Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.a...> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
Hi Darrell! Sorry, there isn't any PDB biological unit fetch … one has to download them from the RCSB website, then open "manually" in Chimera. We have discussed changing from PQS to PISA in the fetch interface (trac ticket #10237), but it hasn't been done. Best regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 2, 2014, at 10:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> wrote:
Hi Chimera friends,
The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates
Thanks, Darrell
Hi Elaine, No problem. We'll work around it. I just wanted you to know that someone else was interested in it, too. :) Thanks, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.a...> Twitter: @niaidbioit<https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Monday, June 2, 2014 5:18 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Fetch biological unit? Hi Darrell! Sorry, there isn't any PDB biological unit fetch … one has to download them from the RCSB website, then open "manually" in Chimera. We have discussed changing from PQS to PISA in the fetch interface (trac ticket #10237), but it hasn't been done. Best regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 2, 2014, at 10:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> wrote: Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell
Hi Darrell, I added a Chimera Fetch dialog entry “PDB biounit” that will fetch all the biological assembly files for a pdb id — there can be more than one. Also they can be fetched using the Chimera command: open pdbbuID:2bbv Will be in tonight’s daily build. Tom On Jun 2, 2014, at 2:19 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Elaine,
No problem. We'll work around it. I just wanted you to know that someone else was interested in it, too.
:)
Thanks, Darrell
-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.a...> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
From: Elaine Meng Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Monday, June 2, 2014 5:18 PM To: Darrell Hurt <> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Fetch biological unit?
Hi Darrell! Sorry, there isn't any PDB biological unit fetch … one has to download them from the RCSB website, then open "manually" in Chimera. We have discussed changing from PQS to PISA in the fetch interface (trac ticket #10237), but it hasn't been done. Best regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2014, at 10:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, Wow! Thanks. I'll give it a try tomorrow. This may really help! Cheers, Darrell -- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559Web: BCBB Home Page <http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb .aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit <https://twitter.com/niaidbioit> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. On 6/2/14 7:53 PM, "Tom Goddard" <goddard@sonic.net> wrote:
Hi Darrell,
I added a Chimera Fetch dialog entry ³PDB biounit² that will fetch all the biological assembly files for a pdb id ‹ there can be more than one. Also they can be fetched using the Chimera command:
open pdbbuID:2bbv
Will be in tonight¹s daily build.
Tom
On Jun 2, 2014, at 2:19 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi Elaine,
No problem. We'll work around it. I just wanted you to know that someone else was interested in it, too.
:)
Thanks, Darrell
-- Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office: 301-402-0095 Mobile: 301-758-3559 Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Page s/bcbb.aspx#niaid_inlineNav_Anchor> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
From: Elaine Meng Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Monday, June 2, 2014 5:18 PM To: Darrell Hurt <> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] Fetch biological unit?
Hi Darrell! Sorry, there isn't any PDB biological unit fetch Š one has to download them from the RCSB website, then open "manually" in Chimera. We have discussed changing from PQS to PISA in the fetch interface (trac ticket #10237), but it hasn't been done. Best regards, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 2, 2014, at 10:18 AM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:
Hi Chimera friends, The PQS server still works well for downloading the biological unit, but (as noted) it doesn't have every structure in it. The PDB itself provides the biological unit(s) for download in their weird ".pdb1", ".pdb2", etc. format for every entry in the database (even if it is redundant). Is there a way to grab those files from the PDB itself using the Chimera interface? The repository is in: ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates Thanks, Darrell
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Hurt, Darrell (NIH/NIAID) [E] -
Tom Goddard