Blast PDB in Chimera version 1.15
Hi there, I am teaching a Protein and Function course this semester, and show students how to use Chimera, and integrated Modeller to carry out homology modeling. I use the older version Chimera 1.11.2 and they downloaded current version Chimera 1.15. For some reason, when they use "info" tool and select "blast proteins" in FASTA file window, the Blast query window show blank and never progressed. I don't have any the problem with the older version Chimera installed in my old laptop. Can you advise how to process from here? Thank you! Feixia _________________ Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire 46 College Road Durham, NH 03824
Hi Feixia, Your students need to download the Chimera daily build. The URL for fetching PDB info for hits from the RCSB changed. Chimera 1.15 uses the old (non-functional) URL whereas the daily build has the new URL. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 6, 2021, at 7:31 AM, Feixia Chu via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hi there,
I am teaching a Protein and Function course this semester, and show students how to use Chimera, and integrated Modeller to carry out homology modeling. I use the older version Chimera 1.11.2 and they downloaded current version Chimera 1.15. For some reason, when they use “info” tool and select “blast proteins” in FASTA file window, the Blast query window show blank and never progressed. I don’t have any the problem with the older version Chimera installed in my old laptop. Can you advise how to process from here? Thank you!
Feixia
_________________ Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire 46 College Road Durham, NH 03824
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Got it! Many thanks for the quick response, Eric! Best, Feixia From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Wednesday, October 06, 2021 11:31 AM To: Feixia Chu <Feixia.Chu@unh.edu> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Blast PDB in Chimera version 1.15 CAUTION: This email originated from outside of the University System. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hi Feixia, Your students need to download the Chimera daily build. The URL for fetching PDB info for hits from the RCSB changed. Chimera 1.15 uses the old (non-functional) URL whereas the daily build has the new URL. --Eric Eric Pettersen UCSF Computer Graphics Lab On Oct 6, 2021, at 7:31 AM, Feixia Chu via Chimera-users <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> wrote: Hi there, I am teaching a Protein and Function course this semester, and show students how to use Chimera, and integrated Modeller to carry out homology modeling. I use the older version Chimera 1.11.2 and they downloaded current version Chimera 1.15. For some reason, when they use "info" tool and select "blast proteins" in FASTA file window, the Blast query window show blank and never progressed. I don't have any the problem with the older version Chimera installed in my old laptop. Can you advise how to process from here? Thank you! Feixia _________________ Feixia Chu, Ph.D. Associate Professor Molecular, Cellular & Biomedical Sciences University of New Hampshire 46 College Road Durham, NH 03824 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplato.cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=04%7C01%7CFeixia.Chu%40unh.edu%7Ca895acef6b9c4e3be16208d988de4ef4%7Cd6241893512d46dc8d2bbe47e25f5666%7C0%7C0%7C637691310777479717%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=uVTMV%2Bjxv0ThKRyauh410qIs%2F4O9W%2Ful3r5pMRePMXA%3D&reserved=0>
participants (2)
-
Eric Pettersen -
Feixia Chu