March 2002 - modeller_usage

How to start
by Jianchao YAO 30 Mar '02

30 Mar '02

Hi, I am a newer for Modeller. After successfully installing Modeller, I wonder how to start modelling. The questions are as follows: 1: Where can I get that alignment files? Need I convert the sequences in FASTA format into PIR format by hands? 2: Where to write those commands? I mean, in other languages, there are developing environments for programmers to write their own commands,however, I don't know how to do it in Modeller. Many thanks Evan

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Inquiry - Modeller (How to begin a program?)
by gt4578a＠prism.gatech.edu 29 Mar '02

29 Mar '02

How are you, sir? My name is Jinseong Cheong, a graduate student at Georgia Tech majoring in Bioinformatics. I think I successfully installed your "MODELLER" on the computer. But when I tried to begin the program by typing 'mod model-default', I got this error message again and again. ****** FORTRAN RUN-TIME SYSTEM ****** Error 1130: zero length file name Location: the OPEN statement at line 372 of "top_mod.F90" Unit: 11 Abort Could you please tell me what the problem is? Thank you. Truly, Jinseong p.s. If possible, could you tell me the beginning procedure in more detail? I'm a kinda novice in this area. Thank you. ------------------------------------------------- Sent through Cyberbuzz- A Server for the Students http://cyberbuzz.gatech.edu/

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(OTCBB: PLRP) Continues to Set Record Volumes
by elco＠8848.net 27 Mar '02

27 Mar '02

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failed to allocate maxcell
by Mateusz Nowak 27 Mar '02

27 Mar '02

Dear All. While running modeller (not standalone, but being a part of InsightII) i get following error after every 4 models produced: pair2____E> failed to allocate maxcell: 136960 I resterted modeller few times with different random number generator seed, but it didn't help. This Modeller runs on SGI R12000 CPU with huge, 40 GB RAM. What does this error message mean? Thanks in advance. Mateusz Nowak Dept. of Medicinal Chemistry Institute of Pharmacology PAN Krakow, Poland

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SKipping models
by Gordon Wells 22 Mar '02

22 Mar '02

Hi Is there any way to make modeller "skip" to the nth model ( in my case #5). I want to do this in order to perform loop modelling on this model only. Alternatively, could I load a previously generated model and run loop modelling, using an alignment to specify the loop regions.

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GPCR
by Rosalia Pascual 22 Mar '02

22 Mar '02

Dear Modellers. I am trying to model a GPCR and I have a doubt about the transmembrane helices. It is known that they contain Pro residues which produce a kink in the helix, so I am not interesting in modelling the seven helices as an ideal helix . My cuestions are: 1) If I do : MAKE_RESTRAINTS RETRAINT_TYPE ='alpha' Can MODELLER take account for these proline kinks ? (I mean if it has specific backbone dihedarl angles for modelling them or should I introduce them as constraints ?) 2) If not, is it a good option to divide the whole helix in segments, excluding the prolines, and to force them to be an ideal alpha helix? Thanks in advance.

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Re: modeler
by Bozidar Jerkovic 22 Mar '02

22 Mar '02

Hi, /home/mansoor/soft/bin/modeller6v1/bin/ is not in your path. What shell are you using? Type source ~/.cshrc after installation is complete, if you are using csh or tcsh and then try again. Type 'which mod6v1' If all fails tell me in detail how you installed MODELLER, and send me a copy of your .cshrc. In future please post your questions through modeller_usage if you can, so that everybody benefits from them. Thanks, Bozidar On 22/3/02 8:36 AM, "msaqi" <m.saqi(a)qmul.ac.uk> wrote: > Hi > > Thnaks for your email re. superpose etc. > > I have moved modeller to another machine and am having some installation > problems - perhasp you can help? I run RedHat linux 7. > > After installation, typing which mod6v1 gives > ~/soft/bin/modeller6v1/bin/mod6v1. OK so far! > but when I try to run a script I get a message like: > > /home/mansoor/soft/bin/modeller6v1/bin/mod6v1: mod6v1_: command not found > > If I do the command "/home/mansoor/soft/bin/modeller6v1/bin/mod6v1" on its > own then I get > "usage: mod script[.top]" > which seems to suggest that it *can* find the executable. > > But why does it not like the run_tops1 example script? > > Any ideas what is wrong? > > best wishes > Mansoor

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Re: RE: pdb format
by Eric Feyfant 20 Mar '02

20 Mar '02

Hi Bozidar; I corrected Stephane error. It was a chain identifier problem. The chain was specified in the pdb but not in the top file, and Modeler could not extrapolate. Eric -------------------------------------------------------- Eric Feyfant, Ph.D. Department of Biological Chemistry WYETH Research 85 bolton St. Cambridge ,MA 02140 tel: (617) 665 8987 fax:(617) 665 8993 email: efeyfant(a)wyeth.com >>> "Bozidar Jerkovic" <bozidar(a)oboe.rockefeller.edu> 03/20 11:51 AM >>> Hi, The .top file looks OK, but I would still add: SET ALIGNMENT_FORMAT = 'PIR' What looks strange is the call: openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm ...after: TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND ...while it should be doing: check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: One more thing: if it fails again, move your .atm files to a directory other then one where is your .top file (keep your .ali in the same dir as your .top file). You can create atom_files dir paraller to the dir where is your .top file. Make sure you replace your ATOM_FILES_DIRECTORY then with: SET ATOM_FILES_DIRECTORY = './:../atom_files' If all this fails, then please send me a complete .log file, .top file, all atom and .ali files and I'll run it here, and see what happens. Thanks, Bozidar -----Original Message----- From: Stephane Coillet-Matillon [mailto:coillet@bri.nrc.ca] Sent: Wednesday, March 20, 2002 8:11 AM To: Bozidar Cc: modeller_usage(a)salilab.org Subject: RE: pdb format Hi Bozidar, Here's what my top file looks like. # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE #Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 #uncomment to produce a large log file SET ALNFILE = 'hpabc.ali' #alignment filename SET KNOWNS = '1G9L' # codes of the templates SET SEQUENCE = 'wPABC' # code of the target SET ATOM_FILES_DIRECTORY = '.' #directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling > -----Original Message----- > From: owner-modeller_usage(a)salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of > Stephane Coillet-Matillon > Sent: Tuesday, March 19, 2002 5:32 PM > To: modeller_usage(a)salilab.org > Subject: pdb format > > > > Hello Modellers, > > I've been trying to run my first modelling, but cannot get any model > so far. Instead, the log file tells me: > > Read the alignment from file : hpabc.ali > Total number of alignment positions: 144 > # Code #_Res #_Segm PDB_code Name > ---------------------------------------------------------------------- > -- > ------- > 1 1G9L 144 1 1G9L PABC > 2 wPABC 72 1 wPABC PABC > > TOP_________> 121 107 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm > rdpdb___303E> No atoms were read from the specified input PDB file: > 1) Possibly because an incorrect/non-existent PDB file > is specified. > 2) Possibly because the segment is specified > incorrectly in the alignment file or by the TOP variable > MODEL_SEGMENT. That is, the beginning residue number and/or chain id > in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT:1 : > To find out more, switch on maximal output by 'SET > OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 144 0 > For alignment entry: 1 recover > ____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > My alignment file is: > > >P1;1G9L > structureN:1G9L:1 : :144 : :PABC:homo sapiens: : > GPLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VLQAHQAKEAAQKAVNSATGVPTV* > >P1;wPABC > sequence:wPABC:1 : :144 : :PABC:wheat: : > --------------------------------------------------EPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VL----------------------* > > Which I trust is the right way to do it. > The top file has nothing that deviates from the example file. My pdb > file was just renamed from 1G9L.pdb to 1G9L.atm, its content was not > edited or changed, and it was located in the right directory. > > So what am I missing there? > > Any suggestion welcomed! > > Thanks, > Stephane >

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pdb format
by Stephane Coillet-Matillon 20 Mar '02

20 Mar '02

Hello Modellers, I've been trying to run my first modelling, but cannot get any model so far. Instead, the log file tells me: Read the alignment from file : hpabc.ali Total number of alignment positions: 144 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1G9L 144 1 1G9L PABC 2 wPABC 72 1 wPABC PABC TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT:1 : To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 144 0 For alignment entry: 1 recover ____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 My alignment file is: >P1;1G9L structureN:1G9L:1 : :144 : :PABC:homo sapiens: : GPLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA VLQAHQAKEAAQKAVNSATGVPTV* >P1;wPABC sequence:wPABC:1 : :144 : :PABC:wheat: : --------------------------------------------------EPLTASMLAS APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA VL----------------------* Which I trust is the right way to do it. The top file has nothing that deviates from the example file. My pdb file was just renamed from 1G9L.pdb to 1G9L.atm, its content was not edited or changed, and it was located in the right directory. So what am I missing there? Any suggestion welcomed! Thanks, Stephane

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problem with BLK residues using multiple templates
by Lucy Forrest 19 Mar '02

19 Mar '02

Hi all, I've been testing out using Modeller to build ferredoxins (some of the ones in the examples, actually) containing 4Fe-4S cluster(s). I wanted to try different levels of description, so to start out I've been describing the FeS clusters as BLK residues. This works very well for single-template modeling, but when I try to use e.g. 3 template structures, I get 3 times as many atoms in the model cluster as I wanted. I've attached the top and alignment files but there are 3 input atom files (plus the model), so I'll send those on request (in the input atom files I use, the residue names have been changed to BLK and some of the atomnames have been changed from the original pdb, so that they all describe the same position: using the original pdbs should still give you the same problem of excess atoms, but the clusters will be distorted). Does anyone have a reason for this, or a way out (apart from deleting the 'extra' atoms afterwards)? I'll be building a new FS4 residue anyway; has anyone done that previously? Many thanks in advance, Lucy Forrest # Modeller input script # LRF 14mar02 # Build models of 2fdn using 3 template pdbs simultaneously # and multiple alignment # # This script should produce one model, 2fdn.B99990016 # try HETERO atoms # SYSTEM COMMAND = 'cp 2fdn_3_template_1.ali~ 2fdn_3_template_1.ali' INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = '2fdn_3_template_1.ali'# alignment filename SET KNOWNS = '1DUR' '1BLU' '1CLF' # codes of the templates SET SEQUENCE = '2fdn' # code of the target SET HETATM_IO = 'on' # use Fe/S heteroatoms SET ATOM_FILES_DIRECTORY = '../atom_files.d/' # directories for input pdb SET STARTING_MODEL= 16 # index of the first model SET ENDING_MODEL = 16 # index of the last model SET FINAL_MALIGN3D = '1' # make fitted structures # thorough MD only #SET MD_LEVEL = 'refine_4' # Repeat the whole cycle x times and do not stop unless obj.func. > 1E6 SET REPEAT_OPTIMIZATION = 3, MAX_MOLPDF = 1E6 CALL ROUTINE = 'model' # do homology modelling >P1;1DUR structureX:1DUR:1 :A:102 :A:::-1.00:-1.00 AYVINDSCIACGACKPECPVNCIQEG-SIYAIDADSCIDC------GSCASVCPVGA-----PNPED-------- -----/..* >P1;1BLU structureX:1BLU:1 : :102 : :::-1.00:-1.00 ALMITDECINCDVCEPECPNGAISQGDETYVIEPSLCTECVGHYETSQCVEVCPVDCIIKDPSHEETEDELRAKY ERITG/..* >P1;1CLF structureN:1CLF:1 : :102 : :::-1.00:-1.00 AYKIADSCVSCGACASECPVNAISQGDSIFVIDADTCIDC------GNCANVCPVGAPVQE-------------- -----/..* >P1;2fdn sequence:2fdn:. :.:. : :::-1.00:-1.00 AYVINEACISCGACEPECPVNAISSGDDRYVIDADTCIDC------GACAGVCPVDAPVQA-------------- -----/..*

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