March 2006 - modeller_usage

Re: [modeller_usage] Protein + Metal Ion
by Anshul Awasthi 21 Mar '06

21 Mar '06

Modeller Caretaker wrote: <mailto:modeller_usage@salilab.org> > Anshul Awasthi wrote: > >> I am trying to model the structure of a protein that contains Zn ion >> in the active site, using modeller 7v7. For the modeling purpose I am >> using 5 templates and one of them contains 2 His residues coordinated >> with Zn ion, and these residues are conserved among all the templates >> and the target sequence. > > > > I suggest that you use the latest version, Modeller 8v2, instead. Not > only does it incorporate a number of bug fixes, but it gives more > informative diagnostics for problems like this one. It will read old > TOP scripts just fine, provided they have the .top file extension. > >> I have put /z* at the end of the alignment file as follows: >> >> P1;1WVR >> structureX:1WVR: 9 :A: 181 ::::: >> PRKPEIQNEIIDLHNSLRRSVN------------PTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGG- >> >> ---IKCGENIYMAT-----YPAKWTDIIHAWHGEYKDFKYGVGAVPSD----AVIGHYTQIVWYKSYRAGCAAAY >> >> CPSSKYS------YFYVCQYCPAGNIIGKTATPYKSGPPCGDCP-SD-C-DN--GLCTN/z/* > > > > The final / is unnecessary here, since nothing follows the ion. > >> ================================================================== >> But when I run the modeller i get an error message stating "SEQUENCE >> DIFFERENCE BETWEEN ALIGNMENT AND PDB " >> >> rdabrk__291E> Sequence difference between alignment and pdb : >> >> STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- >> 2 174 30 ZN2 24 UNK GLCTNz > > > > Your PDB file appears to have an UNK residue rather than a Zn atom > here. It's hard to say what your problem might be, as I'm guessing > your PDB is modified from code 1wvr (since the A chain continues to > residue 221, and the ion is cadmium, not zinc). > > If your problem continues, send me your full input files, and I'll > take a look. > > Ben Webb, Modeller Caretaker Dear Ben, I was able to run the programme and got a model with Zn ion. But I was only able to do it without adding the restraints to the His residues and the Zn ion. But when I put the following subroutine at the end of my .top file, I get an error. SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:420' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:892' 'ZN2:1436' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 RETURN END_SUBROUTINE Following is the last portion of the log file with the error; TOP_________> 231 199 MAKE_RESTRAINTS make_re_417_> Restraint type to be calculated: distance make_re_422_> Number of previous, current restraints : 19104 19104 make_re_423_> Number of previous, current selected restraints: 18913 18913 TOP_________> 232 200 DELETE_ALIGNMENT TOP_________> 233 201 RETURN TOP_________> 234 165 CALL ROUTINE = 'special_restraints' TOP_________> 235 810 SET ATOM_IDS 'NE2:420' 'ZN2:1436' TOP_________> 236 811 ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0; .1 add_res_442E> One or more atoms absent from MODEL: NE2:420 ZN2:1436 top_error__E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 The number of the residues I have used correspond to the modeller numbering system (*.ini file). I am not sure about the RESTRAINT_PARAMETERS I have put in the subroutines as I have duplicated it from one of the earlier posts. I tried to know more about them from the manual but could not understand. I shall be glad if you could also explain the meaning of various fields being used in the parameters. With regards, Anshul

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Protein + Metal Ion
by Anshul Awasthi 19 Mar '06

19 Mar '06

Dear Modeller users, I am trying to model the structure of a protein that contains Zn ion in the active site, using modeller 7v7. For the modeling purpose I am using 5 templates and one of them contains 2 His residues coordinated with Zn ion, and these residues are conserved among all the templates and the target sequence. I have included these lines in my top file SET HETATM_IO = on SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:493' 'ZN:1422' SET ATOM_IDS 'NE2:921' 'ZN:1422' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 RETURN END_SUBROUTINE ================================================================== I have put /z* at the end of the alignment file as follows: P1;1WVR structureX:1WVR: 9 :A: 181 ::::: PRKPEIQNEIIDLHNSLRRSVN------------PTASNMLKMEWYPEAAANAERWAYRCIESHSSRDSRVIGG- ---IKCGENIYMAT-----YPAKWTDIIHAWHGEYKDFKYGVGAVPSD----AVIGHYTQIVWYKSYRAGCAAAY CPSSKYS------YFYVCQYCPAGNIIGKTATPYKSGPPCGDCP-SD-C-DN--GLCTN/z/* ================================================================== But when I run the modeller i get an error message stating "SEQUENCE DIFFERENCE BETWEEN ALIGNMENT AND PDB " Following is the portion of the generated log file: read_al_374_> Non-standard residue type,position,sequence: z 210 2 Read the alignment from file : templates.ali Total number of alignment positions: 210 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1RC9 173 1 1RC9 2 1WVR 174 2 1WVR 3 1XX5 173 1 1XX5 4 1U53 186 1 1U53 5 1QNX 170 1 1QNX 6 GLiPR 181 1 GLiPR TOP_________> 137 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 138 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1RC9.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1WVR.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 174 30 ZN2 24 UNK GLCTNz rdabrk__288W> Protein not accepted: 2 openf5__224_> Open 11 OLD SEQUENTIAL ./1XX5.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1U53.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1QNX.pdb check_a_337E> Structure not read in: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 =================================================================================== Can anyone suggest where things might be going wrong? With regards, Anshul

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build a homopentamer
by Giovanni Grazioso 17 Mar '06

17 Mar '06

Dear Modellers, I'd like to know if mod8v2 is able to build a homopentamer copying only the first chain from the heteropentameric template and then building the remaining 4 chains by axial symmetry. This is important because only one chain is highly conserved while the others are different. Any help will be much appreciated. Thank you Giovanni

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DOPE
by helenaa＠webmail.ibilce.unesp.br 16 Mar '06

16 Mar '06

Does anyone out there know if it is possible to find a description of the DOPE score? I have been searching the manual, the MODELLER web-site and the www... Helen ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/

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ordering of atoms in the PDB
by Robin Stamler 16 Mar '06

16 Mar '06

Hello I'm sure this is answered somewhere but I couldn't find it. The ordering of atoms in a residue in Modeller output as in (a) is different from that usually seen in PDB files (b) This is a problem when using the output in some other servers. Can the Modeller output be changed? Thanks Robin Stamler Dept Molecular Genetics University of Cincinnati (a) ATOM 1 N ALA B 1 10.145 12.378 3.667 1.00 25.81 1SG N+2 ATOM 2 CA ALA B 1 11.592 12.105 3.515 1.00 25.81 1SG C+3 ATOM 3 CB ALA B 1 12.225 11.817 4.886 1.00 25.81 1SG C+4 ATOM 4 C ALA B 1 11.834 10.932 2.631 1.00 25.81 1SG C+5 ATOM 5 O ALA B 1 11.538 10.968 1.437 1.00 25.81 1SG O+6 (b) ATOM 586 N ALA A 86 -33.616 77.292 18.556 1.00 27.93 N ATOM 587 CA ALA A 86 -34.153 76.748 17.311 1.00 27.40 C ATOM 588 C ALA A 86 -33.329 77.134 16.085 1.00 27.32 C ATOM 589 O ALA A 86 -32.386 77.921 16.172 1.00 25.96 O ATOM 590 CB ALA A 86 -35.591 77.205 17.124 1.00 24.83 C

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Perl Script to plot DOPE
by Vimalkumar Velayudhan 16 Mar '06

16 Mar '06

Hello Modeller users, I have written a perl script to plot the energy profiles obtained at the model evaluation step. This script is available at http://salilab.org/modeller/wiki/Plotdope The input for the program is the Alignment of the target and the template and the profile files. The script uses gnuplot to produce the output. Regards, -- Vimalkumar Velayudhan

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Using a Modeller model as input to repeat the process
by Zoe Katsimitsoulia 15 Mar '06

15 Mar '06

Hello all, I am trying to model a protein which has many structures solved in a particular state, and only 1 structure solved in my desired state. I was wondering if it is possible to do the following: 1. Generate a model with Modeller based on the larger number of solved structures (yes, obviously) 2. Run modeller again, this time only with the 1 crystal structure available in my state as a template, but ALSO somehow incorporate my model from step 1 above, without using the model as a second template, because the states are too dissimilar I feel. The reason I do not want to generate a structure solely using the 1 crystal structure is because there is very low sequence identity (just under 30). So, effectively i'm assuming step 1 should give me an accurate enough model of my protein in state A, and i want to use this model plus the only one available structure to get it to state B. Does my theory make sense and is it possible? Any help is much appreciated. Thanks, -Zoe -- Zoe Katsimitsoulia Division of Mathematical Biology National Institute for Medical Research The Ridgeway, Mill Hill, London NW7 1AA zkatsim(a)nimr.mrc.ac.uk +44 (0)20 8816 2507(phone) +44 (0)20 8816 2460 (fax)

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hydrogen atom name
by Zhiqiang Ye 14 Mar '06

14 Mar '06

Dear Sir, I have question about the hydrogen atom name after building the all-atom model. After building the all-atom model, the hydrogen name "HA" means hydrogen bonded to C-alpha, but GLY has two HA, one is 1HA, the other is 2HA. Which one is correponding to the sidechain in other residue types? I checked several GLY in my model, I find always it is 2HA that is corresponding to the side chain of other residue type. Is this the standard criteria, or just modeller's choice? Thank you very much! -- Zhiqiang Ye PHD candidate

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Report of final energy
by 서주현 14 Mar '06

14 Mar '06

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Dope Vs PROSA2003
by jo hanna 14 Mar '06

14 Mar '06

Hi If am trying to model loops within my protein model that seem to correspond to regions of high energy in both DOPE and PROSA analysis. why should it be that aftre modelling the loop with a lower DOPE energy shoud actaully increase in the region of loop modelling with reference to the original model and PROSA analysis? Any advice much appreciated Do people generally prefer DOPE or use PROSA and DOPE to complement each other? Thanks Jo

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