Cc: modeller_usage <modeller_usage>, Tina Yeh <>, ,
Organization: Rockefeller University
Dear Pieter!
Initial alignment is porbably bad which is indicated in diagnostics of
CHECK_ALIGNMENT and MALIGN3D.
Please check your alignment manually or use FIT = on in MALIGN3D to
produce correct alignment. If it won't help, then please send me .top,
.pdb, alignment files and other necessary input files in separate
attachments or as a tar.gz archive.
Happy landings,
Azat
Pieter Stouten wrote:
>
> We have a problem building a 2-domain protein based on multiple (8) other
> proteins. We put a slash between the two domains so that Modeller knows not
> to connect the termini. We have no problems with large distances between
> equivalent CA's of different proteins. the only unusual aspect we notice is
> that the pair of warnings (?) "drmsq1__W> n<2 and drmsq3__W> n<2" occurs 19
> times. No error message occurs, but no model is produced either. Please
> find attached part of the output. Hope this is enough for the experts on
> ths list to give us hints as to how to resolve this issue.
>
> Thanks a million,
>
> Pieter Stouten <>
> DuPont Merck - Computer Aided Drug Design Group
> Web: http://www.halcyon.com/stouten/
>
> ----------------------------------------------------------------------------
>
> chkaln___> Checking pairwise structural superpositions:
> Equivalent CA pairs with distance difference larger than 6.0
> angstroms:
>
> ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST
> ----------------------------------------------------
> drmsq1__W> n<2
> drmsq3__W> n<2
>
> [... repeated 19 times ... /PFWS]
>
> chkaln___> Checking structure-sequence alignments:
> Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:
>
> ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST
> ----------------------------------------------
>
> << end of CHECK_ALIGNMENT.
>
> TOP______> 109 94 CALL ROUTINE = BUILD_METHOD
>
> TOP______> 110 66 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS
>
> [...]
>
> TOP______> 111 67 MALIGN3D FIT = OFF, GAP_PENALTIES_3D = 0 4
>
> malign3d_> Initial framework positions: 9
> fit2xyz_E> number of equivalent positions < 3: 0
> recover__> MODELLER_STATUS >= CONTROL: 1 1
--
- Dr. Azat Badretdinov
- The Rockefeller Univ, Box 270
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail:
- WWW/URL: http://salilab.org/~azat