[Chimera-users] PDB not opening

Eric Pettersen pett at cgl.ucsf.edu
Wed Jun 24 11:09:33 PDT 2015

On Jun 24, 2015, at 1:03 AM, YAikhombA Mutum <yaikhomba.mutum at students.iiserpune.ac.in> wrote:

> 1. I'm not able to fetch pdb's from Chimera by the command 'open 121p'. It just says 'opened 121p' in the reply log while it display a blank black screen. There are no active models displayed too (in the active models panel, there are no active tabs for models (0,1,2...)) despite the status in the reply log.
> The internet connections are ok (my browser is working fine). On checking the preferences (Favorites ---> preferences), everything seems fine (for instance in Category: Fetch (save fetched flie: True and use local files:True/False (I've tried both cases))). Even the category of web access seems ok.
> A day before I'd been able to fetch pdb's by just the command (open 1zik (say)). Now, the only way to retrieve it is to go to the rcsb website, download the pdb from a browser and then run it in chimera.
> Moreover, even if it (the pdb file) is already downloaded it doesn't run by entering the command (again the preferences are fine).
> How can I sort out this?

Hi Yaikhomba,
	Seems mysterious.  Try this:  open Preferences (Favorites->Preferences) and change the "Category" in the resulting dialog to "Preferences".  In that category click the "Reset to factory defaults" button.  Try opening 121p.  Any difference?  If not try removing [or moving elsewhere] your preferences file (the location is given in the dialog).  Restart Chimera.  Any difference opening 121p?


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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