VMD-L Mailing List

From: Anna Lohning (alohning_at_bond.edu.au)
Date: Tue Nov 22 2016 - 18:33:21 CST

Many thanks to all, I will try these great suggestions.
Cheers
Anna

From: Ashar Malik [mailto:asharjm_at_gmail.com]
Sent: Wednesday, 23 November 2016 10:13 AM
To: Anna Lohning <alohning_at_bond.edu.au>
Cc: John Stone <johns_at_ks.uiuc.edu>; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: error loading PDB

Hi,

One fix is to choose to run the program as an administrator by right clicking on the installed program (not the shortcut) and choosing "Run as administrator". That will for that particular instance of the program allow you to by pass the write restrictions.

Hope this helps.

Best,
/A

On Wed, Nov 23, 2016 at 12:44 PM, Anna Lohning <alohning_at_bond.edu.au<mailto:alohning_at_bond.edu.au>> wrote:
Many thanks for taking the time to reply and for the advice. Very much appreciated :)

Cheers
Anna

Dr Anna Lohning
Assistant Professor - Biochemistry
Faculty of Health Sciences & Medicine
Bond University
alohning_at_bond.edu.au<mailto:alohning_at_bond.edu.au>
(07) 5595 4779

> On 23 Nov. 2016, at 9:34 am, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:
>
> Hi,
> Is it possible that the Windows firewall is preventing VMD from
> accessing the network on your computer? The "Windows Defender" firewall
> feature has become progressively more restrictive, and the default behavior
> on most machines today is that Windows will deny applications from opening
> network connections unless you have specifically allowed it. Often, Windows
> will pop open a dialog box that asks for permission at the moment the
> application tries to make a network connection.
>
> We haven't made any recent changes to the software that would affect
> PDB loading that I'm aware of, and it works fine for me when I try
> and load the same structure code, so I would suggest checking whether
> your firewall settings are allowing VMD network access or not.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>
>
>> On Tue, Nov 22, 2016 at 06:56:00AM +0000, Anna Lohning wrote:
>> Hi
>> I am running VMD on a Windows 7 system and receive this error while
>> retrieving pdb files from RCSB server. I cant find anyone having this
>> error on the mailing list. It's most likely a setting but not sure where
>> to look.
>> The detailed error log is:
>> Unable to load file '2hbs' using file type 'webpdb'.
>> Unable to load file '2hbs' using file type 'webpdb'.
>> while executing
>> "mol new $pdbcode"
>> (procedure "::PDBTool::pdbload" line 6)
>> invoked from within
>> "::PDBTool::pdbload"
>> invoked from within
>> ".pdbtool.pdbfile.pdbload invoke"
>> ("uplevel" body line 1)
>> invoked from within
>> "uplevel #0 [list $w invoke]"
>> (procedure "tk::ButtonUp" line 24)
>> invoked from within
>> "tk::ButtonUp .pdbtool.pdbfile.pdbload"
>> (command bound to event)
>> If anyone has any suggestions, it would be most appreciated.
>> Pre-downloading is obvious workaround but I'd like to see if this is
>> something that can be fixed.
>> Many thanks in advance.
>>
>> Kind regards
>> Anna
>>
>> Dr Anna Lohning
>> Assistant Professor - Biochemistry
>> Faculty of Health Sciences & Medicine
>> Ph: 61-7-5995 4779
>>
>> [1][IMG][2][IMG][3][IMG][4][IMG][5][IMG][6][IMG][7][IMG][8][IMG][9][IMG][10][IMG][11][IMG][12][IMG][13][IMG][14][IMG]
>> [15][IMG][16][IMG]
>>
>>
>>
>>
>> References
>>
>> Visible links
>> 1. https://www.youtube.com/user/BondUniversity
>> 2. https://www.youtube.com/user/BondUniversity
>> 3. https://www.pinterest.com/bonduniversity/
>> 4. https://www.pinterest.com/bonduniversity/
>> 5. http://www.linkedin.com/company/bond-university
>> 6. http://www.linkedin.com/company/bond-university
>> 7. https://instagram.com/bonduniversity/
>> 8. https://instagram.com/bonduniversity/
>> 9. https://www.facebook.com/bonduniversity
>> 10. https://www.facebook.com/bonduniversity
>> 11. https://twitter.com/bonduniversity
>> 12. https://twitter.com/bonduniversity
>> 13. http://bonduniversity.tumblr.com/
>> 14. http://bonduniversity.tumblr.com/
>> 15. https://bond.edu.au/now
>> 16. https://bond.edu.au/now
>
>
>
>
>
>
>
>
>
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349<tel:217-244-3349>
> http://www.ks.uiuc.edu/Research/vmd/



--
Best,
/A