- modeller_usage - salilab.org

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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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 39
by Ashish Runthala 01 Mar '11

01 Mar '11

Dear Knut J, Please don't use DOPE as such to evaluate model. NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. Use normalized_dope or GDT to rank models/Clusters/Hybrid Models. Ashish ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Monday, February 28, 2011 5:02:41 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 39 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. Re: Structural alignment using iterative_structural_alignment (Modeller Caretaker) 2. about model rank (albert) 3. Regarding Salign (Ashish Runthala) 4. Re: about model rank (Knut J Bjuland) ---------------------------------------------------------------------- Message: 1 Date: Fri, 25 Feb 2011 16:04:47 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Structural alignment using iterative_structural_alignment To: Seungyeul Yoo <seungyeul.yoo(a)mssm.edu> Cc: modeller_usage(a)salilab.org Message-ID: <4D68439F.3090709(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/25/11 9:48 AM, Seungyeul Yoo wrote: > I was trying to clean two pdb files and superpose them based on the > pairwise structural alignment. ... > But when I replaced it to > 'modeller.salign.iterative_structural_align(aln), I had error message like: My best guess is that every combination of parameters failed for the first loop, so it has no alignment to refine. If you can send me your full inputs (which two PDBs are you trying to align?) I'll see if it can be fixed. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Sun, 27 Feb 2011 23:28:20 +0800 (CST) From: albert <leuven(a)yeah.net> Subject: [modeller_usage] about model rank To: modeller_usage <modeller_usage(a)salilab.org> Message-ID: <2e2442cd.2c66.12e67bc0d5d.Coremail.leuven(a)yeah.net> Content-Type: text/plain; charset="gbk" 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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No template...
by Anna Marabotti 01 Mar '11

01 Mar '11

Dear Marco, have you tried to perform the search for a template using fold recognition tools such as GenThreader, 3D-PSSM and so on? They use a different criterium to find a template with respect to BLAST and PSI-BLAST, and they are effective in finding templates when the similarity of sequences is low. Cheers Anna Date: Tue, 1 Mar 2011 14:31:22 +0000 (GMT) From: Marco Sette <m77it(a)yahoo.it> Subject: [modeller_usage] No template... To: modeller <modeller_usage(a)salilab.org> Message-ID: <286694.64907.qm(a)web24003.mail.ird.yahoo.com> Content-Type: text/plain; charset=iso-8859-1 Dear all, I have a protein consisting of a C-terminal and N-terminal region. While for the C-terminal one I have a good template either Modeller or Blast don't suggest templates for the N-terminal one. I have some suggestion using Modweb (which search performs Modweb?) but not very good. Could ou suggest me a website to search for a template? I looked at the mailing list (very long...) but seems this question has not been posed. Many thanks, Marco Dr.Marco Sette, Ph.D. Department of Chemical Sciences and Technology University of Rome, "Tor Vergata" via della Ricerca Scientifica, 00133, Rome, Italy e-mail: sette(a)uniroma2.it e-mail: m77it(a)yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 10, Issue 41 **********************************************

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 39
by Ashish Runthala 01 Mar '11

01 Mar '11

Dear Albert, It will be really a big mess to select best decoy. Use this line in your modeling script in the loop like this, and use redirectional operator while running the modeller as model_mult.py > modeling.log. That will solve your purpose. knowns=(........), sequence='.....', assess_methods=(assess.DOPE,assess.GA341,assess.normalized_dope)) a.starting_model=1 This will solve your purpose. Take care of loop closure. Good Luck, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 39
by Ashish Runthala 01 Mar '11

01 Mar '11

Dear Seungyeul Yoo I surpassed these errors, when you make a script which provides flexibility in optimal iterative alignment for making the maximal possible satisfaction of unaligned segments. Send me your initial files with the scripts you used. Then i can correct your problems for sure. Good Luck, Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Monday, February 28, 2011 5:02:41 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 39 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. Re: Structural alignment using iterative_structural_alignment (Modeller Caretaker) 2. about model rank (albert) 3. Regarding Salign (Ashish Runthala) 4. Re: about model rank (Knut J Bjuland) ---------------------------------------------------------------------- Message: 1 Date: Fri, 25 Feb 2011 16:04:47 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Structural alignment using iterative_structural_alignment To: Seungyeul Yoo <seungyeul.yoo(a)mssm.edu> Cc: modeller_usage(a)salilab.org Message-ID: <4D68439F.3090709(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/25/11 9:48 AM, Seungyeul Yoo wrote: > I was trying to clean two pdb files and superpose them based on the > pairwise structural alignment. ... > But when I replaced it to > 'modeller.salign.iterative_structural_align(aln), I had error message like: My best guess is that every combination of parameters failed for the first loop, so it has no alignment to refine. If you can send me your full inputs (which two PDBs are you trying to align?) I'll see if it can be fixed. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Sun, 27 Feb 2011 23:28:20 +0800 (CST) From: albert <leuven(a)yeah.net> Subject: [modeller_usage] about model rank To: modeller_usage <modeller_usage(a)salilab.org> Message-ID: <2e2442cd.2c66.12e67bc0d5d.Coremail.leuven(a)yeah.net> Content-Type: text/plain; charset="gbk" 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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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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