- modeller_usage - salilab.org

(no subject)
by Robert Selwyne 27 Apr '06

27 Apr '06

Good Day!!!!!!!!! I had installed modeller software in my computer. I was practising the basic commands. I am comfortable till executing the command. $mod8v2 Target_profile.py Execution was successful and I got the information for Target_profile.log and Target_profile.prf as described in the tutorial. But to the next step when i run the command $mod8v2 Target_compare.py i get these errors!!!!!!!!!!!! ============================================================================= Traceback (most recent call last): File "Target_compare.py", line 7, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting. ============================================================================ I have downloaded the necessary PDB files manually, Could you tell which/where directory to paste these files with a detailed command list since i am beginner to modeller. With Regards Robert Selwyne.

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Modelling of the interface of a protein complex
by Karsten SUHRE 27 Apr '06

27 Apr '06

Dear Modeller users, To study the interface between two proteins in complex (A+B), i.e. to decide whether these proteins may form a complex, I wish to compute a homology model on the basis of an existing, but only remotely homologous, complex (A'+B'), i.e. there are difference in some indels close to the interface. Each of the target proteins has also a closely homologous template, (A" and B"), which I would like to use to model the indels. However, as I am particularly interested in the interface, it is crucial to model the sidechains at the interface correctly, that is to account for the presence of the binding partner. Thus, the remote homologue (A+B) bears some important information as what concerns the complex. The most direct approach would be to use all templates and let MODELLER decide what to do. But is this really the optimal approach? Thank you very much in advance for any suggestion, or reference to similar problems. Kind regards, Karsten.

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Problem with evaluate_model.py
by Eva María Priego 26 Apr '06

26 Apr '06

Dear users, I am trying to obtain the DOPE potential and the corresponding plot for my best model. I am using the evalute_model.py script from the web tutorial, but when I run it I get this error: Traceback (most recent call last): File "evaluate_model.py", line 24, in ? normalize_profile=True, smoothing_window=15) TypeError: assess_dope() got an unexpected keyword argument 'output' Can somebody help me?. Thanks a lot in advance. I am using Modeller 8v0 and here is my scritp (my alignment file is called Ara.ali and the templates structures are located in ../templates/) from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in env.libs.topology.read(file='$(LIB)/top_heav.lib') # read topology env.libs.parameters.read(file='$(LIB)/par.lib') # read parameters # directories for input atom files env.io.atom_files_directory = '../templates/' # read model file mdl = model(env) mdl.read(file='Ara.B99990012.pdb') aln = alignment(env) code = "Ara" # generate topology aln.append_model(mdl, atom_files='Ara.B99990012.pdb', align_codes=code) aln.append_model(mdl, atom_files='Ara.B99990012.pdb', align_codes=code+'-ini') mdl.generate_topology(aln, sequence=code+'-ini') mdl.transfer_xyz(aln) mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file='Ara.profile', normalize_profile=True, smoothing_window=15)

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Regarding > Compare.py < execution
by Robert Selwyne 26 Apr '06

26 Apr '06

ello Modeller Good Day!!!!!!!!! I had installed modeller software in my computer. I was practising the examples on basic modeling with my file name Target.ali, I am comfortable till executing the command. $mod8v2 Target.py Execution was success and I got the information for Target.log and Target.prf as described in the tutorial. But to the next step when i ran the command for comparision $mod8v2 Targetcompare.py i got these errors!!!!!!!!!!!! ============================================================================= [robert@cmm0 basic-example]$ mod8v2 Targetcompare.py Traceback (most recent call last): File "Targetcompare.py", line 6, in ? aln.malign3d() File "/usr/lib/modeller8v2/modlib/modeller/alignment.py", line 210, in malign3d io=io.modpt, libs=libs.modpt, **vars) File "/usr/lib/modeller8v2/modlib/modeller/util/top.py", line 93, in malign3d return _modeller.malign3d(aln, io, libs, *args) _modeller.error: malign3_682E> Structural information is not available for all sequences in the alignment. Aborting.[robert@cmm0 basic-example]$ ============================================================================ Could you please help me in getting rid of this error. I once again thank you for your kind service. With Regards Robert Selwyne.

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Problem with modeller8v2
by Ludovic Pétain 26 Apr '06

26 Apr '06

Hello, I have a problem with MODELLER8v2. Traceback (most recent call last): File "TASSERvsGPR43.py", line 15, in ? a.make() File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\loopmodel.py", l ine 28, in make automodel.make(self, exit_stage) File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 100, in make self.homcsr(exit_stage) File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 318, in homcsr aln = self.read_alignment() File "M:\People\LPetain\Modeller8v2\modlib\modeller\automodel\automodel.py", l ine 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "M:\People\LPetain\Modeller8v2\modlib\modeller\alignment.py", line 68, in __int_append libs=libs.modpt, **vars) File "M:\People\LPetain\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = tasser I have seen in the same problem in the problem list (http://salilab.org/archives/modeller_usage/2006/msg00162.html) But I don't understand this problem since my script is: from modeller.automodel import * log.verbose() env=environ() class myloop(loopmodel): def select_loop_atoms(self): self.pick_atoms(selection_segment=('145:','173:'),selection_status='INITIALIZE') a=myloop(env,alnfile='TASSER_GPR43.ali',knowns='tasser', sequence='GPR43') a.starting_model=1 a.ending_model=1 a.md_level=None a.loop.strating_model=1 a.loop.ending_model=5 a.loop.md_level=refine.fast a.make() and it must be correct. Coulp you please help me? Thanks by advance. Ludovic PETAIN Trainee in Chemoinformatics EUROSCREEN SA Tel +32 71 348 500 Fax +32 71 348 519 Direct +32 71 348 509 http://www.euroscreen.com <http://www.euroscreen.com> This message contains information that may be confidential and privileged and is intended solely for the use of the intended recipient. Unless you are the intended recipient (or authorized to receive for the intended recipient), you may not use, copy or disclose to anyone the message and any attachments or any information contained in the message. If you have received this message in error, please notify Euroscreen at +32 71 348 500 or by reply e-mail and destroy all copies of this message and any attachments.

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Mutiple protein templates
by Sivaram I 25 Apr '06

25 Apr '06

Hi All I have a sequence.Its has about 300 aminoacids.The first 200 aa share sequence homology with one protein and the rest 100 share with other protein .Is there a way to build Homology model using the two protein structures .If yes how do I do it? Thanks in advance Sivaram

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Concatenating models
by Alex Brown 24 Apr '06

24 Apr '06

Hi. A simple question - is it possible to concatenate (add) two models, using a MODELLER script, to create a single file ? I know that two files can be added together using Unix commands or using a text editor, but then the atom numbers are duplicated (I'm not sure this is a problem tho'). Cheers, Alex Brown

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General Question
by Brandon Guida 24 Apr '06

24 Apr '06

Does anyone know whats going on here? I am trying to exit stage 2 but when I add that constriant to the model-single.py file all I get is the following log file and no models being built. As soon as I remove the exit command I get model the models. Here is the log file: check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE read_to_681_> topology.submodel read from topology file: 3 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 23 atom names : C +N atom indices : 175 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 18 23 atom names : C CA +N O atom indices : 175 171 0 176 Dynamically allocated memory at finish [B,kB,MB]: 2152131 2101.690 2.052 Starting time : 2006/04/23 16:51:44.937 Closing time : 2006/04/23 16:51:47.203 Total CPU time [seconds] : 2.20

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rotameric state in MUTATE_MODEL
by Sridhar Acharya 21 Apr '06

21 Apr '06

Hello MODELLERs, I want to know what rotameric state of the mutant residues that the MUTATE_MODEL option of MODELLER generates? What rotameric configuration does the program generates. Is it the most optimum that is possible for the model or is it generated based on some other scoring scheme? Is there any control on the rotameric state of the mutant residue. thanks in advance for your suggessions. sridhar

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Re:plotting dope values
by Prabhakar. G. 21 Apr '06

21 Apr '06

hi, there is a perl script for parsing the dope scrores in the below link http://salilab.org/modeller/wiki/Plotdope run the script, get the output and then plot it using the gnuplot prabhakar On 4/21/06, modeller_usage-request(a)salilab.org < modeller_usage-request(a)salilab.org> wrote: > > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. help (biocompr) > 2. CHAINS_all Updates (Alex Brown) > 3. Re: CHAINS_all Updates (Modeller Caretaker) > > > > ---------- Forwarded message ---------- > From: "biocompr" <biocompr(a)163.com> > To: modeller_usage(a)salilab.org > Date: Thu, 20 Apr 2006 01:22:45 +0800 (CST) > Subject: [modeller_usage] help > hi: > I find the question in the past posts ,bu i do not find the answer. > > I am new user to the modeler, I have started with the basic tutorial, I > have difficulty with plotting the dope scores with GNU plot, > when I plot the two dat files '1bdma_dope.dat','TVLDH_dope.dat'(from the > tutorials folder) I get the graph plotted(Dope score vs Residue Index), but > the two graphs are not aligned, as shown in the tutorial html file. how to > align the graphs. hope someone could help me with this silly doubt. > > Thank you very much. > > > > > > > > > > > > > > 你知道中国每年耗费多少一次性筷子吗？ > 450亿双！相当于170万立方米的木材，大约需要砍伐2500万棵大树！ <http://www.126.com/> > > ---------- Forwarded message ---------- > From: "Alex Brown" <alexander.brown(a)tech.mrc.ac.uk> > To: <modeller_usage(a)salilab.org> > Date: Thu, 20 Apr 2006 13:31:02 +0100 > Subject: [modeller_usage] CHAINS_all Updates > > Hi. > > > > I was wondering if it is possible to get updates to the CHAINS_all.seq > database. > > > > If not, where can I get hold of an updated PIR-formatted file of PDB > sequences with values in the resolution field? > > > > Many thanks, > > > > Alex Brown > > > ---------- Forwarded message ---------- > From: Modeller Caretaker <modeller-care(a)salilab.org> > To: Alex Brown <alexander.brown(a)tech.mrc.ac.uk> > Date: Thu, 20 Apr 2006 14:28:28 -0700 > Subject: Re: [modeller_usage] CHAINS_all Updates > Alex Brown wrote: > > I was wondering if it is possible to get updates to the CHAINS_all.seq > > database. > > > > If not, where can I get hold of an updated PIR-formatted file of PDB > > sequences with values in the resolution field? > > You can rebuild the databases yourself from the original PDB files. See > the relevant page in the Modeller wiki: > http://salilab.org/modeller/wiki/Rebuilding_sequence_databases > > Alternatively, you can download updates, when available, from our > supplemental data file download page, which is linked from that wiki > page and from the main 'download & installation' page. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > -- Prabhakar.G Project Assistant, Bioinformatics and Data Management, National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune-411 007 Maharastra India

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