Hi, Am 17.08.2010 um 15:30 schrieb Ahmadreza Mehdipour:
> Dear Alexander > Thank you in advance for previous email. I worked with server but I > encountered with following problems: > 1- the pymol script file is just including plane and H bonds and there > is no structure of protein itself that correct. You need to download the *_mod.pdb file from the history and load it into PyMOL. Then run the script file via the run command in PyMOL (either run "/path/to/script.py" on the PyMOL console or using Run in the file menu). > 2- when I run the visulization process the server goes to an empty page > without any further process [I am using firefox 3.6.8 in a Mac OS X ver > 10.6 environment which has java for mac ver 1.0) What are you referring to exactly? There is a link "Start protein viewer" when you view a *.hcsummary dataset. This should open the visualization. > 3-number of helices is more than of original number in the pdb, how can > I find that each of number in circles refers to which part of the > sequence? > You spotted some weak spot here. It's complicated to get the numbers directly, but when the "Start protein viewer" link works there is a dropbox 'interface contacts for', which includes the helices and upon selection colors the selected helix pink. Best Alexander > with best wishes > Ahmadreza > -- Charite - Institute of Medical Physics and Biophysics http://proteinformatics.charite.de/ Tel.: ++49 (030) 450 524 170
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