I have been trying to down load it on their server but i found it difficult. Can you please send it into my inbox? Although,am also a learner like you.You are appreciated

[email protected]

maybe you can change the name for PDB file, all characters in upper case or in lower case, i forget

try to check the names of your target and template in alignment file. they should be as provided with the name of your pdb file name and python script: the "known" and the "unknown" one (Lower/Upper case sensitive). for example: if the name of ur pdb file is 1X2Y then do check it must be in the same case in ur alignment file i.e., 1X2Y and not like 1x2y. same thing is applied to ur target sequence. also be sure that all the necessary files (alignment file: *.ali, pdb or ent or atm file, python script: *.py) should be in the same folder say "MOD" and for running Modeler..first change the path in the modeler console to reach the same folder i.e., "MOD" then type the command.

i hope this will help u..if problem persists drop it to my email: [email protected]

You can try SWIFT MODELLER for easy working with modeller

http://bitmesra.ac.in/swift-modeller/swift.htm

Thank you all for your help! These days I’m a little bit caught in some other problems, but I’ will replay you as soon as possible if I manage to fix my problems based on your proposals .

I'm using modeller 9v7. I have the same problem. But i think is just bugs/typo in coding error. It seem that the machine read that .\..\\Modeller9v7\examplestom_files. So what I do, I just create 'examplestom_files' folder and place the pdb file in it. I also tried in modeller 10.1 and it work. Hope it will help you. If any problem that i can help u cam mail me at [email protected].

Thank you for your answer. Right now I started to use swift modeller, it has a friendly interface. I will try also what you proposed and see if it works.

you can try ModWeb server for modeling, which is based on the Modeller. You simply submit your sequence file to the server.

Dear Kibedi Szabo Csaba Zoltan,

swift modeller has very excellent interface with easy working. I will also suggest everyone to try this once.

I-tasser has been the best protein structure predictor in the past 5, 6 years (http://zhanglab.ccmb.med.umich.edu/I-TASSER/).

The modeller and swiss model are also good alternative ones, but not as good as I-tasser from personal experiences !!!

If you are not at all comfortable with scripts (like Python in this case) you can download & try "EasyModeller". Its a GUI vesion of Modeller. URL: http://www.uohyd.ernet.in/uploads/morelinks/downloads/modellergui/index.html

Dear Mr. Shankaracharya,

thank you very much for your advise. I started to use Swift Modeller, and i found it very practical and useful. Although i have a question. After you generate a number of models and you close the program, how can you open the generated models once again for loop optimization?Or you have to perform the loop optimization when you generated the models?

Regards.

Dear Kibedi Szabo Csaba Zoltan,

You can do loop optimization after generated the model and all the models will be saved in the file with the name of current date and time.

Hope this information will solve your problem.

feel free to contact me at my mail

[email protected]

The details of EasyModeller GUI (A graphical interface to MODELLER) is now available at : http://modellergui.blogspot.in/

http://modellergui.blogspot.in/

Article Easymodeller: a graphical interface to MODELLER

Almost exclusively, I use UCSF Chimera which incorporates Modeller in the program and then accesses many other useful software within the same program. Here's the link: https://www.cgl.ucsf.edu/chimera/