May 2002 - modeller_usage

Which loop energy?
by J Simms 30 May '02

30 May '02

Hi all, I have recently started to model GPCRs, but as with everyone else I am having trouble with the loops. I have followed the tutorials , kindly given, and have resulted with a number of files with different loops starting and ending in different locations. I have investingated the log files for energy terms, as I understand it the loop model with the lowest energy term is a good starting point. My problem which energy term in the log file do I use, as there seems to be a number of energy terms even for the same loop model number. > Many thanks for any help > John >

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re:MODELLER for OsX (Was: MODELLER 6v2 available)
by Prevost Martine 30 May '02

30 May '02

Hi, I would also be very interested in getting am Mac OS X version of Modeller. Best, Martine. > >Hi, > >I guess, eventually. We have come a long way since the last year by >increasing a number of executables from 4 to 7, including IBM and Windows. > >OsX is still fairly new, and it's still not quite certain how scientific >community will react to it. Our resources and time are limited and at this >time only if we find someone who is willing to devote their energy to port >it for OsX we will do it. > >I hope this will not prevent you from using MODELLER. > >All the best, >Bozidar > > >On Thu, 30 May 2002, Stefano Ciurli wrote: > >> Hi >> is there any way to get some day the version of Modeller for Mac OS X? >> Stefano. >> > > -------------------------------------------- Martine Prevost Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50 avenue Franklin Roosevelt B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 3606 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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MODELLER for OsX (Was: MODELLER 6v2 available)
by Bozidar Yerkovich 30 May '02

30 May '02

Hi, I guess, eventually. We have come a long way since the last year by increasing a number of executables from 4 to 7, including IBM and Windows. OsX is still fairly new, and it's still not quite certain how scientific community will react to it. Our resources and time are limited and at this time only if we find someone who is willing to devote their energy to port it for OsX we will do it. I hope this will not prevent you from using MODELLER. All the best, Bozidar On Thu, 30 May 2002, Stefano Ciurli wrote: > Hi > is there any way to get some day the version of Modeller for Mac OS X? > Stefano. >

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MODELLER 6v2 available
by Bozidar Yerkovich 30 May '02

30 May '02

Hi everybody, I just wanted to tell you that we finally have all the executables for MODELLER 6v2 ready (including Windows version, thanks to Jaroslaw Pillardy). You will find them at the usual place on MODELLER web site. Happy modeling, Bozidar

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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

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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

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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

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

20 May '02

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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 | ===========================================================================

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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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