I'm trying to get the format right for a multiple alignment I did with a Clustal W server to use as input to modeller. I don't understand the error message; it probably means I don't understand the numbering convention. My sequence has 290 residues & ends up with 316 characters due to alignment gaps. I get exactly the same error message whether I use 290 or 316 as the end residue. Below are various bits of information that might be helpful in debugging what I'm doing.
Thanks for your help!
Irene Newhouse
***The input python script:
[newhoir@localhost rubber]$ cat mod-rubber1.py
# Homology modeling with multiple templates
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
log.verbose() # request verbose output
env = environ() # create a new MODELLER environment to build this model in
# directories for input atom files
env.io.atom_files_directory = ['.', '/home/newhoir/rubber/atom_files']
a = automodel(env,
alnfile = 'multi.ali', # alignment filename
knowns = ('2d2r', '1ueh', '2vg3', '1f75', '2vg0'), # codes of the templates
sequence = '2cpt') # code of the target
a.starting_model= 1 # index of the first model
a.ending_model = 5 # index of the last model
# (determines how many models to calculate)
a.make() # do the actual homology modeling
***The run command:
mod9v8 mod-rubber1.py
***atom_files:
ls -l /home/newhoir/rubber/atom_files
total 2640
-rw-rw-r-- 1 newhoir newhoir 324891 Nov 16 11:17 1f75.pdb
-rw-rw-r-- 1 newhoir newhoir 405810 Nov 16 11:18 1ueh.pdb
-rw-rw-r-- 1 newhoir newhoir 372276 Nov 16 11:19 2d2r.pdb
-rw-rw-r-- 1 newhoir newhoir 707778 Nov 16 11:18 2vg0.pdb
-rw-rw-r-- 1 newhoir newhoir 862326 Nov 16 11:18 2vg3.pdb
*** input file multi.ali
>P1;2d2r
structureX:2d2r:A:3:A:227:UPP :Helicobacter pylori: :
---------------------------------------MLSATQPLSEKLDST-LKHLAIIMDGNGRWAKLKNK
-ARAYGHKKGVKTLKDITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKMLKKYLK---DERSTYLDNNIRFR
AIGDLEGFSKELRDTILQLENDTRHFKDFTQVLALNYGSKNELSRAFKSLLESPPS-NISLLE------------
---------SLENEISNRLDTRNLPEVDLLLRTGGEMRLSNFLLWQSSYAELFFTPILWPDFTPKDLENIISDFY
KRVRKFGELKA-----*
>P1;1ueh
structureX:1ueh:A:13:A:240 :UPP :Erischeria coli : :
--------------------------------------MMLSATQPLSEKLPAHGCRHVAIIMDGNGRWAKKQGK
-IRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALD---SEVKSLHRHNVRLR
IIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQ------------
---------IDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFA
NRERRFGGTEPGDETA*
>P1;2vg3
structureX:2vg3:A:13:A:296:rv2361c decaprenyl PP:M. tuberculosis: :
FPQLPPAPDDYPTFPDTSTWPVVFPELPAAPYGGPCRPPQHTSKAAAPRIPADRLPNHVAIVMDGNGRWATQRGL
-ARTEGHKMGEAVVIDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFNRDVVR---RRRDTLKKLGVRIR
WVGSRPRLWRSVINELAVAEEMTKSNDVITINYCVNYGGRTEITEATREIAREVAAGRLNPER------------
---------ITESTIARHLQRPDIPDVDLFLRTSGEQRSSNFMLWQAAYAEYIFQDKLWPDYDRRDLWAACEEYA
SRTRRFGSA-------*
>P1;1f75
structureX:1f75:A:14:A:242:UPP :Micrococcus luteus: :
-----------------------------------MFPIKKRKAIKNNNINAAQIPKHIAIIMDGNGRWAKQKKM
-PRIKGHYEGMQTVRKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLN---TFLPELIEKNVKVE
TIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDE------------
---------ISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQ
---------------*
>P1;2vg0
structureX:2vg0:A:30:A:256:Rv 1086 farnesyl PP:M. tuberculosis: :
-----------------------------------------------------DLPRHIAVLCDGNRRWARSAGY
DDVSYGYRMGAAKIAEMLRWCHEAGIELATVYLLSTENLQRDPDELAALIEIITDVVE---EICAPANHWSVRT-
-VGDLGLIGEEPARRLRGAVESTPEVASFHVNVAVGYGGRREIVDAVRALLSKELANGATAEELVDA--------
---------VTVEGISENLYTSGQPDPDLVIRTSGEQRLSGFLLWQSAYSEMWFTEAHWPAFRHVDFLRALRDYS
AR--------------*
>P1;2cpt
sequence:2cpt::1: :316:rubber c-prenylxferase:Hevea brasiliensis: :
-----------------------MELYTGERPSVFRLLGKYMRKGLYGILTQGPIPTHLAFILDGNRRFAKKHKL
-PEGGGHKAGFLALLNVLTYCYELGVKYATIYAFSIDNFRRKPHEVQYVMDLMLEKIEGMIMEESIINAYDICVR
FVGNLKLLSEPVKTAADKIMRATANNSKCVLLIAVCYTSTDEIVHAVEESSELNSNEVCNNQELEEANATGSSTV
IQTENMESYSGIKLVDLEKNTYINPYPDVLIRTSGETRLSNYLLWQTTNCILYSPHALWPEIGLRHVVWAVINCQ
RHYSYLEKHKEYLK--*
***The runtime messages:
[newhoir@localhost rubber]$ ./r
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "mod-rubber1.py", line 18, in ?
a.make() # do the actual homology modeling
File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line 98,
in make
self.homcsr(exit_stage)
File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line
424, in homcsr
self.check_alignment(aln)
File "/usr/lib/modeller9v8/modlib/modeller/automodel/automodel.py", line
406, in check_alignment
aln.check()
File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 200, in check
self.check_structure_structure(io=io)
File "/usr/lib/modeller9v8/modlib/modeller/alignment.py", line 209, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.ModellerError: rdpdb___303E> No atoms were read from the specified
input PDB file, since the starting residue number and/or chain id in
MODEL_SEGMENT (or the alignment file header) was not found; requested starting
position: residue number " A", chain " 3"; atom file name:
/home/newhoir/rubber/atom_files/2d2r.pdb
[newhoir@localhost rubber]$
***The file 2d2r.pdb is exactly as I downloaded it from RCSB
**The first lines of the header:
HEADER TRANSFERASE 16-SEP-05 2D2R
TITLE CRYSTAL STRUCTURE OF HELICOBACTER PYLORI UNDECAPRENYL PYROPHOSPHATE
TITLE 2 SYNTHASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UNDECAPRENYL PYROPHOSPHATE SYNTHASE;
COMPND 3 CHAIN: A, B;
**The opening ATOM records:
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.020149 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016974 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006518 0.00000
ATOM 1 N SER A 3 -4.458 53.857 94.802 1.00 59.58 N
ATOM 2 CA SER A 3 -4.745 52.989 93.628 1.00 59.67 C
ATOM 3 C SER A 3 -3.414 52.652 92.952 1.00 59.42 C
ATOM 4 O SER A 3 -2.843 51.569 93.142 1.00 59.53 O