January 2002 - modeller_usage

ask again: disaster
by zhenyisong 15 Jan '02

15 Jan '02

@ I sent this help letter before but no response.I hope some one could help me out of trouble. @ I am I do not know how to get the alignment file even after i read through the tutorial. It seems that if you have a @ template (preferred PDB code) and target seqeunce, and the alignment file in PIR format, you could run homology @ modeling. Am I rignt ? @ If i know the sequence of targets and template , what should i do next ? /* *# Homology modelling by the MODELLER TOP routine 'model'. *INCLUDE # Include the predefined TOP routines (like c languange include <math.h>) *SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file *SET ALNFILE = 'alignment.ali' # alignment filename (where the pre-aligned file, "alignment.ali" come *from?) *SET KNOWNS = '5fd1' # codes of the templates *SET SEQUENCE = '1fdx' # code of the target *SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files *SET STARTING_MODEL= 1 # index of the first model *SET ENDING_MODEL = 1 # index of the last model * # (determines how many models to calculate) *CALL ROUTINE = 'model' # do homology modelling */

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stepwise top
by Dan Thomas Major 10 Jan '02

10 Jan '02

Hi, Is it possible in a modeller top file to calculate, let's say 100 models, and then tell modeller to refine the best 10 and then to add loops for the best 5 (all in one run). Thanks, Dan -- Dan Thomas Major (at Dr. B. Fischer's lab) Bar-Ilan University Ramat-Gan, Israel

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MD refinement
by Giulio Rastelli 09 Jan '02

09 Jan '02

Dear modellers, it is not clear to me whether the 'model' routine in modeller6 performs MD refinement or not. Even setting the .log verbosity to a debugger level, I cannot see the details of MD equilibration in the log file. Thanks in advance, Giulio Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena e Reggio Emilia Via Campi 183 41100 Modena - ITALY ------------------------------------- tel 0039-059-2055145 fax 0039-059-2055131 -------------------------------------

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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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