September 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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Restraining a disulphide bridge
by Marc BAADEN 11 Sep '01

11 Sep '01

Dear Professor Sali, although I tried to thoroughly read through your documentation, and found several references (and examples) to patching disulphide bridges, I could not get it to work for my particular case. I tried to use Modeller v6a (but we also have Modeller4 in the lab, if that would make any difference). My case might be a bit special: I have got an Xray structure, with missing sidechains+residues. One Cysteine is present, the second missing, There are only 2 in the structure, and there has to be a disulphide bridge between them. I only need a homology model where missing residues and sidechains are completed. So my usual modeller script looks like this: INCLUDE SET ALNFILE = '1fep.ali' SET KNOWNS = '1fep_xr' SET SEQUENCE = '1fep_ok' SET ATOM_FILES_DIRECTORY = '.' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET DEVIATION = 2.0 SET RAND_SEED = -12312 CALL ROUTINE = 'model' Using xray coordinates from 1fep_xr.atm. Now I wanted to add something like PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '487' '494' which leads to an error of Run READ_TOPOLOGY and GENERATE_TOPOLOGY first. Now I wonder, is this the right way to add my disulphide restraint ? If yes, then what kind of topology should I use and how ? Do I need to build an initial complete model first, and my 10 models afterwards ? Thank you very much in advance, Best wishes, Marc Baaden -- Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University mailto:baaden@smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de FAX/Voice +49 40333 968508 - Tel: +44 1865 275380 or +33 609 843217

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ref f2c
by Delmiro Fernandez-Reyes 07 Sep '01

07 Sep '01

Hi I am running under linux suse kernel 2.4.x What I did was just install the rpm from suse for the package f2c which contains that libray object. Check the Debian distribution on this package Check on your system under the path where mod binaries are ldd -d mod_xxx Anyway even after a suscesfull linking of that objects to produce the binary for modeller I have an error that I reported to Dr Sali and I am awaiting for his reply Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

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Linux Debian/libf2c
by Decha Enkvetchakul 06 Sep '01

06 Sep '01

I installed Modeller for Debian Linux, but when I try to run the program, it gives the following error: "libf2c.so.0: cannot open shared object file: No such file or directory" I found a file with the above name on the internet, but putting the file on my computer does not work. I still get the same error, even if the file is in the PATH. Any suggestions? Thanks. Decha Enkvetchakul

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DOUBLE
by Delmiro Fernandez-Reyes 05 Sep '01

05 Sep '01

Hi It is possible to get code or the exec for mod_i486-linux-MAXSEQ=10_MAXRES=1000_DOUBLE instead of the SINGLE mod_i486-linux-MAXSEQ=10_MAXRES=1000.Z Also I am cofused because it is a web page of a release5 but the link to the software is the one of number 4? Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

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problem with share libraries under linux 2.4.x
by Delmiro Fernandez-Reyes 04 Sep '01

04 Sep '01

Hi I just installed Modeller4 under linux kernel 2.4.x the only problem I have is executing > soft/modeller4/bin/mod4 model-default /soft/modeller4/bin/mod_i386-linux: error while loading shared libraries: /soft/modeller4/bin/mod_i386-linux: undefined symbol: acos check libs and it seems I have the right set of linked libs ldd -d mod_i386-linux /lib/libNoVersion.so.1 => /lib/libNoVersion.so.1 (0x40017000) libf2c.so.0 => /usr/lib/libf2c.so.0 (0x40034000) libc.so.6 => /lib/libc.so.6 (0x4004b000) /lib/ld-linux.so.2 => /lib/ld-linux.so.2 (0x40000000) Any ideas on this Delmiro -- Dr. Delmiro Fernandez-Reyes National Institute for Medical Research Division of Mathematical Biology The Ridgeway, Mill Hill, London NW7 1AA Tel: +44 020 89593666 ext. 2632 Tel: +44 020 89138711 Direct Fax: +44 020 89138545 http://mathbio.nimr.mrc.ac.uk/

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