- modeller_usage - salilab.org

Loop refinement: setting the right anchors in multichain models
by Jérôme Hénin 01 May '12

01 May '12

Hi everyone, I am trying to do loop refinement on a multi-chain protein. My problem is that Modeller tries to anchor C-ter loops to the N-ter of the next chain, yielding unrealistic starting configurations, and making the whole refinement fail. How can I instruct Modeller that the C-ter and the following N-ter "loops" are to be modeled separately? Thanks, Jerome

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procheck problem.
by vishal Nemaysh 30 Apr '12

30 Apr '12

Respected Sir, I have tried to minimize my pdb structure which is modeled by Modeller9v8. i use the Discovery Studio plateform to minimize this pdb structure by applying CHARMm force field and applying steepest descent and after that conjugate gradient algorithm. but the problem here is that the procheck result is not good as earlier. such as in Ramachandran plot 87% amino acids are in favorable region before minimization but after minimization only 55% amino acids are in favorable range...so plz sir suggest me some solutions.... Thanking you, Your Sincerely -- Vishal Research Scholar, University of Delhi, North Campus Delhi-110007 M: 91+9650736653

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Re: [modeller_usage] (no subject)
by sree jyothi 27 Apr '12

27 Apr '12

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Invitation to connect on LinkedIn
by Uday Kumar 26 Apr '12

26 Apr '12

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Uday Uday Kumar Manager-Health and Safety at Compass Group - ESS Bengaluru Area, India Confirm that you know Uday Kumar: https://www.linkedin.com/e/-xaf1me-h1iu5mec-5r/isd/6855298703/Yx6fI_Q6/?hs=… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-xaf1me-h1iu5mec-5r/3GpqQCFu9Ujj9Gys3027RLVJQStjD… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Invitation to connect on LinkedIn
by Uday Kumar 26 Apr '12

26 Apr '12

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Uday Uday Kumar Manager-Health and Safety at Compass Group - ESS Bengaluru Area, India Confirm that you know Uday Kumar: https://www.linkedin.com/e/-xaf1me-h1iu4l3v-4a/isd/6855298703/Yx6fI_Q6/?hs=… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/-xaf1me-h1iu4l3v-4a/3GpqQCFu9Ujj9Gys3027RLVJQStjD… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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Regarding Model Building
by Ashish Runthala 23 Apr '12

23 Apr '12

Dear Modellers, I have a pretty small question. Is there a way in MODELLER where i can completely use a single template along with its side-chain topology? So while aligned with target, I would expect that the template's backbone and side-chain relative orientations, topology and architecture is properly copied from the considered template, and then I would expect MODELLER to model the unaligned flexible chunks through the exactly copied scaffolds from the template. In normal modelling scripts, it simply harness the peptide backbone localization information from the template and then fixes the side-chains with its own algorithms. HOW CAN I GET MY QUERY SOLVED WITH AN ADDITIONAL LINE IN MODEL-SINGLE.PY TO COMPLETELY EMPLOY TEMPLATE WITH ITS PEPTIDE BACKBONE ALONG WITH SIDE-CHAINS? 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 11, Issue 44
by Ashish Runthala 10 Apr '12

10 Apr '12

Script is wrong, Use knowns='5fd1A' (with ChainID) because this is a protein. For ligand bound residue put a . in the alignment file, so that MODELLER can include the attached ligand too in the model. Then it will correctly call assess_methods=(assess.DOPE, assess.GA341)) (Last line of your initial set of lines). If you are using 5FD1 as the PDB file to model your sequence 1fdx, then you should definitely have the DOPE Score calculated. 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: Tuesday, April 10, 2012 11:12:30 AM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 44 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: modeller_usage Digest, Vol 11, Issue 42 (Modeller Caretaker) 2. calculating DOPE score (NUTAN CHAUHAN) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 20:35:37 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: <4F83AA89.9080408(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 4/9/12 8:00 PM, Ashish Runthala wrote: > MODELLER based on your constructed alignment file > parsing the reliable template residues mapped against the target > ones, constructs and fixes the average alpha carbon backbone Actually all atoms that have the same name in target and template will be simply copied into the model in this case. Usually this means all backbone atoms, not just alpha carbons. > On increased sampling, > MODELLER tries best to satisfy the Lennard Jones and all the > energetic equations composing its DOPE energy function. In fact the optimization tries to minimize the molecular PDF, which includes contributions from soft sphere (not Lennard Jones). DOPE is a separate, atomistic pairwise statistical potential. It is not used in comparative modeling. 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: Tue, 10 Apr 2012 13:29:27 +0800 (SGT) From: NUTAN CHAUHAN <nutanbt(a)yahoo.co.in> To: "modeller_usage(a)salilab.org" <modeller_usage(a)salilab.org> Subject: [modeller_usage] calculating DOPE score Message-ID: <1334035767.17687.YahooMailNeo(a)web192502.mail.sg3.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, I am trying to build a protein-ligand model using align-ligand.ali file. . Below is ?the python script to generate 5 model and to ?calculate the Dope and GA score.?but I am unable to calculate the DOPE score and GA score. Plz help from modeller import * from modeller.automodel import * log.verbose() ? ?# request verbose output env = environ() ?# create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env = environ() a = automodel(env, alnfile='alignment.ali', ? ? ? ? ? ? ? knowns='5fd1', sequence='1fdx', ? ? ? ? ? ? ? assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() ? Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Tuesday, 10 April 2012 8:58 AM Subject: modeller_usage Digest, Vol 11, Issue 43 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: In what are the initial structures different? ? ? ? (Modeller Caretaker) ? 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ? 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: BIN ZHANG <zhngbn(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] In what are the initial structures ??? different? Message-ID: <4F832E6A.5020001(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual. See http://salilab.org/modeller/9.10/manual/node470.html, in particular step 3 and substep 3. The initial structures are simply randomized by calling selection.randomize_xyz(). ??? 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: Tue, 10 Apr 2012 08:33:02 +0530 (IST) From: Ashish Runthala??? ? <ashishr(a)bits-pilani.ac.in> To: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: ??? <15240798.16751334026982399.JavaMail.root(a)mailserver.bits-pilani.ac.in> ??? Content-Type: text/plain; charset=utf-8 Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: ??? <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(? ? ? 2) =? 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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calculating DOPE score
by NUTAN CHAUHAN 09 Apr '12

09 Apr '12

Hello all, I am trying to build a protein-ligand model using align-ligand.ali file. . Below is the python script to generate 5 model and to calculate the Dope and GA score. but I am unable to calculate the DOPE score and GA score. Plz help from modeller import * from modeller.automodel import * log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] env = environ() a = automodel(env, alnfile='alignment.ali', knowns='5fd1', sequence='1fdx', assess_methods=(assess.DOPE, assess.GA341)) a.starting_model = 1 a.ending_model = 5 a.make() Regards, Nutan Chauhan Research Scholar Department of Biotechnology BIT, Mesra Ranchi-835215, Jharkhand ________________________________ From: "modeller_usage-request(a)salilab.org" <modeller_usage-request(a)salilab.org> To: modeller_usage(a)salilab.org Sent: Tuesday, 10 April 2012 8:58 AM Subject: modeller_usage Digest, Vol 11, Issue 43 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: In what are the initial structures different? (Modeller Caretaker) 2. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) 3. Re: modeller_usage Digest, Vol 11, Issue 42 (Ashish Runthala) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Apr 2012 11:46:02 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: BIN ZHANG <zhngbn(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] In what are the initial structures different? Message-ID: <4F832E6A.5020001(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 04/08/2012 11:58 PM, BIN ZHANG wrote: > I have a question about the differences of the initial structure built > for homology modeling. Can anyone tell me how exactly are these initial > structures different? Do they differ in the secondary structures in > uncertain regions? I cannot find this information in the manual. See http://salilab.org/modeller/9.10/manual/node470.html, in particular step 3 and substep 3. The initial structures are simply randomized by calling selection.randomize_xyz(). 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: Tue, 10 Apr 2012 08:33:02 +0530 (IST) From: Ashish Runthala <ashishr(a)bits-pilani.ac.in> To: modeller usage <modeller_usage(a)salilab.org> Subject: Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42 Message-ID: <15240798.16751334026982399.JavaMail.root(a)mailserver.bits-pilani.ac.in> Content-Type: text/plain; charset=utf-8 Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
by Ashish Runthala 09 Apr '12

09 Apr '12

Dear BIN ZHANG, MODELLER based on your constructed alignment file parsing the reliable template residues mapped against the target ones, constructs and fixes the average alpha carbon backbone (if you choose a single template) or an average backbone topology (for Multiple templates' local aligned chunks). Then it fits in the side chains and backbone atoms to make the model complete. However, easy saying but really a vicious circle problem, the alignment could have actually been wrong to incorrectly fit target against parsed template residues. Regardless of the earlier problems, On increased sampling, MODELLER tries best to satisfy the Lennard Jones and all the energetic equations composing its DOPE energy function. The non-physical local atomic clashes are thus minimized with every such iteration. So only you see, Restraints earlier, now with end of every such iterative step. That in fact, is the trial to leap the energetic landscape, precisely focusing on the probably erroneous regions encompassing the higher local steric clashes. The story continues until the number of iterations are over. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA Message: 1 Date: Sun, 8 Apr 2012 23:58:13 -0700 From: BIN ZHANG <zhngbn(a)gmail.com> To: modeller_usage(a)salilab.org Subject: [modeller_usage] In what are the initial structures different? Message-ID: <602A5241-132A-4319-81BA-94C238A459AF(a)gmail.com> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Dear All: I have a question about the differences of the initial structure built for homology modeling. Can anyone tell me how exactly are these initial structures different? Do they differ in the secondary structures in uncertain regions? I cannot find this information in the manual. For example, by using a = automodel() a.starting_model = 1 a.ending_model = 50 I can built 50 different homology models starting from different initial structures, but I have want to know how these different initial structures are constructed. Thanks very much for help. Best, Bin

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42
by Ashish Runthala 09 Apr '12

09 Apr '12

Focus on the statement with ALIGN_CODES, as it is inclusive of the PDB_ID and the PDB_CHAIN used in the alignment file. So it could probably be '2AHNA' or '2AHNB'. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ------------------------------ Message: 2 Date: Mon, 9 Apr 2012 17:21:12 +0530 From: Sumedha Roy <sumedharoy(a)gmail.com> To: modeller usage <modeller_usage(a)salilab.org> Subject: [modeller_usage] Error in ALIGN_CODES(i) Message-ID: <CABFmE0dNMawUwZgsh07bsRd43+-O3Yrzq6VhfkSQJOTjp=NECA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hello all, When I try to model my protein-DNA complex, I get the error: _modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 2) = 2AHN But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!! -- Sumedha Roy

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