[Chimera-users] Regarding generating a .pdb file of peptide (Diglycine)

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 21 17:44:01 PDT 2017


Hi,
	We can reproduce the problem you’re having (only occurs on Linux) and are working on a solution.  Until we fix it, you have three options:

1) Use a non-Linux machine
2) Since PubChem 11163 is simply a diglycine, use the “peptide” option in Build Structure with the sequence “GG”.  This will differ slightly from the PubChem structure in that the PubChem one will be protonated as neutral, whereas the Build Structure one (if you later add hydrogens) will be protonated for biological pH.
3) Assuming you installed Chimera in the default location on your Linux box, run it as “SSL_CERT_DIR=/etc/ssl/certs ~/.local/UCSF-Chimera64-<VERSION>/bin/chimera”.  You will have to look in your ~/.local directory and replace <VERSION> with the Chimera version number you see there.  Then you should be able to use a PubChem fetch successfully.

—Eric


	Eric Pettersen
	UCSF Computer Graphics Lab


> On Aug 20, 2017, at 11:03 AM, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
> 
> Hello,
> I have installed chimera in ubuntu 14.04..
> I am finding difficult to get the .pdb format for diglyicne peptide (and further to create the topology and run the simulation in gromacs)... 
> 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:-
> Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590)
> 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error..
> 
> So can anybody kindly help....i am a novice here..
> Any suggestions are highly appreciated..
> 
> Thank you... 
> 
> 
> 
>   <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
> 
> On Sun, Aug 20, 2017 at 11:15 PM, Dilip H N <cy16f01.dilip at nitk.edu.in <mailto:cy16f01.dilip at nitk.edu.in>> wrote:
> Hello,
> I have install chimers in ubuntu 14.04..
> I am finding difficult to get the .pdb format for diglyicne peptide... 
> 1] If in Build Structure i select PubChem CID and type 11163 (Diglycine PubChem CID) i am getting error as:-
> Error fetching 11163:[Errno socket error] [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssi.c:590)
> 2] I even tried through File - Fetch by ID - Pubchem and typed 1163 (Diglycine PubChem CID).. but in vain..i am getting the same error..
> 
> So can anybody kindly help....i am a novice here..
> 
> Thank you...
> -- 
> With Best Regards,
> 
> DILIP.H.N
> Ph.D Student
> 
> 
> 
>   <https://mailtrack.io/>Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22>
> 
> 
> -- 
> With Best Regards,
> 
> DILIP.H.N
> Ph.D Student
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