[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[modeller_usage] tutorial on mod7v7

Hi,

I am trying to do the modeller tutorial on a linux machine,
with version mod7v7.

After running seq_search for the TvDLH model the seqsearch.dat
is empty, and I get the .log file as shown below.

Would you know why I can't get any answer from my search?

Thanks, Paula.



Kind, OS, HostName, Kernel, Processor: 4, Linux japiim.cbi.cnptia.embrapa.br 
2.4.20-42.9.legacysmp i
686
Date and time of compilation         : 09/14/2004 11:06:39
Job starting time (YY/MM/DD HH:MM:SS): 2005/04/11  16:50:46.106


Dynamically allocated memory at         amaxseq [B,kB,MB]:        69639      
68.007     0.066
TOP_________>     2    2 SET SEARCH_RANDOMIZATIONS = 100 
 
TOP_________>     3    3 SET MAXRES = 300 
 
TOP_________>     4    4 SET FILE = 'TvLDH.seq' 
 
TOP_________>     5    5 SEQUENCE_SEARCH ALIGN_CODES = 'TvLDH', DATA_FILE = 
ON 
 

Dynamically allocated memory at         amaxseq [B,kB,MB]:       614337     
599.938     0.586

Dynamically allocated memory at         amaxbnd [B,kB,MB]:     32806393   
32037.492    31.287
openf5__224_> Open       11  OLD  SEQUENTIAL  
${MODINSTALL7v7}/modlib//as1.sim.mat
rdrrwgh_268_> Number of residue types:       20
openf5__224_> Open       11  OLD  SEQUENTIAL  TvLDH.seq



Searching a list of chains for similarity with a given sequence:

   Target sequence       : TvLDH.seq
   List of test chains   : ${MODINSTALL7v7}/modlib//CHAINS_3.0_40_XN.cod
   Number of test chains :        0
   Residue-residue metric: ${MODINSTALL7v7}/modlib//as1.sim.mat
   Gap penalties U, V    :  -900.00  -50.00
   Randomizations        :      100
   +/- range for sig2&3  :       10
   SIGNIF_CUTOFF         :     4.00    5.00
   Top chains are listed :       20
   (see the corresponding $MODINSTALL/modlib/seqfilt_*.grp 
    file for more related PDB codes)


RELATED_SEQUENCES

   # CODE_1      CODE_2 LEN1 LEN2 NID   %ID   %ID    SCORE  SIGNI SIGNI2 
SIGNI3
-----------------------------------------------------------------------------
---



openf5__224_> Open       14  UNKNOWN  SEQUENTIAL  seqsearch.dat

Dynamically allocated memory at          finish [B,kB,MB]:     32806393   
32037.492    31.287
Starting time                                            : 2005/04/11  
16:50:46.106
Closing time                                             : 2005/04/11  
16:50:46.882
Total CPU time [seconds]                                 :       0.58







Paula Kuser Falcão
Laboratório de Bioinformática Estrutural
Embrapa Informática Agropecuária


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.