-------- Original Message -------- Subject: Re: [modeller_usage] The models miss the 40 first aa of the sequence Date: Thu, 02 Aug 2007 15:03:17 -0400 From: Dany Naranjo Feliciano dany@censa.edu.cu To: Modeller Caretaker modeller-care@salilab.org References: WorldClient-F200708021350.AA50150418@censa.edu.cu 46B21D98.2020806@salilab.org
When I visualized the models using vmd, I can't see the first 40aa of the sequence. Thanks,
Dany Naranjo Feliciano Lic. Bioquímica Grupo Biología Molecular Centro Nacional de Sanidad Agropecuaria (CENSA) Apartado 10. San José de las Lajas. La Habana. CP 32700. Cuba Teléfono 53-47-863014 ext 28
-----Original Message----- From: Modeller Caretaker modeller-care@salilab.org To: Dany Naranjo Feliciano dany@censa.edu.cu Cc: modeller_usage@salilab.org Date: Thu, 02 Aug 2007 11:08:24 -0700 Subject: Re: [modeller_usage] The models miss the 40 first aa of the sequence
Dany Naranjo Feliciano wrote: > The models miss the 40 first aa of the sequence. > What might be wrong?
What do you mean by "miss the 40 first aa" ?
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
"Participe en Universidad 2008 del 11 al 15 de febrero del 2008. Palacio de Convenciones. La Habana. Cuba. http: //www.universidad2008.cu".
Ben Webb, Modeller Caretaker
> From: Dany Naranjo Feliciano dany@censa.edu.cu > When I visualized the models using vmd, I can't see the first 40aa of > the sequence.
You should first check the generated PDB files with a text editor, to make sure the first 40aa are actually there. If they are, then either VMD is doing something weird (try a different PDB viewer) or the PDB file is corrupt in some way, which should be obvious from a visual inspection.
If they are not there, it's probably because you didn't ask Modeller to build those residues in the first place. Check your alignment.
Ben Webb, Modeller Caretaker
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Modeller Caretaker