Messages

1

General discussions (Q&As) / Re:stacking diagrm

« on: November 06, 2010, 02:30:49 pm »

Hi
My question was something specific about the generating the stacking diagram. How we can generate different color diagram other than the default and also how one can hide hydrogen atoms in the generated stacking diagram. I was trying to search in the manual but couldn't locate it.

I will appreciate any help.

Regards
Raman

2

General discussions (Q&As) / Re: Re:pdb problem in 3DNA

« on: August 18, 2010, 03:52:23 pm »

Thanks Xiang for your help. You are right that it is the format issue problem. I generated these files using CYANA. I was looking for various program for converting to the right format but I came to conclusion using script in sed, vim or the one you did in ruby are the best solutions. Does anyone know any webserver or any other program for generating proper pdb format files?

Regards
raman

3

General discussions (Q&As) / Re:pdb problem in 3DNA

« on: August 12, 2010, 03:32:13 pm »

I was trying to use 3DNA web server for analyzing of the RNA double stranded   (CCGCUGCGG)2 but the server seems not to recognize the file.
 I am not able to figure out the error source. I think it might be some atom types are not recognized. I will appreciate if you can give me any insight into how I can modify the files for proper format for  3DNA. I have attached the pdb file.
Help will be highly appreciated.
Regards
Raman