- modeller_usage - salilab.org

muliplay cpu
by Knut J Bjuland 21 Jan '10

21 Jan '10

How do I use multiple cpu when doing loop which I have shown in a script below. I am trying to use several cpus to get a faster build of a model. Knut J rom modeller import * from modeller.automodel import * from modeller.parallel import * env = environ() j= job() j.append(local_slave()) #cpu 1 j.append(local_slave()) #cpu 2 j.append(local_slave()) #cpu 3 j.append(local_slave()) #cpu 3 j.start() class Model(automodel): def select_atoms(self): return selection(self.residue_range('1:','180:')) a=Model(env,alnfile='hNaa10p.ali', knowns='2OB0', sequence='hnaa10', assess_methods=assess.DOPE) a.starting_model=1 a.ending_model=200 a.use_parallel_job(j) a.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: %s (DOPE score %.3f)" % (m['name'], m[key])

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good book about modeller.
by Knut J Bjuland 18 Jan '10

18 Jan '10

I am looking for a good book about molecular modellering, and in particular a good book about modeller. Knut J

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Re: [modeller_usage] Modeling a larger protein in several steps
by nornik 17 Jan '10

17 Jan '10

I noticed that the alignment made no sense at all so I resend the message with a new one with mono space characters and hope it will be easier: Hello I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template ----BBBBSBBBBBBB--------------------------------------------------- template2 ----------CCCCCCCCCSCCCCC------------------------------------------ template3 ----------------------------------DDDDDSDDDDDDDSDDDDDD------------- template4 ----------------------------------------------------------EEEESEEEE template5 sulfur bridge sulfur bridge sulfur bridge Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "deletions" with the other four templates and still maintain the sulfur bridges. Any other suggestions are of course also welcome in trying to solve this problem. Thank you

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Modeling a larger protein in several steps
by nornik 13 Jan '10

13 Jan '10

Hello I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this MMMMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMMMMMMMMMMMMMM Model AAAAAAAAAAA---------------------------AAAAAAAAAAAAAAAAAAAAA------------------------AAAAAAAAASAA------------------------------- core template --------------BBBBSBBBBBBB------------------------------------------------------------------------------------------------------------------------- template2 ---------------------------CCCCCCCCCSCCCCC----------------------------------------------------------------------------------------------------- template3 -------------------------------------------------------------------------DDDDDSDDDDDDDDDSDDDDDD-------------------------------------------- template4 ---------------------------------------------------------------------------------------------------------------------EEEEEEEEEEEEEEEEESEEEEEEE template5 __sulfur bridge___ _sulfur bridge_ ___sulfur bridge___ Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "deletions" with the other four templates and still maintain the sulfur bridges. Any other suggestions are of course also welcome in trying to solve this problem. Thank you Niklas

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question about Modeling with cryo-EM compare.
by Knut J Bjuland 12 Jan '10

12 Jan '10

When you read the second part of this tutorial at http://salilab.org/modeller/ncmi_2008/select.html. How do you read this table, or is there any function in modeller that use the table and output sequence identity. Sequence identity comparison (ID_TABLE): Diagonal ... number of residues; Upper triangle ... number of identical residues; Lower triangle ... % sequence identity, id/min(length). 1b8pA @11y7tA @11civA @25mdhA @27mdhA @23d5tA @21smkA @2 1b8pA @1 327 201 146 152 152 249 50 1y7tA @1 61 327 158 170 160 210 58 1civA @2 45 48 374 140 304 148 55 5mdhA @2 46 52 42 333 140 164 58 7mdhA @2 46 49 87 42 351 148 50 3d5tA @2 78 65 46 51 46 321 50 1smkA @2 16 19 18 19 16 16 313 I am not able to read the this table manually and I can not see how I can extract sequence_identity from it. Best regards Knut J _________________________________________________________________ Windows Live Hotmail: Your friends can get your Facebook updates, right from Hotmail®. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/so…

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mutipule cpu run errors.
by leuven 12 Jan '10

12 Jan '10

hello all: I try to use multiple cpu with modeller, but it fails, here is my srcipts: # Example of changing the default optmization schedule from modeller import * from modeller.automodel import * from modeller.parallel import * # Load the parallel class, to use multiple processors j = job("/usr/lib/modeller9v7/bin/modslave.py") j.append(local_slave()) # 1 Processor j.append(local_slave()) # 2 Processors And here is the error: /soft/python/lib/python2.5/site-packages/modeller/__init__.py:69: RuntimeWarning: Python C API version mismatch for module _modeller: This Python has API version 1013, module _modeller has version 1012. import _modeller /soft/python/lib/python2.5/site-packages/modeller/__init__.py:69: RuntimeWarning: Python C API version mismatch for module swig_runtime_data4: This Python has API version 1013, module swig_runtime_data4 has version 1012. import _modeller

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how to build mutations with different resiudes to different target residues?
by leuven 11 Jan '10

11 Jan '10

I want to build mutation model with 5 residues. The no. of this residues is : 16, 42 56, 88, 152, and they are mutated into different residues. How to achieve this? I found something at http://salilab.org/modeller/manual/node234.html, but I don't think this example is suitable for my situation. Thank you very much.

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how to get log file in windows
by 龚云国 11 Jan '10

11 Jan '10

Dear Modeller， I used windows XP system, and mod9v7, I can't receive the log file. I take refernce of the down following, and modify the file of "modenv.bat"(no "mod.bat" file) change to the style "%MODINSTALL9v7%\bin\modeller6v2 %1 %2 %3 %4 %5 %6 %7 %8 %9 > %1.log" or "%Modeller9v7%\bin\modeller6v2 %1 %2 %3 %4 %5 %6 %7 %8 %9 > %1.log" Can not succeed. Can you tell me how to solve it? Thank you! Yunguo Gong -- To: Nataraj Balkrishnan < natarajmtech(a)yahoo.co.uknatarajmtechATyahoo.co.uk> Subject: Re: [modeller_usage] How to get log file in windows From: Mensur Dlakic < mdlakic(a)montana.edumdlakicATmontana.edu> Date: Mon, 09 Feb 2004 08:13:44 -0700 Cc: modeller_usage(a)salilab.orgmodeller_usageATsalilab.org Hi The solution is simple. In your C:\mod6v2\bin directory there is a file mod.bat. Change it so it looks something like this: %MODINSTALL6v2%\bin\modeller6v2 %1 %2 %3 %4 %5 %6 %7 %8 %9 > %1.log As simple as this is, I think it should be documented as not all people know UNIX :-)) At 03:50 AM 2/9/2004, you wrote: Dear modellers, I am doing my modelling of protein in modeller uder MS-DOS version ,the log information is visualized while I run my TOP script but could not be stored ,how can I retrive my log file after task been executed in window version of modeller. .. yours, B.Nataraj ==================================================== Department of Medicinal Chemistry, School of Pharmacy, FudanUniversity ,826 Zhangheng Road, Shanghai, PRC.210203

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Request
by rasoul nasiri 08 Jan '10

08 Jan '10

Hi, I want to add residues 1-4 and 583-85 on protein which have been missed in X-ray structure. How can I do it? Thanks for helping! Regards Rasoul

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Error In Align Codes
by Muthiah I 04 Jan '10

04 Jan '10

Hi, I am trying to model a hetero dimer protein using modeller and I couldnt make it up.. the error which i was not able to rectify is "PROTEIN SPECIFIED IN ALIGN CODES WAS NOT FOUND IN THE ALIGNMENT FILE" The alignment file is as follows: >P1;queryAB sequence:queryAB:1: :1691: : : : : MGPRAKTISSLFFLLWVLAEPAENSDFY-----LPGDYLLGGLFSLHANMKGIVHLNFLQ VPMCKEYEVKV-IGYNLMQAMRFAVEEINNDSSLLPGVLLGYEIVDVCYISNNVQPVLYF LAHEDNLLPIQEDYSNYISRVVAVIGPDNSESVMTVANFLSLFLLPQITYSAISDELRDK VRFPALLRTTPSADHHIEAMVQLMLHFRWNWIIVLVSSDTYGRDNGQLLGERVARRDICI AFQETLPTLQPNQNMTSEERQRLVTIVDKLQQ--STARVVVVFSPDLTLYHFFNEVLRQN FTGAV-WIASESWA-IDPVLHNLTELRHLGTFLGITIQSVPIPGFSEF-----------R EWGPQAGPPPL-----SRTSQSYTCNQECDNCLNATLSFNTILRLSGERVVYSVYSAVYA VAHAL----HSLLGCDKSTC-TKRVVYPWQLLEEIWKVNFT-LLDHQIFFDPQGDVALHL EIVQWQWDRSQNPFQSVASYYPLQRQLKNIQDISWHTINNTIPMSMCSKRCQSGQKKKPV GIHVCCFECIDCLPGTFLNHTEDEYECQACPNNEWSYQSETSCFKRQLVFLEWHEAPTIA VALLAALGFLSTLAILVIFWRHFQTPIVRSAGGPMCFLMLTLLLVAYMVVPVYVGPPKVS TCLCRQALFPLCFTICISCIAVRSFQIVCAFKMASRFPRAYSYWVRYQGPYVSMAFITVL KMVIVVIGMLATGLSPTTRTDPDDPKITIVSCNPNYRNSLLFNTSLDLLLSVVGFSFAYM GKELPTNYNEAKFITLSMTFYFTSSVSLCTFMSAYSGVLVTIVDLLVTVLNLLAISLGYF GPKCYMILFYPERNTPAYFNSMIQGYTMRRD-------------------------- / MLGPAVLGLSLWALLHPGTGAPLCLSQQL-----RMKGDYVLGGLFPLGEAEEAGLRSRT RPSSPVCTRFSSNGLLWALAMKMAVEEINNKSDLLPGLRLGYDLFDTCSEPVVAMKPSLM FLAKAGSRDIAAYCNYTQYQPRVLAVIGPHSSELAMVTGKFFSFFLMPQVSYGASMELLS ARETFPSFFRTVPSDRVQLTAAAELLQEFGWNWVAALGSDDEYGRQGLSIFSALAAARGI CIAHEGLV---PLPRADDSRLGKVQDVLHQVNQSSVQVVLLFASVHAAHALFNYSISSRL ---SPKVWVASEAWLTSDLVMGLPGMAQMGTVLGFLQRGAQLHEFPQY-VKTHLALAT-D PAFCSALGEREQGLEEDVVGQRCPQCDCITLQNVSAGLNHHQTFS---VYAAVYSVAQAL HNTLQCNASG----CPAQDPVKPWQLLENMYNLTF-HVGGLPLRFDSSGNVDMEYDLKLW VWQGSVPRLHDVGRFNGSLRTERLKIRWHTSDNQKPVSRCSRQCQEGQVRRVKGFHSCCY DCVDCEAGSYRQNPDDIACTFCGQDEWSPERSTRCFRRRSRFLAWGEPAVLLLLLLLSLA LGLVLAALGLFVHHRDSPLVQASGGPLACFGLVCLGLVCLSVLLFPGQPSPARCLAQQPL SHLPLTGCLSTLFLQAAEIFVESELPLSWADRLSGCLRGPWAWLVVLLAMLVEVALCTWY LVAFPPEVVTDWHMLPTEALVHCRTRSWVSFGLAHATNATLAFLCFLGTFLVRSQPGCYN RARGLTFAMLAYFITWVSFVPLLANVQVVLRPAVQMGALLLCVLGILAAFHLPRCYLLMR QPGLNTPEFFLGGGPGDAQGQNDGNTGNQGKHE--------------------------- ---- * >P1;1ewkAB structureX:1ewkAB:36:A:512:B: : : : ----------------------------RSVARMDGDVIIGALFSVHHQPPAE------K VPERKCGEIREQYGIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSS-------- VALEQSIEFIRKP-------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLSDK TLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGLCI AHSD---KIYSNAGEKSFDR-----LLRKLRERLPKARVVVCFCEGMTVRGLLSAMRRLG VVGEFSLIGSDGWADRDEVIEGYEVEANGG--ITIKLQSPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLENPNFKKVCTG--NESLEENYV----QDSKMGFVINAIYA MAHGLQNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRY DIMNLQY----------------------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ -------------------------------TEANRYDYVHVGTWHEGVLNIDDYKI / -----------------------------QRSVARMDGDVIIGALFSVHHQPPAE-KVPE RKCGEIREQY---GIQRVEAMFHTLDKINADPVLLPNITLGSEIRDSCWHSSVALEQSIE FIRKP-----------------IAGVIGPGSSSVAIQVQNLLQLFDIPQIAYSATSIDLS DKTLYKYFLRVVPSDTLQARAMLDIVKRYNWTYVSAVHTEGNYGESGMDAFKELAAQEGL CIAHSDKIYSNAGEKSFDRLLRKLRERL-----PKARVVVCFCEGMTVRGLL--SAMRRL GVVGEFSLIGSDGWADRDEVIEGYEVEANGGITIKLQ-SPEVRSFDDYFLKLRLDTNTRN PWFPEFWQHRFQCRLPGHLLEN-PNFKKVCTGNESLEENYVQDSKMGFVINAIYAMAHGL QNMHHALCPGHVGLCDAMKPIDGRKLLDFLIKSSFVGVSGEEVWFDEKGDAPGRYDI--- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ---------------------------------MNLQYTEANRYDYVHVGTWHEGVLNID DYKI * Please help me to overcome this and to get a best model. thanks in advance. MUTHIAH. _________________________________________________________________ New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop

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