Your problem is that your PDB file has more then one chain. > rdpir___648E> Alignment sequence not found in PDB file: 1 1fxy means that you haven't specified which chain you want to read. Even your .ali files says: '> structureX:1fxy: :A : : : : : :', so I guess you are after A chain.
After you fix this, the same problem will appear for the next sequence in ali file (1npm), so be careful. Please refer to the manual for details.
Good luck, Bozidar
On Wednesday May 22 2002 04:16 am, Rajesh Reddy wrote: > Hi Bozidar > > I had posted this message on modeller usage list, but didn't got any help. > Please help me to overcome this problem. I have problem in modeller(6v1). > The error is "Alignment sequence not found in PDB file:". The file names > are correct and I have downloaded the PDB files from PDB and looks nothing > wrong with the PDB files . I am encountering this problem for most of the > jobs. I am enclosing the alignment, top files and error message in log > file. I also like to know how to specify the chain ID when working with > reference protein with more than one chain. > > > > Alignment File > > >P1;p00760 > > sequence:p00760: : : : : : : : > KIVGGYTCGANTVPYQVSLNS--GYHFCGGSLINSQWVVSAAHCYKSG--IQVRLGEDNI > NVVEGNEQFISASKSIVHPSYNS---NTLNNDIMLIKLKSAASLNSRVASISLPTSCASA > GTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDS > CQGDSGGPVVCSGKLQGIVSWGSG-CAQKNKPGVYTKVCNYVSWIKQTIASN- > * > > >P1;1fxy > > structureX:1fxy: :A : : : : : : > -IVGGYNCKDGEVPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNT > EQEEGGEAVHEVEVVIKHNRFTK---ETYDFDIAVLRLKTPITFRMNVAPASLPTAPPAT > GTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDS > CQGDSGGPVVCNGQLQGVVSWGDG-CAQKNKPGVYTKVYNYVKWIKNTIAANS > * > > >P1;1npm > > structureX:1npm: :A : : : : : : > -ILEGRECIPHSQPWQAALFQG-ERLICGGVLVGDRWVLTAAHCKKQK--YSVRLGDHSL > QSRDQPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKV > GQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNG-ADT > CQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD--- > * > TOP file > INCLUDE > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = 'p00760.ali' > SET KNOWNS = '1fxy' '1npm' > SET SEQUENCE = 'p00760' > SET ATOM_FILES_DIRECTORY = '/home/rajesh/alcproj' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 1 > CALL ROUTINE = 'model' > Error message > Dynamically allocated memory at amaxseq [B,kB,MB]: 2210071 2158.272 2.108 > openf5__224_> Open 11 OLD SEQUENTIAL p00760.ali > openf5__224_> Open 13 OLD SEQUENTIAL 1fxy > openf5__224_> Open 13 OLD SEQUENTIAL 1npm > Dynamically allocated memory at amaxbnd [B,kB,MB]: 5790067 5654.362 5.522 > openf5__224_> Open 11 OLD SEQUENTIAL p00760.ali > openf5__224_> Open 13 OLD SEQUENTIAL 1fxy > rdpir___648E> Alignment sequence not found in PDB file: 1 1fxy > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > can someone help > > Thanks > > Rajesh R > Research Assistant > Univerisity of Agricultural Sciences > BANGALORE - INDIA > > > > Send and receive Hotmail on your mobile device: Click Here
Dear modeller users,
I am having a doubt and i want to get idea from your people. The problem is:
We have a protein which has a domain called DED domain and this domain interacts with other proteins that has DED domain by means of hydrophobic interactions.
we have a organic molecule (a polyphenolic compound) and i want to know the hydrophobic interactions of this organic compound with the protein that has DED domain (mainly with the DED domain of the protein).
Kindly can anydoby suggest me how i can proceed to address this problem. Expecting for your reply.
R.Senthil Kumar, Junior Research Fellow(JRF), c/o Dr.Akash Ranjan, Computational & Functional Genomics Group, Centre For DNA Fingerprinting & Diagnostics (CDFD), Hyderabad-500 076.
Ph:040-7151344-Extn(Lab:1304) (Hostel:2300) E-mail:firstname.lastname@example.org