modeller_usage

modeller_usage@salilab.org

3151 discussions

Modeling ligands in the binding site
by Qinghua Liao 03 Nov '09

03 Nov '09

Hi Modeller users, I have a problem of Modeling ligands in the binding site, I have read the manual online, but I still can't understand exactly! my question is what the differences of alignment between that of with and without ligand! Is it just the value of env.io.hetatm? And how to set the atoms with restraint? Could somebody share the all python scripts used during the entire process of Modeling ligands in the binding site? Any response will be highly appreciated! All the best, Qinghua Liao

2 1

Basic tutorial
by Marco 03 Nov '09

03 Nov '09

Dear all, I'm following the basic tutorial and I have a couple of question: a) some times ago Modeller grouped similar structures and scanned against the representative protein of each group: is this still valid? b) where I find the data on cristallografic resolution of the chosen proteins? The pdball.pir file does not contain this data. Thanks for your help, Marco

2 1

(no subject)
by Steve Seibold 03 Nov '09

03 Nov '09

Hello Modeller I believe I figured out the problem with the on-line tutorial. In the tutorial on-line in writes in the python script: env.io.atom_files_directory = ['.', '../atom_files'] However, I got it to work with only with: env.io.atom_files_directory = './:../atom_files' At least I hope this is the answer. Thanks, Steve

3 2

(no subject)
by madhavi choudary 02 Nov '09

02 Nov '09

"bunny.bindumadhavi(a)gmail.com" is ma email id -- m@d#@v|

1 0

(no subject)
by Steve Seibold 02 Nov '09

02 Nov '09

Hello I have been doing the tutorial http://salilab.org/modeller/wiki/Missing%20residues I have generated the alignment.ali file containing the pdb file 1qg8 and the 1qg8_fill sequences. (I basically copied them from the web site). I have gotten "automodel" to work without any problems. However, when I try run "loopmodel" it fails. Again, I am using the script directly from the web site for loop modeling (attached). When I attempt to run it, Modeller loads it libraries etc but then fails with the following error printed, not in log, but to the screen. File "loop-refine.py", line 19, in ? a.make() Does anyone have any insights as to what I could be doing incorrect? Thanks, Steve

1 0

Basic tutorial
by Marco 31 Oct '09

31 Oct '09

1 0

Re: [modeller_usage] Bad Contacts and Dimeric symmetry
by nornik 28 Oct '09

28 Oct '09

Hello again. I am now making new models with only symmetry restraints on the alpha carbons. However, I still think it's strange that when i have a model with 26 or even 38 bad clashes they are all 2.5 or 2.6 Å. Do you know why this is? Another thing is that the alignment should not be poor. There are only three small deletions and one large insert and they are all in surface exposed loop regions. My alignment has a 57 % identity so it could not be drastically changed. I also do not think that the bad contacts are in positions close to the deletions/inserts and moving these would greatly decrease the % identity. I guess I could use just my automodel models since they are rather good but the template is fully symmetric and it's for my Master's thesis so I want to do as nice models as possible. Thank you for putting such effort in helping all of us /Niklas

2 1

Permission denied message
by Manoel Arcisio-Miranda 28 Oct '09

28 Oct '09

Dear Ben, I am beginner in modeling of proteins. I downloaded the Modeller 9v7 (Windows package) and I am following the tutorials. I just started the Basic Modeling tutorial, but when I type any command at the command line, for example: mod9v7 build_profile.py, the following message appear: Cannot open logfile build_profile.log: Permission denied I also tried to run the command: mod9v7 model.py. and I got the same message. I downloaded all input and output files for this tutorial. So, what should I do? P.S.: the list of systems that I am using: Windows Vista, Modeller 9v7 and Phython 2.3.5 Thanks so much, Manoel ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

3 4

Stop renumbering of new model
by João Rodrigues 26 Oct '09

26 Oct '09

Dear all, When MODELLER creates a new model, it renumbers it. The first residue is 1, second is 2, etc. How can I force these residues to obey the original template numbering? Say, if the template starts at residue 54, MODELLER's models will start with 54? Regards! João [ .. ] Rodrigues (Blog) http://doeidoei.wordpress.com (MSN) always_asleep_(a)hotmail.com (Skype) rodrigues.jglm

2 2

Model missing residues in a trimer
by Panagiotis Kastritis 26 Oct '09

26 Oct '09

Dear all, I would like to ask you how is it possible to model missing residues in a trimer that I have. All the monomers have missing residues and each chain has numbering from 1 to 100 let's say. I searched the archive but I haven't found such question. I can try this one /from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('133', '135'), self.residue_range('216', '230')) a = MyModel(env, alnfile = 'alignment.ali', knowns = '1qg8', sequence = '1qg8_fill') a.starting_model= 1 a.ending_model = 1 a.make() /but how can I expand it to more than one chain? I would like only to fill the missing residues, with only local minimization of the structure and not global. Is it possible to do it in modeller? Thank you in advance, Panagiotis

3 5

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modeller_usage