- modeller_usage - salilab.org

Modeller 9.10 release
by Modeller Caretaker 29 Sep '11

29 Sep '11

The new version of Modeller, 9.10, is now available for download! Please see the download page at http://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 9.10 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9.10 is primarily a bugfix release relative to the last public release (9.9). Major user-visible changes include: # Add Python 3 support. # Add support for Mac OS X 10.7 (Lion). # Modeller on 64-bit Macs is now built with Intel Fortran, resulting in a roughly 2x speedup compared to 9.9. # Add Unicode support; all filenames should be UTF-8 encoded. See the Modeller manual for a full change log: http://salilab.org/modeller/9.10/manual/node38.html If you encounter bugs in Modeller 9.10, please see http://salilab.org/modeller/9.10/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 http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Restricting parts of the protein to alpha helix
by Kalavera＠gmx.net 06 Sep '11

06 Sep '11

Dear modeller users, my current project involves the refinement of an tertrameric protein, which is already an homology model generated with modeller. Now, I tried to refine the existing model, because its N-terminus should be alpha helical. My strategy involved creating an alpha-helix and generating a new chimeric protein with this. Maybe my strategy is bad or do carry some failure. Searching your archives, I found no fitting topic. I hope this community might be able to help me with my issues. There must be a slightly more elegant way to receive an helical n-terminus. My strategy in detail:(all files/examples/scripts are shown below). In a first step I created an alpha-helix (22 AA) matching the N-terminal AA sequence of my template pdb. The helix was created based on an script tutorial I found here : http://salilab.org/modeller/wiki/Make%20alpha%20helix In a second step I created a pir file, which seems to cause the problems. I followed the Pir-format on the modeller webpage, but the python script exits pointig at problems in the pir file. At least a simple pythonscript should create my chimera. I figured out, that there is a problem in the pir file. I don't know, how to create four helices or assign the already created to all four monomers. Thanks for all your help, Kalavera Information: My Pir file in principle:(Original residues are masked) >P1;My-PDB structureX:My-PDB:1:A:82:D:::0.00:0.00 AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/* >P1;alpha-helix structureX:alpha-helix:1: :22: :::0.00:0.00 ----------------------------------------------- -----------------------------------/ ----------------------------------------------- -----------------------------------/ ----------------------------------------------- -----------------------------------/ XAAAAAAAAAAAAAAAAAAAAA------------------------- -----------------------------------/* >P1;chimera sequence:chimera:::::::0.00:0.00 AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ AAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/ XAAAAAAAAAAAAAAAAAAAAMMMMMMMMMMMMMMMMMMMMMMMMMM MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/* my *.py script: from modeller.automodel import * from modeller import * log.verbose() env = environ(rand_seed=-42) env.io.atom_files_directory = '.' #env.io.hetatm = env.io.hydrogen = True a = automodel(env, alnfile = 'my_pir_file.pir', knowns = ('My-PDB','alpha-helix'), sequence = 'chimera') a.repeat_optimization = 1 a.starting_model= 1 a.ending_model = 1 a.final_malign3d = True a.make() a.energy(output='VERY_LONG') Parts of My-PDB: ATOM 1 N MET 1 9.237 -14.594 13.390 1.00133.02 1SG 2 ATOM 2 CA MET 1 10.424 -14.242 12.577 1.00133.02 1SG 3 ATOM 3 CB MET 1 9.978 -13.883 11.150 1.00133.02 1SG 4 ATOM 4 CG MET 1 11.111 -13.752 10.133 1.00133.02 1SG 5 ATOM 5 SD MET 1 10.531 -13.360 8.454 1.00133.02 1SG 6 ATOM 6 CE MET 1 9.496 -14.845 8.300 1.00133.02 1SG 7 ATOM 7 C MET 1 11.086 -13.059 13.198 1.00133.02 1SG 8 ATOM 8 O MET 1 10.511 -12.420 14.078 1.00133.02 1SG 9 ATOM 9 N LEU 2 12.328 -12.738 12.784 1.00173.80 1SG 10 ATOM 10 CA LEU 2 12.915 -11.582 13.388 1.00173.80 1SG 11 ATOM 11 CB LEU 2 14.364 -11.293 12.962 1.00173.80 1SG 12 ATOM 12 CG LEU 2 15.370 -12.347 13.459 1.00173.80 1SG 13 ATOM 13 CD1 LEU 2 15.119 -13.714 12.806 1.00173.80 1SG 1 ..... ATOM 634 CH2 TRP 82 -2.392 -10.968 17.703 1.00228.90 1SG 635 ATOM 635 C TRP 82 -1.256 -4.168 15.227 1.00228.90 1SG 636 ATOM 636 O TRP 82 -1.869 -3.238 14.636 1.00228.90 1SG 637 ATOM 637 OXT TRP 82 -0.880 -4.112 16.427 1.00228.90 1SG 638 TER 637 TRP 82 1SG 639 ATOM 638 N MET 83 -9.978 -14.264 9.752 1.00140.79 2SG 640 ATOM 639 CA MET 83 -11.395 -14.650 9.550 1.00140.79 2SG 641 ATOM 640 CB MET 83 -11.772 -14.541 8.059 1.00140.79 2SG 642 ATOM 641 CG MET 83 -11.766 -13.103 7.529 1.00140.79 2SG 643 ..... -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de

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MODELLER thinks HSEs are ATOM instead of HETATM
by Yingjie Lin 02 Sep '11

02 Sep '11

Hi Modellers, I ran into a problem with PDB file 1j9n, which contains HSE residues. Each HSE line starts with "HETATM". However, when I read them into MODELLER, MODELLER thinks HSEs are ATOMs. env = environ() env.io.hydrogen = False env.io.hetatm = True mdl = model(env) mdl.read(file = '1j9n.pdb') for chain in mdl.chains: for residue in chain.residues: if residue.name=='HSE': print residue.name, residue.hetatm ... <Residue 16:C (type HSE)> False ... Does anyone know what is happening here? Where can I find MODELLER's lists/libraries of HETATM/ATOM residue types? Thank you. Yingjie - Yingjie

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To generate P(r) of SAXS from a PDB model
by Zhong Huang 30 Aug '11

30 Aug '11

Hi folks, I am trying to generate P(r) of SAXS from PDB models using the following code. However, the P(r) does not look like corrected one. The computed 1-D curve decreases monotonically from 0-300 Angstrom, which is against published curve obtained from the experimental data. Is there any thing wrong with my code? Thank you in advance. env=environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') #print env env.libs.parameters.read(file='$(LIB)/par.lib') from sys import exit log.verbose() ### Calculate SAXS spectrum of correct structure mdl = complete_pdb(env, 'PDB') atmsel = selection(mdl) saxs = saxsdata(env) saxs.ini_saxs(atmsel=atmsel, s_min= 0.0, s_max=0.5, maxs=500, nmesh=400, natomtyp=15, represtyp='heav', filename='$(LIB)/formfactors-int_tab_solvation.lib', wswitch = 'uniform', s_low=0.5, s_hi=0.0, s_hybrid=0.0,nr = 5000,dr=.1,nr_exp=300,dr_exp=1.0, spaceflag= 'real', use_lookup=False) ### append SAXS data to energy structure mdl.env.edat.saxsdata.append(saxs) mdl.saxs_intens(saxsd=saxs, filename='i_s.txt', fitflag=False) mdl.saxs_pr(saxsd=saxs,filename="pr.txt") -- Best Zhong

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build profile problem
by Bishwajit Das 26 Aug '11

26 Aug '11

Dear modeller when i use this build profile program, then when its terminate the result shown hit one found but in result file that mean this template.ali file not showing the hit .how can i solve this problem. *** input file and program file attach here.Please help me as soon as possible. -- * BISHWAJIT DAS*** KOLKATA

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GA341 score vector?
by R K Belew 22 Aug '11

22 Aug '11

using for an automodel a, and using a.outputs to get access to its output details, i find m['GA341 score'] gives a VECTOR of values. > (Pdb) p m['GA341 score'] > [0.066255435347557068, 0.40340045094490051, 21.524829864501953, -1.6095080375671387, 0.29580554366111755, -2.9327836036682129, -3.012000560760498, -3.6851351261138916] m['GA341 score'][0] seems to be the actual value reported as the GA341 metric, but what are the other seven values?

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GA341 score vector - PS
by R K Belew 22 Aug '11

22 Aug '11

looking through Modeller's generated output: > % sequence identity : 8.397000 > Sequence length : 131 > Compactness : 0.393804 > Native energy (pair) : 26.327664 > Native energy (surface) : -0.742166 > Native energy (combined) : 0.798566 > Z score (pair) : -2.285661 > Z score (surface) : -2.854515 > Z score (combined) : -3.209596 > GA341 score : 0.040909 i'm now guessing it is probably the compactness,native energy and Z scores?

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plot_profiles.py run error
by 刘吉元 22 Aug '11

22 Aug '11

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I need some information about an salign module
by Ashish Runthala 15 Aug '11

15 Aug '11

Dear Modellers, The script salign_multiple_struc.py works on sub-optimal alignments as given on page http://computing.bio.cam.ac.uk/local/doc/modeller/node294.html Tell me, is this script similar to the consistency and sub-optimal alignment generation, as cited by Travis Wheeler for MAFFT, PROBCONS, TCOFFEE. Other than their hydrophobic gap penalties, what is the other difference focusing on alignment strategy between this script and these three servers. Thank you Ashish -- Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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ranking loop scores
by flavio seixas 15 Aug '11

15 Aug '11

Hi Ben, I wanto to carry out with loop refinement from the "best" model generated by modeller. However, the log file from loop.py script only ranks a modpdf score. I edited the script to generate other assessment scores as follow: m = MyLoop(env, inimodel='PROTEIN.B99990220.pdb', sequence='PROTEIN', assess_methods=(assess.DOPE, assess.GA341)) m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 20 # index of the last loop model m.loop.md_level = refine.very_fast # loop refinement method m.make() # Get a list of all successfully built models from a.outputs ok_models = filter(lambda x: x['failure'] is None, a.outputs) # Rank the models by DOPE score key = 'DOPE score' ok_models.sort(lambda a,b: cmp(a[key], b[key])) # Get top model m = ok_models[0] print "Top model 1: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[1] print "Top model 2: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[2] print "Top model 3: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[3] print "Top model 4: %s (DOPE score %.3f)" % (m['name'], m[key]) m = ok_models[4] print "Top model 5: %s (DOPE score %.3f)" % (m['name'], m[key]) However, the assess_methods seems bo be ignored and loopy.log file does not list the models ranked by DOPE socore. root@hercules:~/modeller/set7/loop# mod9.9 loop.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "loop.py", line 30, in ? ok_models = filter(lambda x: x['failure'] is None, a.outputs) TypeError: iteration over non-sequence root@hercules:~/modeller/set7/loop# Is there a problem with the way I set the scritp? Regards, Flavio

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