March 2011 - modeller_usage

Re: [modeller_usage] how to rank model if log file missing
by albert 02 Mar '11

02 Mar '11

Thanks for kind reply. Here I found this script: http://salilab.org/modeller/9v8/manual/node194.html But it just contains one PDB file for rank. However, I contains 1000 structures, how can I rank them in one time? THX On Tue, 2011-03-01 at 13:53 +0530, Ashish Runthala wrote: > 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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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 42
by Ashish Runthala 02 Mar '11

02 Mar '11

Benn, CASP winners used HMM based profiles for target as well as template to rank and consider the template hits. Their approach is better when the target sequence identity to known templates lie below the twilight zone mark. 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: Tuesday, March 1, 2011 11:41:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 42 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: about model rank (Modeller Caretaker) 2. Re: Regarding Salign (Modeller Caretaker) 3. Re: No template... (Modeller Caretaker) 4. No template... (Anna Marabotti) ---------------------------------------------------------------------- Message: 1 Date: Tue, 01 Mar 2011 08:10:37 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] about model rank To: modeller usage <modeller_usage(a)salilab.org> Message-ID: <4D6D1A7D.70809(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/1/11 12:23 AM, Ashish Runthala wrote: > NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. Such a strong statement needs to be backed up by a publication... particularly given that it is contradicted by both your next sentence and our own study (Prot Sci 17, 1881-1893, 2008). > Use normalized_dope Normalized DOPE is derived from the raw DOPE score. Thus the ranking of models, given the same sequence, will be the same with DOPE or normalized DOPE. However, since raw DOPE is an "energy", you should certainly not use it to rank models that differ in sequence. For that, normalized DOPE would be more appropriate. > or GDT to rank models/Clusters/Hybrid Models. GDT is a structural measure, like RMSD, so it requires another structure to compare against. This makes it useless for assessing comparative models unless you already know the answer (as in CASP). 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, 01 Mar 2011 08:12:08 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Regarding Salign To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4D6D1AD8.2060606(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/28/11 2:33 AM, Ashish Runthala wrote: > How does align2d_mult actually adds the target sequence onto the > aligned templates ali file. The algorithm is fully described in Prot. Eng. Des. & Sel. 19, 129-133. 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: 3 Date: Tue, 01 Mar 2011 08:19:46 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] No template... To: Marco Sette <m77it(a)yahoo.it> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4D6D1CA2.5020502(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/1/11 6:31 AM, Marco Sette wrote: > 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, Since Modeller is a package for comparative modeling, if you don't have a template, you cannot model that region of your model. I don't know what you mean by "Modeller ... doesn't suggest templates" since Modeller doesn't suggest templates for you. Perhaps you mean you are doing a sequence-sequence search to look for templates (step 1 of the basic tutorial) and you didn't find any? BLAST does essentially the same thing - except that it's using an approximation rather than "real" dynamic programming, so it runs faster - so is also unlikely to find a template if this search doesn't work. ModWeb supplements this basic sequence-sequence search with more sensitive profile-based searches (it also tries PSI-BLAST, which is a similar method). But there are many other methods available to search for templates - e.g. HMM-based. One thing you could do is look at the best performers for the last CASP contest and see how they detect templates - some of those are available as web servers. 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: 4 Date: Tue, 01 Mar 2011 16:45:45 +0100 From: Anna Marabotti <anna.marabotti(a)isa.cnr.it> Subject: [modeller_usage] No template... To: modeller_usage(a)salilab.org Message-ID: <01NYEM52EMMQPZ8FR2(a)mx.isti.cnr.it> Content-Type: text/plain; charset=us-ascii 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 ********************************************** ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 10, Issue 42 **********************************************

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 42
by Ashish Runthala 02 Mar '11

02 Mar '11

But Benn, you answer my simple question then. Suppose you have 2 protein sequences for each of which you generated 1000 decoys. To select the best model, won't you consider normalized_DOPE. Energy & GA341 can discriminate bad and correct overall model fold to some extent, but it can't cluster/select best model especially, when we consider TBM-HA targets. And, By the way i designed an algorithm for which i am writing the script which does calculate most likely GDT-TS or GDT-HA score to actual native unknown conformation. And yes, don't mind about my comments on DOPE. I experienced it, So wrote it. 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: Tuesday, March 1, 2011 11:41:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 10, Issue 42 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: about model rank (Modeller Caretaker) 2. Re: Regarding Salign (Modeller Caretaker) 3. Re: No template... (Modeller Caretaker) 4. No template... (Anna Marabotti) ---------------------------------------------------------------------- Message: 1 Date: Tue, 01 Mar 2011 08:10:37 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] about model rank To: modeller usage <modeller_usage(a)salilab.org> Message-ID: <4D6D1A7D.70809(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/1/11 12:23 AM, Ashish Runthala wrote: > NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE. Such a strong statement needs to be backed up by a publication... particularly given that it is contradicted by both your next sentence and our own study (Prot Sci 17, 1881-1893, 2008). > Use normalized_dope Normalized DOPE is derived from the raw DOPE score. Thus the ranking of models, given the same sequence, will be the same with DOPE or normalized DOPE. However, since raw DOPE is an "energy", you should certainly not use it to rank models that differ in sequence. For that, normalized DOPE would be more appropriate. > or GDT to rank models/Clusters/Hybrid Models. GDT is a structural measure, like RMSD, so it requires another structure to compare against. This makes it useless for assessing comparative models unless you already know the answer (as in CASP). 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, 01 Mar 2011 08:12:08 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] Regarding Salign To: Ashish Runthala <ashishr(a)bits-pilani.ac.in> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4D6D1AD8.2060606(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/28/11 2:33 AM, Ashish Runthala wrote: > How does align2d_mult actually adds the target sequence onto the > aligned templates ali file. The algorithm is fully described in Prot. Eng. Des. & Sel. 19, 129-133. 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: 3 Date: Tue, 01 Mar 2011 08:19:46 -0800 From: Modeller Caretaker <modeller-care(a)salilab.org> Subject: Re: [modeller_usage] No template... To: Marco Sette <m77it(a)yahoo.it> Cc: modeller <modeller_usage(a)salilab.org> Message-ID: <4D6D1CA2.5020502(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 3/1/11 6:31 AM, Marco Sette wrote: > 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, Since Modeller is a package for comparative modeling, if you don't have a template, you cannot model that region of your model. I don't know what you mean by "Modeller ... doesn't suggest templates" since Modeller doesn't suggest templates for you. Perhaps you mean you are doing a sequence-sequence search to look for templates (step 1 of the basic tutorial) and you didn't find any? BLAST does essentially the same thing - except that it's using an approximation rather than "real" dynamic programming, so it runs faster - so is also unlikely to find a template if this search doesn't work. ModWeb supplements this basic sequence-sequence search with more sensitive profile-based searches (it also tries PSI-BLAST, which is a similar method). But there are many other methods available to search for templates - e.g. HMM-based. One thing you could do is look at the best performers for the last CASP contest and see how they detect templates - some of those are available as web servers. 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: 4 Date: Tue, 01 Mar 2011 16:45:45 +0100 From: Anna Marabotti <anna.marabotti(a)isa.cnr.it> Subject: [modeller_usage] No template... To: modeller_usage(a)salilab.org Message-ID: <01NYEM52EMMQPZ8FR2(a)mx.isti.cnr.it> Content-Type: text/plain; charset=us-ascii 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 ********************************************** ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 10, Issue 42 **********************************************

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Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 41
by Ashish Runthala 02 Mar '11

02 Mar '11

Dear Marco, Your question is very nice. But to make a good prediction, better check out structural similarity in templates based on the both N & C terminal. I guess you are modeling a big sequence, which may have multiple domains. So you should consider many things. If you upload other details of the sequence along with its length, it will be better to suggest the best way to screen significant template folds. Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA 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 --- Gio 27/1/11, Modeller Caretaker <modeller-care(a)salilab.org> ha scritto: > Da: Modeller Caretaker <modeller-care(a)salilab.org> > Oggetto: Re: [modeller_usage] Loop modeling > A: "bharat lal" <monu46010(a)yahoo.com> > Cc: "modeller" <modeller_usage(a)salilab.org> > Data: Gioved? 27 gennaio 2011, 21:44 > On 01/27/2011 06:22 AM, bharat lal > wrote: > > 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 ??? > > You can't *force* it, but if you unalign the target and > template in this > region, loop/coil is the most likely secondary structure > you'll end up > with. See > http://salilab.org/archives/modeller_usage/2009/msg00170.html > > ??? Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org? > ? ? ? ? ???http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage > ------------------------------ _______________________________________________ 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 41
by Ashish Runthala 02 Mar '11

02 Mar '11

Dear Albert, Then i think instead of running MODELLER again, better make a batch file in windows to individually call each target*.pdb file from the current folder to save the log file again to check the results Ashish Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA

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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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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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