August 2006 - modeller_usage

pdb output
by yalini.pathy＠yale.edu 02 Sep '06

02 Sep '06

Hi, I ran a test modeller script to generate 2 models. From running this script, I only got the Dxxxxx files and not the PDB output files. The log file didn't contain any error messages for generating PDB files - might anyone be able to suggest a solution please? Thanks, Yalini

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top to python (+ symmetry restraints)
by yalini.pathy＠yale.edu 30 Aug '06

30 Aug '06

Hi, I have a top file from Modeller v6.0 (or possibly older). The top script defines a tetramer and then applies alpha-helical restraints to the same residue range in each monomer. I have been trying to convert this to use with the newest version of Modeller. I've been unsuccessful so far - might someone be able to help please? The top script is attached to this e-mail; Many thanks in advance! Yalini

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Re: [modeller_usage] CHARMM atom type is out of range
by Modeller Caretaker 29 Aug '06

29 Aug '06

zzj wrote: > Hi, the problem was solved by deleting "inifile = 'mgl.pdb'" in my > script. mgl.pdb is my template pdb file, without any further change. If > you still think this is not normal, I'll send the input files towrrow > when I get to lab. If you specify an "inifile" it needs to be a set of coordinates of your model (usually from a previous optimization), not a template. If you leave out "inifile", then Modeller will automatically build an initial model (with a .ini file extension) based on your template(s) and the alignment. This is usually what you want, although sometimes the .ini file has such a bad structure (e.g. knots in the sequence or other bad clashes) that the optimization is unable to recover, and you may be able to manually tweak the initial model to correct this. Unfortunately, Modeller does very little checking on a user-provided initial model, and expects it to match the .ini file (i.e. same residue and atom order, just with different coordinates). So you can get weird errors if this is not the case. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Hello,everyone, what are CA CB atoms?
by li bai 29 Aug '06

29 Aug '06

Hello,everyone! Today I study manual of modeller.I found a question! It says:"non-hydrogen mainchain (N, C,CA,O)and CB atoms" what are CA and CB atoms? How analyse CA and CB atoms? Sincerely！ --------------------------------- 抢注雅虎免费邮箱-3.5G容量，20M附件！

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CHARMM atom type is out of range
by zzj 28 Aug '06

28 Aug '06

Hellow everyone, I am learning how to use Modeller. It gives me the following infor in the log file: ..... preppdf_203E> CHARMM atom type is out of range; Probably because model.generate_topology() was not called. Atom index, atom type: 0 >> Summary of failed models: hgl.B99990001.pdb preppdf_203E> CHARMM atom type is out of range; Probably because model.generate_topology() was not called. Atom index, atom type: 0 Dynamically allocated memory at finish [B,kB,MB]: 4148015 4050.796 3.956 Starting time : 2006/08/28 16:17:29.348 Closing time : 2006/08/28 16:17:48.589 Total CPU time [seconds] : 17.68 I believe my alignment is ok. Here's my script: # Modeling using a provided initial structure file (inifile) from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = automodel(env, alnfile = 'alignment.ali', # alignment filename knowns = 'mgl', # codes of the templates sequence = 'hgl', # code of the target inifile = 'mgl.pdb') # use 'my' initial structure a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do homology modelling Can somebody give me a hint? Thanks alot. JOE -- _________________________________________ Joe (zhaocai) Zhou Department of Pathology & Laboratory Medicine University of Pennsylvania, School of Medicine 252 John Morgan Building 36th Street & Hamilton Walk Philadelphia, PA 19104-6082 Tel: 215-898-2870 Fax:215-898-2401 Cell:781-330-2409 -------------------------------------------------------------

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Assess model quality with multi chains
by bmbbl＠leeds.ac.uk 23 Aug '06

23 Aug '06

Dear all, I have remodelled a loop on a tetramer model, and kicked out 40 of 100 loops which had bad objective functions. As pointed out in the manual, either DOPE or GA341 function is recommended to assess a model with multi chains. So how to assess the 60 loop models? Many thnx. Binbin

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dope energy of template
by caj 18 Aug '06

18 Aug '06

Hi all, The evaluate-model.py was used for a few of my models but I would like to compare the DOPE energies to my template and where do I find that data-set? Hope it is not too obvious.... Best wishes Caroline

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enforcing symmetry in loop refinement
by Mike White 10 Aug '06

10 Aug '06

I have modeled a homopentamer using automodel with enforcing pentameric symmetry, and everything looks fine. There are two regions of each subunit that have 3 and 5 residue long loops that aren't in the templates. When I do loop modeling of all 10 of these loops at the same time using a script based on the one in the Advanced tutorial, I get a set of models where the loops are no longer symmetric. I then introduced the same symmetry constraints in the loop modeling that I used in the original model, and it produced models with the appropriate symmetry. However, it took much longer (765 seconds of cpu time to generate 5 loop models without the symmetry , but 8629 seconds to generate 2 loop models with symmetry). I don't mind letting things run overnight to generate models, but the hugh increase in computational time suggests that I might not be doing this right. Below is the python script: ******************************************************************* # Loop refinement of an existing model of the receptor from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './:../atom_files' def defsym(mdl, aln, seg1, seg2): for (set,seg) in [(2,seg1), (3,seg2)]: mdl.pick_atoms(aln, pick_atoms_set=set,selection_segment=seg, atom_types='ALL',selection_status='INITIALIZE', selection_search='SEGMENT') mdl.symmetry.define(symmetry_weight=1.0,add_symmetry=(True,False)) segsize = 217 #number of residues per chain # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 4 residue insertion in Loop C in each subunit self.pick_atoms(selection_segment=('198:', '201:'), selection_status='INITIALIZE') self.pick_atoms(selection_segment=('415:', '418:'), selection_status='ADD') self.pick_atoms(selection_segment=('632:', '635:'), selection_status='ADD') self.pick_atoms(selection_segment=('849:', '852:'), selection_status='ADD') self.pick_atoms(selection_segment=('1066:', '1069:'), selection_status='ADD') # 3 residue insertion in Loop F in each subunit self.pick_atoms(selection_segment=('162:', '164:'), selection_status='ADD') self.pick_atoms(selection_segment=('379:', '381:'), selection_status='ADD') self.pick_atoms(selection_segment=('596:', '598:'), selection_status='ADD') self.pick_atoms(selection_segment=('813:', '815:'), selection_status='ADD') self.pick_atoms(selection_segment=('1030:', '1032:'), selection_status='ADD') def special_restraints(self, aln): #identify the seqments to maintain symmetry: A-B, B-C, C-D, D-E defsym(self,aln,seg1=('1',str(segsize)), seg2=(str(segsize+1),str(2*segsize))) defsym(self,aln,seg1=(str(segsize+1),str(2*segsize)), seg2=(str(2*segsize+1),str(3*segsize))) defsym(self,aln,seg1=(str(2*segsize+1),str(3*segsize)), seg2=(str(3*segsize+1),str(4*segsize))) defsym(self,aln,seg1=(str(3*segsize+1),str(4*segsize)), seg2=(str(4*segsize+1),str(5*segsize))) m = myloop(env, inimodel='ReceptorBEST.pdb', # initial model of the target sequence='Receptor') # code of the target m.loop.starting_model= 11 # index of the first loop model m.loop.ending_model = 12 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() ******************************************************************************** The only difference between the two scripts is the inclusion of the definition of the defsym operation and the mdl.symmetry.define operation and the "def special_restraints" block. The cutting and pasting into this message screwed up the indentation, but the "mdl.symmetry.define" command is lined up with the "for (set, seg).." line. Have I done this right? I'm still at the "copying other scripts and trying to adapt them to my needs stage." There was an earlier post about this topic (http://salilab.org/archives/modeller_usage/2005/msg00381.html )but I didn't quite understand how this was to be implemented in loop modeling. Thanks! Mike White

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How analyse "model_segment"
by li bai 07 Aug '06

07 Aug '06

Dear, everyone! Could you tell how analyse like: model_segment=('FIRST:A','LAST:A') model_segment=('FIRST:@,'END:') model_segment=('2','50') model_segment=('!2','!50') Could give me an answer? Thank you very much! Sincerely! Yours, --------------------------------- Mp3疯狂搜-新歌热歌高速下

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Help:analyse .profile
by li bai 06 Aug '06

06 Aug '06

Dear,everyone! How do I analyse a plot of .profile in the 'basic tutorial'? It says 'This profile is written to a file `TvLDH.profile', which can be used as input to a graphing program such as GNUPLOT', but when a plot it ,I get a straight line.How do I analyse it???What does mean? Does it sense?Thank you! Sincerely --------------------------------- 雅虎免费邮箱-3.5G容量，20M附件

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