June 2006 - modeller_usage

Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ COPA 2006: (¯`·._.·[ Ooooooola ]·._.·´¯) e + frases para seu MSN Clique aqui! http://copa.br.msn.com/extra/frases/

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rdpir___648E> Alignment sequence not found in PDB file
by Michael Mazanetz 14 Jun '06

14 Jun '06

Dear MODELLER users, I get this error message " rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb " in my log file when I try and run a homology model. When I reduce the number of residues in the sequence to just four the model runs OK. What is wrong, can anyone suggest anything?? I've enclosed my files :screen output, B04_2742_111_002.ali, Loop-005.py and Loop-005.log And the -v command always gives an error too?? regards and thanks in advance. Mike The screen output is: C:\Program Files\Modeller8v2\examples\automodel>mod8v2 loop-005.py -v 'import site' failed; use -v for traceback Traceback (most recent call last): File "loop-005.py", line 24, in ? a.make() # do the actual homology modelling File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\loopmodel.py", line 28, in make automodel.make(self, exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 100, in make self.homcsr(exit_stage) File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 318, in homcsr aln = self.read_alignment() File "C:\Program Files\Modeller8v2\modlib\modeller\automodel\automodel.py", line 312, in read_alignment aln.append(file=self.alnfile, align_codes=self.knowns+[self.sequence]) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 36, in append return self.__int_append('alignment.append', io, libs, vars) File "C:\Program Files\Modeller8v2\modlib\modeller\alignment.py", line 68, in__int_append libs=libs.modpt, **vars) File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line 33, in read_alignment return _modeller.read_alignment(aln, io, libs, *args) _modeller.error: rdpir___648E> Alignment sequence not found in PDB file:1 ../atom_files\1ba4.pdb B04_2742_111_002.ali file >P1;1ba4 structureX:1ba4:.:.:.:.: MENFQKVEKI GEGTYGVVYK ARNKLTGEVV ALKKIRXDTE TEGVPSTAIR EISLLKELNH PNIVKLLDVI HTENKLYLVF EFLHQDLKKF MDAS------* >P1;1M8Qb structureX:1M8Qb:.:.:.:.: ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ----KQPRQY* >P1;1bb2 sequence:1ba2:.:.:.:. MEDYTKIEKI GEGTYGVVYK GRHKTTGQVV AMKKIRLESE EEGVPSTAIR EISLLKELRH PNIVSLQDVL MQDSRLYLIF EFLSMDLKKY LD-SIPPGQY* Loop-005.py file # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './:../atom_files' a = loopmodel(env, alnfile = 'B04_2742_111_002.ali', # alignment filename knowns = ('1ba4','1M8Qb'), # codes of the templates sequence = '1ba2') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 1 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() # do the actual homology modelling Loop-005.log file rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files\1ba4.pdb This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Modeling a Chimera
by Toty Santos 14 Jun '06

14 Jun '06

Hi dears, I am a starting model buiter and i´d like to know how i can make a model like this : I have a bifuncional enzime with two domains. But in the PDB i have as a model different structures : One for domain A and other to domain B. And i´d like to build a model with this two domains together. It is not a dimer, it a single enzime with two diferente domains. And i´d like to know tto, what i will do with the linker resudues between this both domains !! I anybody can help me, please be detalist cause i am a start user i am using Modeller 8v0 thanks a Lot Marcos Tadeu dos Santos Undergratuated Student UNICAMP - BRAZIL _________________________________________________________________ Você sabe em qual Copa o Pelé vestiu a camisa 10 pela 1a. vez? http://copa.br.msn.com/extra/curiosidades/1958/

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Imposing dihedral restraints
by Vivek Sharma 14 Jun '06

14 Jun '06

Dear Benn, I am having some troubles in putting dihedral restraints in the system I am modelling. Firstly, I should say I want to put backbone angles (phi/psi) into a stretch of 5 amino acid residues. I mention the values (these values are from database, in fact are right and do exist in one protein) with the std. deviation value ~ 15deg. And, I am using Modeller 7v7, sorry I am slow in updating myself ;). So for e.g. I put a dihedral restraint (say phi for e.g.) for a residue like this: SET ATOM_IDS = 'C:317' 'N:318' 'CA:318' 'C:318' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 11 4 2 0 -1 0.261 So now you can see here; Form is 3 Modality is 1 Feature is 3 (dihedral angle) group is 11 (Mainchain phi dihedral restraints) Numb_atoms = 4 Numb_parameters = 2 0 Value of angle in radians Std. deviation in radians. Now when I run modeller with such restraints, in the finally obtained models, I dont see these exact values of restraints, which we mentioned explicitly, taken in by the model. Why this is so? The values of these mentioned dihedral restraints in the modelled models are far from the prescribed values. Secondly, though I dont see any violation also in concern to these values, i.e. if I have understood correctly, then violation will be reported in the log file if (optimized value - value mentioned by used)/(std. deviation) > 4.5 (approximately something like that). So this makes clear that why violation is not reported, because our values (diff/std. devn) are less than 4.5. But the question is, that when I give value of 15 degree as std. deviation (which I have to, I will come to this point later!) , then difference between optimsed value and mentioned value ~ 60 degrees, and that is very much. So again what I say is that I want to put certain values of dihedrals (backbone angles in fact) in the model, but values obtained for these angles in optimised models are far from the values mentioned in by me (because range of difference is ~60 degrees), though there are no violations reported, probably because of the above mentioned reason. PLease tell me what to do in this concern. Now as I said above that I am giving 15deg as std. deviation,but when I use smaller values like 5deg or so, the program is getting failed, it seems that it is getting difficult for it to optimise the system, with smaller values of std. deviation. Also, please tell me how to solve this problem. Last but not least, what I tried or trying is that creating the gaps in this section of 5 residues, where I am imposing backbone dihedrals, so that MODELLER doesnt find any equivalent residues in that position in templates and probably reduces the number of restraints, and in that case I may be able to impose my restraints well enough for these five residues, but still results doesnt seems to go hand in hand. Any comments in this concern also will be helpful. Details: there are two templates, MD_LEVEL is refine_3, our own alignment and paramters are used. So overall these are the problems I am at the moment facing, so any comments/details, will be very helpful. PS: The subject is different from 'Problem', :). Thanks in advance, br, Vivek Sharma University of Helsinki.

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Modeling core residues without loop regions
by Vimalkumar Velayudhan 13 Jun '06

13 Jun '06

Dear MODELLER users, I was looking for answers to the following questions? 1. What is the best approach to model proteins with large insertions (approximately 50residues) at different parts of the protein. Example AAAAAA---------------------------------BBBBBB---------------------------------------------CCCC Even if the alignment is good, I get an exceeded maxmolpdf error in the model building stage. I am not sure what value to set for the maxmolpdf . 2.Is it possible to build only the core residues without the insertions? It would be helpful if you can point me to references related to the same. -- Vimalkumar Velayudhan

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Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model
by Modeller Caretaker 09 Jun '06

09 Jun '06

Yun He wrote: > On Thursday 08 June 2006 09:40, you wrote: >> The PDB files produced by Modeller also contain the molpdf, as a REMARK >> at the top of the file, so you can just read this. If you refine the >> structure, you should write out a new PDB file, which will contain the > ~~~~~~~~~~~~~ write out?? If I refine this model with > Refmac5 in CCP4, the refined model written by Refmac5 doesn't contain any > header remark about molpdf, how should I get the molpdf? Is this molpdf the > same as the one of the model not refined, or there are any ways to > re-calculate its molpdf? Scoring functions used by different programs are almost never comparable, so you can't do this. All you can do is to, like I said, write out the refined structure and then recalculate its molpdf in Modeller. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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loop modelling
by hori koshii 08 Jun '06

08 Jun '06

Does MODELLER has a limitation for loop modelling up to 12 or 14 residues? What if I have 20 residues? Could you please give me some suggestions how to model a loop like this please? Thanks in advance! :) __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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DOPE profile
by Tom Burghardt 07 Jun '06

07 Jun '06

Modellers I would like to make a DOPE profile for a modeled protein containing a chemically modified side chain. I used the script suggested in the Advanced Tutorial with the following lines to read the library files containing information about the modified residue. env = environ(restyp_lib_file='${LIB}/restyp_tom.lib') env.libs.topology.read(file='$(LIB)/top_heav_tom.lib') # read topology env.libs.parameters.read(file='$(LIB)/par_tom.lib') # read parameters The DOPE profile is created by the script but the modified residue is left out of the profile. Any suggestions would be appreciated. Tom -- Tom Burghardt Department of Physiology and Biomedical Engineering Mayo Clinic

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How can I get MolPDF of an existed PDB file of an model
by Yun He 07 Jun '06

07 Jun '06

When I use automodel class to generate N models, the energy MolPDF of every model will be displayed in the log file, e.g. =========================================== >> Summary of successfully produced models: Filename molpdf ---------------------------------------- T0291.B99990001.pdb 2029.54651 T0291.B99990002.pdb 2719.03467 T0291.B99990003.pdb 2009.53479 T0291.B99990004.pdb 2688.20435 T0291.B99990005.pdb 2311.00342 =========================================== But, sometimes, after the models got be refined by some other means, how can I get those changed molpdf by handling the existed PDB files, rather than to involve the automodel class again to rebuild such models? I think "examples/commands/energy.py" in node151.html of the manual may help me, but I wonder whether the molpdf got by this method is identical to that recorded in log file.

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Re: [modeller_usage] loop optimization problem
by Agnieszka Szarecka 07 Jun '06

07 Jun '06

Hello Modeller Users, I am trying to run the loop structure refinement using loop_refine.py. I have several 3-5 residue long gaps in my pdb structure and I am trying to get them "patched". The program crashes with "..... ddihedr_262E> Central bond too short: 0.000" I checked the structures (they seem fine) and actually tried running three different loops and the same error pops up. Would anyone have an idea what the problem is and how I should fix it? Also: I ran the same time type of calcs with mod8v1 and had no such problems. The only difference is that I switched from Linux to Windows for this run. tons of thanks for help, Agnieszka

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