- modeller_usage - salilab.org

Help
by matziast＠med.uth.gr 06 Apr '08

06 Apr '08

Thank you for your immediate reply, I am trying to install modeller9v3 on Scientific Linux(2.6-18-53.1.4.3I5xen). It doesn't have any glibc, only glib=2.0 but I think that it has to be installed glib=2.2. And a last question, the scripts must be written in Python and they also have to be finished with .py? Thank you in advance and I am sorry for my so simple and boring questions.

2 1

Help
by matziast＠med.uth.gr 04 Apr '08

04 Apr '08

Hi, I am a new user of modeller and specifically modeller9v3. I am a student of Biochemistry and Biotechnology in Greece and I need this program for my diploma thesis. I read in the page of modeller that I must install python and I have to write my scripts in this language. On top of that, I must install glib>=2.2 and glibc>=2.3 but I have some problems in their installation. If I do not install them, the modeller9v3 will not work? (I am sorry for my errors in English). Thank you in advance. Maria.

2 1

inducing kink in a helix
by Marta Rossini 01 Apr '08

01 Apr '08

Hi all, I am using Modeller to model a structure in which there is a portion - not present in the template - that I want to force to be an alpha-helix. If I introduce the secondray structure restraints in the entire corresponding region of sequence, I obtain a straightened helix. In the sequence, however, there is a Proline in correspondence of which I want to induce a little distortion of the helix. If I force the secondary structure only before and after the proline, by excluding it, I obtain some very strange angles of an helix with respect to the other, that is a too pronounced bending. Is there in Modeller a way to induce a "controlled" distortion (that in my case corresponds to control the angle between the CO and NH groups of the proline!)? thanks _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE

2 1

FW: inducing kink in a helix
by Marta Rossini 01 Apr '08

01 Apr '08

> > Hi all, > I am using Modeller to model a structure in which there is a portion - not present in the template - that I want to force to be an alpha-helix. > If I introduce the secondray structure restraints in the entire corresponding region of sequence, I obtain a straightened helix. In the sequence, however, there is a Proline in correspondence of which I want to induce a little distortion of the helix. > If I force the secondary structure only before and after the proline, by excluding it, I obtain some very strange angles of an helix with respect to the other, that is a too pronounced bending. > Is there in Modeller a way to induce a "controlled" distortion (that in my case corresponds to control the angle between the CO and NH groups of the proline!)? > thanks > _________________________________________________________________ > Explore the seven wonders of the world > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx

1 0

MODELLER and USER FORMAT restraints
by Yingang Feng 29 Mar '08

29 Mar '08

Hi, In modeller9v3, the USER FORMAT of rsr file is not supported. However, it seems MODELLER FORMAT rsr file do not support the atom selection with name like 'CA:10' but have to use the number indice of atom. This makes the NMR restraint conversion difficult. How to deal with large number restraints easily? Best Wishes, Yingang Feng National Laboratory of Biomacromolecules Institue of Biophysics, Chinese Academy of Sciences Datun Road 15, Beijing 100101, P. R. China

2 1

symmetry and molecular dynamics
by JEAN WATERMEYER 28 Mar '08

28 Mar '08

Hi all We are trying to build a homotetramer model but having some difficulty maintaining symmetry. I've read the previous posts but maybe someone can help me further - I'm new to Modeller and to Python. I have imposed symmetry: s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) but when I run automodel the molecular dynamics step pulls the monomers away from the template - so that although the subunits are identical, the symmetry is broken. We can think of a few ways to get around this: 1) do no molecular dynamics, only minimisation (maybe someone can tell me how?) 2) run molecular dynamics only on selected regions of the model so that the core remains fixed in place (again, how would I do this?) 3) learn Python and write restraints using symmetry matrices (if someone has implemented something like this before I'd love to see their code!) Looking forward to your input Jean Jean Watermeyer Division of Medical Biochemistry IIDMM University of Cape Town Health Sciences Anzio Rd Observatory 7925 South Africa Tel. 021 4066832

2 1

What are the considerations to model a cytosol protein using nuclear protein.
by Saravanan 20 Mar '08

20 Mar '08

I would like to model a protein which subcellular location is cytosol. I have found a better template which subcellular location is nuclear. My queries: 1) What are the considerations or constrainsts to be used to model a cytosol protein using nuclear protein. Is is correct to do like this. 2) Is it possible to specify constrainsts to model the environment based on tissue specific. Thank you in advance for any help Please don't print this e-mail unless you really need to. Save Trees.. P.Saravanan --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

1 0

DOPE profile of target structure
by Hanudatta Atreya 19 Mar '08

19 Mar '08

Dear all, Should the residue-wise DOPE profile of the target modeled structure necessarily match that of the template? This is because in the tutorial online, the DOPE profile shown indeed follows very closely that of the template. In my case, the modeled structure has 1.0 Angstrom RMSD with the template. However, the residue wise DOPE profile do not match with that of template. Also, other structure quality scores as I checked with PROCHECK, MOLPROBITY etc. are poor. So does this indicate non-optimal modeling? Especially the Clash-scores are high. Should I carry out one more mimimization step myself to loosen the distortions? Thanks With regards Atreya --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

2 1

long loops modeling
by Ivan Anishchenko 17 Mar '08

17 Mar '08

Good day, Modellers! I'm a student and not yet rather familiar with Modeller. I've faced some difficulties when modeling long loops. My target sequences are 35 residues long and have just slight differences (approximately five residues) from the template. The only restraint to the models is a disulfide bond connecting the first and the last residues. Several known structures (completely different) are used as templates; the result of the modeling each time are structures similar to the one used as template. The structures are supposed to be variable: nothing is known about their preferable conformation. Also there is no suggestion of elements with definite secondary structure. 1) whether it is possible somehow to obtain a set of possible conformations (not only those similar to the initial ones) by making changes in initial conditions or with the help of any other means? 2) can the tools for loop modeling be applied here, because the length of the loop seems to be excessive. Taking into account the low accuracy of the models obtained is it then possible using some assessment method (DOPE for example) to pick out more reliable models? 3) does the DOPE assessment method have any limitations on the minimal length of the structure and how does its accuracy change with length if it does? Thank you a lot for any help. Ivan

2 1

Modelling extra residues, not present in template
by Hanudatta Atreya 15 Mar '08

15 Mar '08

Dear all, I am trying to model a protein which has 70% sequence similarity to the template sequence. However, there are ~20 residues in the target/query sequence which is not present in the template. Now, from Secondary Structure Prediction algorithms, this region seems to be partly helical. But the model generated by Modeller (9v3) gives a random-coil or loop for these residues. Is it not possible to feed the secondary structure info. into the program to improve the structural quality of this extra region? Thanks Regards Hanudatta --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

2 1