- modeller_usage - salilab.org

Re: Question
by Eric Feyfant 07 Jan '02

07 Jan '02

Yes Paolo there is a way, Just use the variable , STARTING_MODEL, and ENDING_MODEL: Example, SET STARTING_MODEL = 57 SET ENDING_MODEL = 100 SET RAND_SEED = XXXX (your choice for the random seed number). It is important to give a new random see, if not your 54 new models will be the same that the 56 model you already built. Eric Feyfant -------------------------------------------------------- Eric Feyfant, Ph.D. Department of Biological Chemistry WYETH / Genetics Institute 85 bolton St. Cambridge ,MA 02140 tel: (617) 665 8987 fax:(617) 665 8993 email: efeyfant(a)genetics.com >>> Paolo Daniele <daniepao(a)yahoo.it> 01/07 11:49 AM >>> Hi, I have a problem. Using Modeller program to make 100 models of my protein following the loop routine, the program was stopped because of an electric interruption, so I have now just 56 of 100 models! Is there a way to restart the program without loosing the 56 models yet obtained? Thanks in advance for your help. Best regards, Paolo Daniele ______________________________________________________________________ Iscriviti al gruppo ufficiale di Tomb Raider: http://it.groups.yahoo.com/group/gruppoufficiale_tombraider/

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Re: GPCR
by Dan Thomas Major 07 Jan '02

07 Jan '02

Hi Jose, The modelling of the TMs themselves shouldn't be a problem, if you have a reliable template which is from the same family (e.g. GPCR). For instance, I'm modelling a GPCR using rhodopsin as a template and for each of the 7 TMs the sequence alignment is clear. That means the relative positioning (TM orientations) of the helices should be correct. Moreover, certain key residues that connect the helices are conserved within the GPCR family and I'm planning to add additional constraints to these interhelical distances in the modeller optimization. As far as I can see, the modeller energy function doesn't contain any term that should be biased towards globular proteins such as hydrophobic/hydrophilic terms, solvent accessability term or the like. The only problem that I see is that the data for some parameters (e.g. side-chain conformation) is inherently different in globular and membrane proteins, due to packing. The statistical data used in the modeller energy function is solely based on globular proteins as far as I understand. All other energy terms used in modeller seem to me to be general to all proteins. I would like the confirmation about this from the modeller team, though, since this is only my uneducated understanding. My main question was that the homology of GPCRs is relatively low, but the topology is better conserved than in globular proteins of similar homology. Thus the "greater than 40% homology rule" shouldn't apply to GPCRs. I hope this helps, Dan José Saldanha wrote: > Hi dan, > I saw your message on the modeller list. Unfortunately I cannot > answer it, but have a question to you. Can you use modeller's > optimisation for TM regions? I have done it myself, but feel > uneasy since I imagine it is meant for globular proteins, not > TM regions. > regards, > -josé- > ================================================================= > José W. Saldanha (PhD) Tel: (+44)(0)208 913 8635 > Division of Mathematical Biology Fax: (+44)(0)208 913 8545 > National Institute Ema: jsaldan(a)nimr.mrc.ac.uk > for Medical Research (NIMR) Cel: 07762 340964 > Mill Hill, London NW7 1AA (UK) > > Humanisation bY Design > http://www.cryst.bbk.ac.uk/~ubcg07s > ================================================================= -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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GPCR
by Dan Thomas Major 07 Jan '02

07 Jan '02

Hi, I'm modelling a GPCR based on rhodopsin as a template. The sequence similarity is relatively low (<20%), but the conserved residues are located in the 7 Transmembrane Helices, and the alignment of the TMs is obvious. It is assumed that the topology is well conserved (more so than expected from the sequence similarity), because of the known folding pattern in the GPCR-family. The question is this: Is there any way to assign greater weight to the conserved residues in the TM-regions in the distance constraints in the pdf, or in any other way assure that the information about the conserved residues won't get lost in the optimization? Thanks, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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[Fwd: GPCR]
by Dan Thomas Major 07 Jan '02

07 Jan '02

-- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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(no subject)
by Alexander Farley 05 Jan '02

05 Jan '02

subscibe Alexander_Farley afarley(a)mail.med.upenn.edu

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GPCR
by Dan Thomas Major 02 Jan '02

02 Jan '02

Hi, I'm modelling a GPCR based on rhodopsin as a template. The sequence similarity is relatively low (<20%), but the conserved residues are located in the 7 Transmembrane Helices, and the alignment of the TMs is obvious. It is assumed that the topology is well conserved (more so than expected from the sequence similarity), because of the known folding pattern in the GPCR-family. The question is this: Is there any way to assign greater weight to the conserved residues in the TM-regions in the distance constraints in the pdf, or in any other way assure that the information about the conserved residues won't get lost in the optimization? Thanks, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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Hai regarding ali file
by R Senthil Kumar 22 Dec '01

22 Dec '01

Dear modellers, I kindly request any one of you to send the example ali file for model building to build homodimer molecule along with heteroatoms. I mainly want to know sequence:1fdx: 1 : : 54 : :ferredoxin:Peptococcus aerogenes:-1.00:-1.00 how this line will look like when modelling homodimer template along with heteroatoms.Please help me in this regard. friendly from, Senthil kumar.R R.Senthil Kumar, Junior Research Fellow(JRF), c/o Dr.Akash Ranjan, Computational & Functional Genomics Group, Center For DNA Fingerprinting(CDFD), Hyderabad-500 076 Ph:040-7151344-Extn(Lab:1304) (Hostel:2300) E-mail:skumar@www.cdfd.org.in

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about restraints
by Paola D'Alessio 14 Dec '01

14 Dec '01

Dear modellers, I'd like to use the "make_restraint" command in my top file, in order to obtain five models that have a b-sheet in a particular region, but it doesn't work, in the final five models (after doing 100 cicles of VTFM) the b-sheet disappears (and the two strands too), while it is present in the .ini file, please, can you tell me something about this problem? the top file I used is the following: INCLUDE SET ALNFILE = 'align.ali' SET KNOWNS = 'E1' 'M1' ' SET SEQUENCE = 'abs' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '148:' '150:' MAKE_RESTRAINTS RESTRAINT_TYPE = 'STRAND', RESIDUE_IDS = '158:' '160:' #antiparallel sheet MAKE_RESTRAINTS RESTRAINT_TYPE = 'SHEET', ATOM_IDS = 'N:148' 'O:160', SHEET_H-BONDS = -5 RETURN END_SUBROUTINE -- dott. Paola D'Alessio Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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segmentation fault in Linux
by Rockey, William 13 Dec '01

13 Dec '01

Hi, Has anyone had trouble with Modeller crashing with segmentation faults under RedHat Linux 7.0? The specific error message is /usr/local/bin/modeller4/bin/mod4: line 39: 3410 Segmentation fault (core dumped) /usr/local/bin/modeller4/bin/${EXECUTABLE} $STEERF >$LOGF The log file has a 0 byte size when this occurs. I've tried setting the stacksize up to 512M, but this doesn't help. Both the MAXSEQ=6 and MAXSEQ=10 versions of the executables have the problem. The problem occurs both with my own job that I set up and the example file ./examples/tutorial-model/model-fast.top. Thanks in advance for any advice! Bill Rockey

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modeling problem
by Stephane Vandevuer 11 Dec '01

11 Dec '01

Hi, I'm performing homology modelling with Modeller. My template file is a Ca-only file, but this doesn't seem to be a problem. The .ini, .rsr and .sch files are correctly generated and the optimization begins for the first model (.D00000001) but does not succeed. Here is the end of the .log file : TOP_________> 327 234 OPTIMIZE pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 89694 89694 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I do search a little bit for the MPAIRS variable but I don't find it. Furthermore I was already successfull in modeling systems larger than the one I'm working now. Thanks for any help. Stephane.

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