modeller_usage

modeller_usage@salilab.org

3151 discussions

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

2 1

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

2 1

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/

2 1

Sintax error in script
by virginia miguel 29 Dec '09

29 Dec '09

Hi; I am trying to run the following script : # Homology modeling with multiple templates from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class 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' a = automodel(env, alnfile = ’align.ali’, # alignment filename knowns = (’1bkn’, ’1b62’, ’1b63’, ’1nhh’, ’1nhi’, ’1nhj’), # codes of the templates sequence = ’PAOI’) # code of the target a.starting_model= 1 # index of the first model a.ending_model = 50 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modeling and I get the following error: warning: Non-ASCII character '\xe2' in file model-multiple2.py on line 14, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details File "model-multiple2.py", line 14 alnfile = ’align.ali’, # alignment filename ^ SyntaxError: invalid syntax How do I fix my script? Thanks, Virginia Yahoo! Cocina Encontra las mejores recetas con Yahoo! Cocina. http://ar.mujer.yahoo.com/cocina/

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mailing list
by 陈颢 21 Dec '09

21 Dec '09

test -- 陈颢国家海洋局第一海洋研究所青岛市高科园仙霞岭路6号邮编：266061

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homology modelling vs protein threading
by Thomas Evangelidis 21 Dec '09

21 Dec '09

Dear modellers, I want to build models of ATP-binding domains with sequence identity ranging between 40% and 50%. In the FAQs it says that one needs 35-40% at least to build reliable models. However these models will be used for inhibitor design, therefore the accuracy of the structure prediction method will determine the outcome. Do you reckon the sequence similarity is enough to get a good model of the domain, or should I try other programs based on threading? Is there a way to compare the quality of the structures derived from these 2 different methodologies? I would greatly appreciate any advice. Thomas

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HIS and HSE
by Francesco Musiani 15 Dec '09

15 Dec '09

Hello, I would like to calculate an all atoms (including hydrogens) model of a metallo protein containing zinc. In particular, I would like to bind Zn2+ ion to ND1 atom of an histidine residues. I try to replace the residue "H" with "6" in the alignment (I referred to restyp.lib library found in modlib directory) but I obtain the following error in the log file. getpdf__392E> Your library requires all bins zero; nbinx: 5 can you help me? regards, Francesco -- Francesco Musiani -- Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna, Italy Phone: +39-051-2096236 - Fax: +39-051-2096203 E-mail: francesco.musiani(a)unibo.it

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rigid.txt for PDBs with multiple subunits
by Robin Zhang 15 Dec '09

15 Dec '09

Hi, I'm trying to create a rigid.txt file for an antibody PDB file that contains multiple subunits (ie subunit A, subunit B, subunit C, and subunit D). However, the example in the ncmi_2008_files folder only contains a single subunit. Is there any way one can specify subunit as well as residue number in an rigid.txt file?

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modeller_usage