.verbose() env = environ() # Give less weight to all soft-sphere restraints: env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['.', '../atom_files'] a = Mymodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1') a.starting_model =1 a.ending_model = 60 # Very thorough VTFM optimization: a.library_schedule = autosched.slow a.max_var_iterations = 300 # Thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 8 a.max_molpdf = 1e8 a.use_parallel_job(j) a.make() error: 'module' object has no attribute 'Mymodel' from <Slave on localhost>

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disulfide building problem
by leuven 06 Dec '09

06 Dec '09

Dear All, I want to build a model including 3 disulfide bridges, but my script could not build bridges while modelling. Can you give me some suggestion on how to make the bridges-making script work? from modeller import * from modeller.automodel import * log.verbose() env = environ() env.schedule_scale = physical.values(default=1.0, soft_sphere=0.7) env.io.atom_files_directory = ['.', '../atom_files'] a = automodel(env, alnfile='GBSS1-mult.ali',knowns=('2r4tA','3copA','3cx4A'), sequence='GBSS1') class automodel: def special_patches(self, aln): self.patch(residue_type='DISU', residues=(self.residues['151'],self.residues['181'])) self.patch(residue_type='DISU', residues=(self.residues['422'],self.residues['448'])) self.patch(residue_type='DISU', residues=(self.residues['420'],self.residues['482'])) a.starting_model =1 a.ending_model = 60 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level = refine.very_slow a.repeat_optimization = 8 a.max_molpdf = 1e8 a.use_parallel_job(j) a.make()

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how to enbale mutiple CPU for modeller?
by leuven 28 Nov '09

28 Nov '09

Dear all: I found that Modeller just use ony one CPU on my computer but the CPU is four-core. how to enbale mutiple CPU for modeller? Thank you

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how to assign different template for different regions?
by leuven 25 Nov '09

25 Nov '09

Dear Sir: I would like to build models assining different templates for different regions. For exmple: PDB-A for 1-150aa, PDB-B for 151-220aa and so on. How to achieve this? Because different template has different homolog with different regions. Thank you very much.

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Mutate and refine residue placement
by Steve Seibold 18 Nov '09

18 Nov '09

Hello Modeller. Having successfully install the newest version of Modeller on my new machine (I ran some test cases), I would like to attempt the construction of a mutant of my protein using the tutorial: http://salilab.org/modeller/wiki/Mutate%20model. However, my protein has metal and DNA with it and, so, I am not sure how Modeller will deal with this. Can you inform me? I am worried that Modeller will simple fail with the error that it can not recognize certain atoms. If it does, is there away I can get around this? Could I do only a local (around the mutated site) minimization only, ignoring the rest of the protein? I tried to investigate this in the archives but didn't find it. Sorry if this is a repeat. Thanks ,Steve

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Re: [modeller_usage] Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hello Yes. It seems to be working fine now. I just thought the error message I was getting ( "Could not find platform independent libraries" etc.) was DUE to the KEY ID problem. But they are evidently two separate issues and neither is a *Fatal* error. I am now attempting to run sample scripts to verify installation. Thanks, Steve _____ From: Forlemu, Neville [mailto:neville.forlemu@mssm.edu] Sent: Tuesday, November 17, 2009 1:33 PM To: Steve Seibold Subject: RE: [modeller_usage] Installation problem? Hi Steve, I guess it installed fine. Just locate the executable file and you are good to go -----Original Message----- From: modeller_usage-bounces(a)salilab.org on behalf of Steve Seibold Sent: Tue 11/17/2009 11:28 AM To: modeller_usage(a)salilab.org Subject: [modeller_usage] Installation problem? Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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modelling with ligands (FAD FMN and NADP)
by Yerko Escalona 17 Nov '09

17 Nov '09

Hi I have a problem when i model the structure of proteins with ligands (hetatm = NADP, FAD and FMN), because some residues have improper bond, like the Asparagine make bond between the N and C(gamma), or Phenyalanine with wrong position of aromatic carbon. I try resolve this with the optimization of models with VTFM and MD&SA but the error in the bonds of residues is the same. Also try without ligands and that's work. I think the problem is of the ligands that make incorrect restriction to the protein and make that errors. I hope that you can help me. Bye (My native language is the Spanish, so sorry for the mistakes)

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Installation problem?
by Steve Seibold 17 Nov '09

17 Nov '09

Hi Paul I installed "Modeller" using the info on http://salilab.org/modeller/9v7/release.html#rpm. However I get the error message "warning modeller9v7-1.x86_64.rmp: Header V4 DSA signature: NOKEY, Key ID" . I have obtain a license key and attempted the install as follows: "env KEY_MODELLER9v7=licensekey -Uvh modeller-9v7-1.x86_64.rpm". I have also tried, as suggested by web site: "env KEY_MODELLER9v7=licensekeyx86_64 -Uvh modeller-9v7-1.x86_64.rpm". And "env KEY_MODELLER9v7=licensekey x86_64 -Uvh modeller-9v7-1.x86_64.rpm". However, nothing seems to be working. I must be doing something incorrect? I did check my machine using "uname -m" to verify by system's specs. Can you help me? Thanks Steve

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rotation!!!
by Cool Hunk 13 Nov '09

13 Nov '09

Dear Ben n all, i have got an issue about the side chain of some of the aminoacids that are part of some beta-strands in my predicted model.. is there any way that i can rotate specific amino acids so that their side chains orientation can flip outward which is inward in my predicted model... or can i rotate the whole strand to fix that issue.. second question regarding some loops in my model is that one loop kind of intersect the other or you can say passes in between/ thru the other and that makes my model unreal.. can you tell me, how can i resolve this issue???? Also can you suggest some tools, web or any way to validate my structure and look for the bad contacts if any, so that i could use this model for futher work.... Thanking in advance... Muhammad

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Installation in Ubuntu
by Dinesh 13 Nov '09

13 Nov '09

*I am trying to install Modeller in in Ubuntu 9.10 with the alien command and I get the below errors:* $ sudo env KEY_MODELLER9v7=<My Educational License Key> alien -ic modeller-9v7-1.i386.rpm warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 error: incorrect format: unknown tag warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 warning: modeller-9v7-1.i386.rpm: Header V4 DSA signature: NOKEY, key ID 745e6093 chown: cannot access `modeller-9v7//usr/lib/modeller9v7/modlib/modeller/config.py': No such file or directory failed chowning /usr/lib/modeller9v7/modlib/modeller/config.py to 0:0: Illegal seek at /usr/share/perl5/Alien/Package/Rpm.pm line 265, <GETPERMS> line 104 *I tried importing the public key of Ben Webb and still its the same... Any help will be appreciated* -- Dinesh Cyanam

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