January 2010 - modeller_usage

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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links generation
by subarna thakur 04 Jan '10

04 Jan '10

Hello, I am using modeller-ligand.py script of Modeller9v6 for generation of a ligand (FE4S4 cluster ) for my modelled protein. The co-ordinates of the FE atoms and S atoms have been generated but the connect information are missing. Is there a way that somehow the ligands co-ordinates along with the connect information can be generated by the Modeller? regards Subarna Thakur The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/

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