- modeller_usage - salilab.org

Problems about disulfide bonds
by 饶�� 03 Jan '07

03 Jan '07

Dear Mr.: I have some questions about two commonds model.patch_ss_templates() and model.patch_ss().First,I don't know what exactly does these two commonds want to do.In my opinion,the earler can indicate wether the disulfide bonds exist and where are they and the later has the same function of which the target is the protein which is modeled.But after I have run the commond and used the mdl.energy() commond,I don't how to understant the output file.I don't know what information I can get from the .log file. In fact,what I am doing now is to model a protein which has a hign homology with another protein of which the structure has been known.The template is thermophilic and has a disulfide bond.The target has two cys amino acids in the same places where the template form the disulfide bond.However,after the target model has been established,the Chimera software indicate that no disulfide bond exists.The target protein has no ability of thermostability.So I want to use the MODELLER software to explore the differences between them and find out what factors influence the target protein and make it can't be thermophilic.The disulfide bond is the first element I take into account. How do I solve the problems above? I am very appreciate your advises. Yours sincerely, Rao Ben __________________________________________________ 赶快注册雅虎超大容量免费邮箱? http://cn.mail.yahoo.com

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homodimer modelling
by drugdesign 31 Dec '06

31 Dec '06

modeller_usage(a)salilab.org Dear Modeller users, I need to model a homodimer from a homodimer templare. How my alignment file must look like? I mean I have problems with aminoacids numbers and chain names. How to solve this problems? I've attached all input files. Do I need to rename and renumber sequence or I can complete the task without it? Respectively yours, Andrew MODELLER 8v1, Jun 20, 2005 11:37am PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2005 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux Home 2.6.8-24-default i686 Date and time of compilation : 06/20/2005 12:25:12 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2006/11/18 01:06:28.018 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['mfzd', 'fzd1'], atom_files=[], file='fzd1.pir', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open fzd1.pir Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124923 2075.120 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2126623 2076.780 2.028 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2130023 2080.101 2.031 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2136823 2086.741 2.038 openf5__224_> Open 13 OLD SEQUENTIAL mfzd.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 mfzd.pdb

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Re: [modeller_usage] modeller_usage Digest, Vol 4, Issue 109
by S.Sundar Raman 22 Dec '06

22 Dec '06

dear modeller creater friends i am regular user of modeller8v1. i am also member of the modeller usage group. resenctly my system get crashed. so i installed modeller again. i forgot the password for the modeller8v1. pls kindly send me the password to me thank u

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Question about DOPE
by Wei Chen 15 Dec '06

15 Dec '06

Hello, Everyone, I read something about DOPE. I understand it is a statistical potential. I followed tutorials to calculate the DOPE profile. Someone said that DOPE profile is calculted by Potential Energy / Restriction. In the tutorial, it seems that DOPE profile should be above -0.03. My question is why it shoud be above -0.03. Why is the potential energy positive if it is above -0.03? Thanks for your help! Wei Chen

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wrong column range?
by Attila Gulyas-Kovacs 05 Dec '06

05 Dec '06

Hi there, I am using the model.write_data function with output='PSA' to calculate the atomic solvent accessibility. The 'output.sol' pdb file has two new columns on the right. I figured out that the rightmost column must be the atomic solvent accessibility values. But what is the meaning of the one to the left (the second rightmost column)? Second question: these two new columns seem 'right shifted' as compared to the Occupancy value (should have column range 55-60) and B-value (expected between 61-66). This shift messes up with other applications that use these arrays. Am I wrong about this shift? If now, can the model.write_data function easily be corrected? thanks Attila

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Re: [modeller_usage] HowTo Fix Position of Atoms?
by SaTa 05 Dec '06

05 Dec '06

Dear Mr. Webb, thank you very much for your quick and accurate answer. >You seem to be confused between atom selections and restraints. Actually, I was thinking of fixing the position of atoms in space. To me, this means adding constraints. Since I learned, that Modeller features no constraints, my next idea was to add a upper-bond harmonic potential, i.e. restraints to the r(1),r(2),r(3)-components in space. Studying this mailinglist, I found out that in Modeller, deselection would be the appropiate way. > I don't know where you got that link from; My apologize, I thought this was an official mirror, sorry for that. > I can't give you an example that does "exactly what has been requested" because you didn't give the exact problem. Anyway, your example tackled "exactly what has been requested" ;-) I was just confused by the first redefinition of the member actually *initializing* the selection_status parameter. However, I got it, now: The status is initializes *before* selecting the residues selected in selection_segment ;-) *That* was my confusion... Sincerly yours

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HowTo Fix Position of Atoms?
by SaTa 04 Dec '06

04 Dec '06

Dear all, having spend a couple of hours in reading the FAQ (e.g. http://salilab.org/modeller/FAQ.html#5 ), the manual (e.g.http://www.msg.ucsf.edu/local/programs/modeller/node29.html) this Mailinglist (e.g. http://salilab.org/archives/modeller_usage/2005/msg00143.html http://salilab.org/archives/modeller_usage/2003/msg00265.html ...) it is still a complete mystery to my how to fix the position of atoms when annealing. It was suggested to simply DESELECT the atoms I do not want to move at all (http://salilab.org/archives/modeller_usage/2005/msg00155.html) but the link to the manual given did not made clear HOW TO deselect atoms. However, I made my way to http://www.msg.ucsf.edu/local/programs/modeller/node29.html (Refining only part of the model). Still, this did not help. I simply do not understand how to realize this: Do Not Move The Position Of The Atoms Of Residue 75 to 80 in All Chains! >From the mailing-list I deduced, that quite a number of other people have been messing with the same question , and that referring to the manual or the F.A.Q doesn't really help. Instead, an example that does exactly what has been requested would be a pleasure! Thank you very much in advance

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(no subject)
by SaTa 04 Dec '06

04 Dec '06

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Please remove me from the mailing list, Thank you!
by Omid Khalouei 30 Nov '06

30 Nov '06

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structure not read in
by Nicolas Fusseder 30 Nov '06

30 Nov '06

Hello, I have an application which models protein sequences based on template structures which are found by blasting the query sequence against all sequences from pdbaa. The entire modeling process works fine, only when one of the templates structures found via blast was solved with Cryo-EM the modelling process fails with the following error (sorry for the nasty formatting): C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks>mod8v2 C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks.py C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks 'import site' failed; use -v for traceback Traceback (most recent call last): File "C:\bea\user_projects\domains\mydomain\applications\tools\temp\FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks\model_FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks. py", line 8, in ? a.make() File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 331, in homcsr aln.check() File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 153, in check io=io.modpt, libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 37, in check_alignment return _modeller.check_alignment(aln, io, libs, *args) _modeller.error: check_a_337E> Structure not read in (please consult the log file for more details): 1 1D3E1 ExitValue: 0 Status(3): Loading file... Status(1): Load failed! alignment file looks like this: C; Produced by MODELLER >P1;1D3E1 structureE:1D3E:1 :1:285 :1:MOL_ID 1; MOLECULE INTERCELLULAR ADHESION MOLECULE-1; CHAIN I; FRAGMENT:MOL_ID 1; FRAGMENT 1 - 185; ORGANISM_SCIENTIFIC HOMO SAPIENS; ORGANISM_CO:28.00:-1.00 APVAAYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQTLDEMSVESFLGRSG CIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDSEITMVPSVAAKDGHIGHIVMQYMYVPPGAP IPTTRDDYAWQSGTNASVFWQHGQPFPRFSLPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSE QLHKVKVVTRIYHKAKHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV* >P1;FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks sequence:FtrMBC2L1CdcGjpJ81FsjT0qXGb4yTRYks:1 : :113 : :::-1.00:-1.00 ----VGHD------------SGGFSTTVSTGQSVPDPQVGITTM---KDLKANR-----GKMDVSGVQAPVG--- ----AITTIED---------------------------------------PVLAKK------------------- VPET---------------------FPELK-----------------PGE---SRH----------------TSD HM-------SIYKFMGRSHFLC---------TFTFNSNNK---EKEYTFPI---TL----* I also noticed that unlike sucessful modelling attemps, when I attempt to model with 1D3E (Cryo-EM structure) as a template structure the .RSR as well as a .D00000001 file are never created. All help would be greatly appreciated, Sincerely, -- Nicolas Fusseder

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