- modeller_usage - salilab.org

Re:
by Bozidar Yerkovich 29 May '02

29 May '02

Hi, 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

2 1

model evaluation
by Giselle Knudsen 24 May '02

24 May '02

Dear Modeller users, I have generated some models using Modeller, and I wonder if you could recommend the best way to evaluate them. My sequence homology between modeled protein and the templates is about 30%, so the confidence in some regions of the sequence alignments is low. I have generated several plots for energy versus residue number using ProsaII, and these show quite nicely which regions have poorer structure. These correlate to regions of low sequence conservation in the alignments. My question to you is how valid the more specific analyses of atomic-level contacts in the models would be. I have run Procheck and Whatif analyses as well, and the quality check scores are within acceptable ranges. In cases with 30% homology I would expect many errors in atom placements, so should I even consider these stereochemical and packing constraints? Can you recommend a good reference that discusses these issues? Thanks very much for your help. Sincerely, Giselle Knudsen graduate student, CCB Program University of California San Francisco knudsen(a)cgl.ucsf.edu

4 4

SYMMETRY
by Valeria Costa 21 May '02

21 May '02

Hi, I have problems to obtain symmetric models. Initially I do an asymmetric model, then, starting form this model, I run a second job which includes the symmetry. Even if the asymmetric model is good, the symmetric models are really bad, all atoms lengths are wrong. I would like to know if someone had the same problem and what is the way to obtain good symmetric models. Thanks for help, Valeria Costa

1 0

Alignment sequence not found in PDB file
by Rajesh Reddy 20 May '02

20 May '02

1 0

Better Prosa Z-scores for models than template
by Mensur Dlakic 17 May '02

17 May '02

Hi, I have observed an interesting thing with some recently produced models. When I evaluate them using Prosa, they all have excellent Z-scores (-5.5 to -6 for 81 residue protein). The strange part is that the template, also 81 residues long and solved to 2 A, has a Z-score of -4.28. When compared using Procheck, the template and models are just about indistinguishable in terms of stereochemistry, even though they share only 17% identity (40% similarity). Is it "normal" that all models have better Prosa Z-scores than the template, and what could be the reason for this "improvement"? Thanks for your time, Mensur =========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur(a)umich.edu | ===========================================================================

2 1

Topology and parameter files for sugar residues in glycoproteins
by Bozidar Yerkovich 17 May '02

17 May '02

> > >> >> From: "Andersen, Kim Vilbour (KVA)" <kva(a)maxygen.dk> >> To: <modeller_usage(a)salilab.org> >> Content-Transfer-Encoding: 8bit >> X-MIME-Autoconverted: from quoted-printable to 8bit by >> salilab.org id g4HCeIDD023046 >> >> Hi >> >> I'm trying to model a glycoprotein with Modeller and would like to >> include the glyco-part in the modelling. >> >> I'm fighting with the creation of topology files (and parameter files) >> creating the topology of the different involved sugar residues as well >> as patch residues to create the relevant bonds. >> >> Has anybody out there done this already and are willing to share? >> >> I'm mainly interested in N-acetylglucosamine, N-acetylgalactosamine, >> Mannose, Galactose and Sialic acid as well as the relevant patchings. >> >> Any input will be appreciated, >> >> thanks >> >> Kim >> >> ------------------------------------------------------------------------ >> Kim Vilbour Andersen, PhD >> Principal Scientist >> Maxygen >> Agern AllÈ 1 >> DK-2970 H¯rsholm >> Denmark >> ------------------------------------------------------------------------ >> >

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Topology and parameter files for sugar residues in glycoproteins
by Andersen, Kim Vilbour (KVA) 17 May '02

17 May '02

Hi I'm trying to model a glycoprotein with Modeller and would like to include the glyco-part in the modelling. I'm fighting with the creation of topology files (and parameter files) creating the topology of the different involved sugar residues as well as patch residues to create the relevant bonds. Has anybody out there done this already and are willing to share? I'm mainly interested in N-acetylglucosamine, N-acetylgalactosamine, Mannose, Galactose and Sialic acid as well as the relevant patchings. Any input will be appreciated, thanks Kim ------------------------------------------------------------------------ Kim Vilbour Andersen, PhD Principal Scientist Maxygen Agern Allé 1 DK-2970 Hørsholm Denmark ------------------------------------------------------------------------

1 0

None
by Mensur Dlakic 15 May '02

15 May '02

Hello, There is a bug in iris4d v6.2 when fitting models to the original structure using SET FINAL_MALIGN3D = 1. To be more precise, original models are reoriented properly, but loop-optimized models are not. It looks something like this: HETATM 323 PCA 6.BL0 58.234 76.175 42.150 1.00110.73 1SG 324 HETATM 324 PCA 6.BL0 58.860 77.458 42.113 1.00110.73 1SG 325 HETATM 325 PCA 6.BL0 59.060 78.039 43.525 1.00110.73 1SG 326 HETATM 326 PCA 6.BL0 57.719 78.207 44.162 1.00110.73 1SG 327 HETATM 327 PCA 6.BL0 57.087 77.136 44.752 1.00110.73 1SG 328 HETATM 328 PCA 6.BL0 57.092 79.431 44.186 1.00110.73 1SG 329 HETATM 329 PCA 6.BL0 55.854 77.282 45.346 1.00110.73 1SG 330 HETATM 330 PCA 6.BL0 55.861 79.586 44.775 1.00110.73 1SG 331 HETATM 331 PCA 6.BL0 55.238 78.509 45.357 1.00110.73 1SG 332 HETATM 332 PCA 6.BL0 60.210 77.157 41.537 1.00110.73 1SG 333 HETATM 333 PCA 6.BL0 60.927 76.297 42.048 1.00110.73 1SG 334 while the original file before MALIGN looks like this: ATOM 323 N PHE 42 58.234 76.175 42.150 1.00110.73 1SG 324 ATOM 324 CA PHE 42 58.860 77.458 42.113 1.00110.73 1SG 325 ATOM 325 CB PHE 42 59.060 78.039 43.525 1.00110.73 1SG 326 ATOM 326 CG PHE 42 57.719 78.207 44.162 1.00110.73 1SG 327 ATOM 327 CD1 PHE 42 57.087 77.136 44.752 1.00110.73 1SG 328 ATOM 328 CD2 PHE 42 57.092 79.431 44.186 1.00110.73 1SG 329 ATOM 329 CE1 PHE 42 55.854 77.282 45.346 1.00110.73 1SG 330 ATOM 330 CE2 PHE 42 55.861 79.586 44.775 1.00110.73 1SG 331 ATOM 331 CZ PHE 42 55.238 78.509 45.357 1.00110.73 1SG 332 ATOM 332 C PHE 42 60.210 77.157 41.537 1.00110.73 1SG 333 ATOM 333 O PHE 42 60.927 76.297 42.048 1.00110.73 1SG 334 If this is not informative enough, I can send whole files as attachments and also my .TOP scripts, though nothing seems to be wrong with them and everything else got executed fine. Mensur =========================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Department of Biological Chemistry | Fax: (734) 615-3397 | | University of Michigan Medical School | http://www.umich.edu/~mensur/ | | 5416 Medical Science I | http://myprofile.cos.com/mensur | | Ann Arbor, MI 48109-0606 | E-mail: mensur(a)umich.edu | ===========================================================================

1 0

modeller4
by sasson iris 13 May '02

13 May '02

Hi I want to use modeller to expand CA models to full atom model. When i give modeller an alignment of the query with a sequence from a pdbfile it changes the position of the CAs, that is , my original model changes. Can i give modeller a parameter that sets restrictions regarding where the atoms around the backbone are positioned ? Can i set this restraint to some interval ? Thanks alot !!!! Iris. I

1 0

Re: Modeller 4
by Dinesh Soares 13 May '02

13 May '02

1 0