February 2011 - modeller_usage

Loop modeling
by bharat lal 01 Mar '11

01 Mar '11

Hi, I have modelled a protein using secondary structure restrained script... The model seems to be perfectly fine .. but one portion of the model is converted into a helix which has to be a loop according to the template .. how can I force that region to be a loop ??? ------------ Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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Regarding Salign
by Ashish Runthala 01 Mar '11

01 Mar '11

Dear Modellers, How does align2d_mult actually adds the target sequence onto the aligned templates ali file. What is the logic considered by align2d_mult to align the target sequence onto the structurally aligned templates' ali file.It just considers topology of coordinates but no structural information is known for target. So how does it considers restraints from templates to align target sequence? Thanks Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS Pilani Rajasthan - INDIA

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about model rank
by albert 27 Feb '11

27 Feb '11

Hello: I've built 1000 models by modeller and I forgot save the log file. So I cannot obtain the DOPE or MOLPDF information for each residues. I am wondering, is it possible to rank then manually? Thank you very much

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Structural alignment using iterative_structural_alignment
by Seungyeul Yoo 25 Feb '11

25 Feb '11

I was trying to clean two pdb files and superpose them based on the pairwise structural alignment. The script is like followings: from modeller import * from modeller.scripts import complete_pdb import sys import modeller.salign log.verbose() env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') env.io.atom_files_directory = './' if len(sys.argv) != 5: print "Usage: superpose_pdbs.py code1 chain1 code2 chain2" sys.exit(1) code1,chain1,code2,chain2 = sys.argv[1:] file1 = code1+'.pdb' file2 = code2+'.pdb' aln = alignment(env) mdl1 = complete_pdb(env,file1,model_segment=('FIRST:'+chain1,'LAST:'+chain1)) mdl1.chains.name = chain1 mdl1.write(file=code1+'_'+chain1+'_complete.pdb',model_format='PDB') mdl2 = complete_pdb(env,file2,model_segment=('FIRST:'+chain2,'LAST:'+chain2)) mdl2.chains.name = chain2 mdl2.write(file=code2+'_'+chain2+'_complete.pdb',model_format='PDB') aln.append_model(mdl1,atom_files=file1,align_codes=code1+chain1) aln.append_model(mdl2,atom_files=file2,align_codes=code2+chain2) modeller.salign.iterative_structural_align(aln) #for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), # ((1., 0.5, 1., 1., 1., 0.), False, True), # ((1., 1., 1., 1., 1., 0.), True, False)): # aln.salign(rms_cutoff=3.5, normalize_pp_scores=False, # rr_file='$(LIB)/as1.sim.mat', overhang=30, # gap_penalties_1d=(-450, -50), # gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, # alignment_type='PAIRWISE', # If 'progresive', the tree is not # # computed and all structues will be # # aligned sequentially to the first # feature_weights=weights, # For a multiple sequence alignment only # # the first feature needs to be non-zero # improve_alignment=True, fit=True, write_fit=write_fit, # write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file=code1+chain1+'_'+code2+chain2+'.ali',alignment_format='PIR') atmsel = selection(mdl1).only_atom_types('CA') r = atmsel.superpose(mdl2,aln) mdl2.write(file=code2+'_'+chain2+'_complete.pdb',model_format='PDB') When I used three iterative cycles of 'salign' above (commented) I could successfully run the script. But when I replaced it to 'modeller.salign.iterative_structural_align(aln), I had error message like: Traceback (most recent call last): File "clean_pdb.sh", line 33, in ? modeller.salign.iterative_structural_align(aln) File "/Library/modeller-9v7/modlib/modeller/salign.py", line 122, in iterative_structural_align aln.append(file=opfile) File "/Library/modeller-9v7/modlib/modeller/alignment.py", line 79, in append allow_alternates) IOError: openf______E> Cannot open file /var/folders/nx/nx+3eBsLGB4bYzOn5I3FjE+++TY/-Tmp-/tmp4FqRw9/salign_local_mid.ali: No such file or directory Could you please let me know what I did wrong with this? Thanks, Best regards, Seungyeul Yoo

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 37
by Ashish Runthala 24 Feb '11

24 Feb '11

Hi Benn, Check it out. I want to consider maximal/average occupancy of a residue at a position to select the better possible residue conformation, augmenting the overall accuracy of the model. Tell me a way to consider all templates in a script, develop iterative optimal alignment based only on sequence, i.e. without your RMS or cutoff thresholds for superimpositions. This alignment considers maximal propensity of a residue at every location, among available residues of considered templates, and put gaps for others at same locus in the alignment file for other templates. Thanks Ashish ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, February 25, 2011 12:01:29 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 37 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://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. bad occupancy from loop refinement (albert) 2. Re: bad occupancy from loop refinement (Modeller Caretaker) 3. Regarding Iterative Sequence Alignment (Ashish Runthala) 4. Re: Regarding Iterative Sequence Alignment (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Feb 2011 03:08:12 +0800 (CST) From: albert <leuven(a)yeah.net> Subject: [modeller_usage] bad occupancy from loop refinement To: modeller_usage <modeller_usage(a)salilab.org> Message-ID: <7f59a41d.528d.12e499f311b.Coremail.leuven(a)yeah.net> Content-Type: text/plain; charset="gbk" Hello: I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1. here is some list, can you tell me why? THX -----------------------------Loop refinement---------------------------------------------- EXPDTA THEORETICAL MODEL, MODELLER 9v8 2011/02/18 21:54:47 REMARK 6 MODELLER OBJECTIVE FUNCTION: -11.8879 ATOM 1 N SER A 1 53.405 4.206 73.937 59.86 59.86 ATOM 2 CA SER A 1 54.091 5.156 73.036 59.86 59.86 ATOM 3 CB SER A 1 53.358 5.255 71.687 59.86 59.86 ATOM 4 OG SER A 1 53.443 4.020 70.992 59.86 59.86 ATOM 5 C SER A 1 54.148 6.519 73.639 59.86 59.86 ATOM 6 O SER A 1 54.469 6.679 74.816 59.86 59.86 ATOM 7 N ALA A 2 53.848 7.547 72.824 39.90 39.90 ATOM 8 CA ALA A 2 53.862 8.892 73.313 39.90 39.90

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Regarding Iterative Sequence Alignment
by Ashish Runthala 24 Feb '11

24 Feb '11

Dear Modellers, I want to generate iterative sequence alignment of Templates before being integrated with the target sequence. How to use salign for optimal iterative alignment only based on sequences, with no consideration of overhang folds. Thanks Ashish Ashish Runthala Lecturer, Structural Biology Cell, Biological Sciences Group, BITS Pilani, Rajasthan - INDIA

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bad occupancy from loop refinement
by albert 22 Feb '11

22 Feb '11

Hello: I am using loop refinement protocol based on known PDB file method for loop refinement. What surprised me is that: the occupancy for each atom in the refined structure is more than 1. here is some list, can you tell me why? THX -----------------------------Loop refinement---------------------------------------------- EXPDTA THEORETICAL MODEL, MODELLER 9v8 2011/02/18 21:54:47 REMARK 6 MODELLER OBJECTIVE FUNCTION: -11.8879 ATOM 1 N SER A 1 53.405 4.206 73.937 59.86 59.86 ATOM 2 CA SER A 1 54.091 5.156 73.036 59.86 59.86 ATOM 3 CB SER A 1 53.358 5.255 71.687 59.86 59.86 ATOM 4 OG SER A 1 53.443 4.020 70.992 59.86 59.86 ATOM 5 C SER A 1 54.148 6.519 73.639 59.86 59.86 ATOM 6 O SER A 1 54.469 6.679 74.816 59.86 59.86 ATOM 7 N ALA A 2 53.848 7.547 72.824 39.90 39.90 ATOM 8 CA ALA A 2 53.862 8.892 73.313 39.90 39.90

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loop model error
by albert 18 Feb '11

18 Feb '11

Hi: I am using model loop based on initial PDB files, but there is a error: Traceback (most recent call last): File "model.py", line 41, in ? a.make() File "/usr/lib64/python2.4/site-packages/modeller/automodel/loopmodel.py", line 36, in make automodel.make(self, exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 411, in homcsr aln = self.read_alignment() File "/usr/lib64/python2.4/site-packages/modeller/automodel/automodel.py", line 401, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "/usr/lib64/python2.4/site-packages/modeller/alignment.py", line 81, in append allow_alternates) IOError: openf______E> Cannot open file : No such file or directory

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how seed influence the Modeller results?
by albert 18 Feb '11

18 Feb '11

Hi: I've got a question about how seed influence the Modeller results? If I start from the same seed in the same computer, does it means it should get the same results? If two job both start from random seed or different seeds, they will get different results, and those results is comparable with running model building jobs with doubled model number building? THX

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plot_profiles.py errors
by hari krishna 18 Feb '11

18 Feb '11

I installed MatPlotLib 2.6v. (python2.6) Still it is showing me the error: File "plot_profiles.py", line 1, in ? import pylab Importerror: No module named pylab Please help me to over come this problem. *Thanks in advance..*

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