Hi Tom, Thanks again for adding this functionality. I'm running the script on a server behind a firewall. Can you tell me the address(es) (and port(s), if applicable) that must be available to my server if I want to use this new direct fetching of biological assemblies? 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: 301-758-3559Web: 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 6/3/14 2:52 PM, "Tom Goddard" <goddard@sonic.net> wrote:

Hi Darrell, Boaz,

I made a few improvement to the fetching of PDB biological unit files that will be in tonight¹s daily build.

1) Made fetching biounit give each assembly a separate top level model id number and separate color. Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel.

2) Renamed biounit file type and prefix from pdbbuID to biounitID. So use Chimera command ³open biounitID:1hho².

3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2. This works in the Fetch by Id dialog and on the command-line. Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number. Used "." instead of comma since commas separate multiple identifiers in the fetch dialog.

Tom

On Jun 3, 2014, at 5:52 AM, Boaz Shaanan <bshaanan@bgu.ac.il> wrote:

...

Hi Tom,

This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think?

Cheers,

Boaz

Fantastic! Thank you! 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 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) 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. ----- Original Message ----- From: Tom Goddard [mailto:goddard@sonic.net] Sent: Thursday, June 12, 2014 06:22 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; Boaz Shaanan <bshaanan@bgu.ac.il> Subject: Re: [Chimera-users] About direct fetc hing biological assemblies into Chimera Hi Darrell, The new Chimera fetch PDB biounit code does an ftp fetch of a url that looks like ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/all/391d.pdb1.gz using urlretrieve() from the Python urllib module. Here’s the code http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/FetchBioUnit/fetch... http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/chimera/fetch.py Tom On Jun 12, 2014, at 12:56 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:

Hi Tom,

Thanks again for adding this functionality. I'm running the script on a server behind a firewall. Can you tell me the address(es) (and port(s), if applicable) that must be available to my server if I want to use this new direct fetching of biological assemblies?

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: 301-758-3559Web: 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 6/3/14 2:52 PM, "Tom Goddard" wrote:

...

Hi Darrell, Boaz,

I made a few improvement to the fetching of PDB biological unit files that will be in tonight¹s daily build.

1) Made fetching biounit give each assembly a separate top level model id number and separate color. Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel.

2) Renamed biounit file type and prefix from pdbbuID to biounitID. So use Chimera command ³open biounitID:1hho².

3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2. This works in the Fetch by Id dialog and on the command-line. Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number. Used "." instead of comma since commas separate multiple identifiers in the fetch dialog.

Tom

On Jun 3, 2014, at 5:52 AM, Boaz Shaanan wrote:

...

Hi Tom,

This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think?

Cheers,

Boaz

Thanks Darrell, I’ve fixed the code so that fetching pdb biounit files uses the lower-case 4-letter id. Fix will be in tonight’s daily build. Oddly for some entries upper and lower case work, while for others, only lowercase works. Tom On Jun 16, 2014, at 9:27 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

Hi Tom,

Thanks again for this. I found that when I specify a PDB using uppercase letters via a script, the command doesn't work. But lowercase letters do work. I catch it in my script, but you may want to build this into the command for other users, kind of like how regular PDB fetch does it.

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: 301-758-3559Web: 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 6/12/14 6:35 PM, "Hurt, Darrell (NIH/NIAID) [E]" wrote:

...

Fantastic! Thank you!

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 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)

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.

----- Original Message ----- From: Tom Goddard Sent: Thursday, June 12, 2014 06:22 PM To: Hurt, Darrell (NIH/NIAID) [E] Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu>; Boaz Shaanan <bshaanan@bgu.ac.il> Subject: Re: [Chimera-users] About direct fetc hing biological assemblies into Chimera

Hi Darrell,

The new Chimera fetch PDB biounit code does an ftp fetch of a url that looks like

ftp://ftp.wwpdb.org/pub/pdb/data/biounit/coordinates/all/391d.pdb1.gz

using urlretrieve() from the Python urllib module. Here’s the code

http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/FetchBioUnit/fet ch_biounit.py http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/chimera/fetch.py

Tom

On Jun 12, 2014, at 12:56 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:

...

Hi Tom,

Thanks again for adding this functionality. I'm running the script on a server behind a firewall. Can you tell me the address(es) (and port(s), if applicable) that must be available to my server if I want to use this new direct fetching of biological assemblies?

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: 301-758-3559Web: BCBB Home Page

<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bc bb .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 6/3/14 2:52 PM, "Tom Goddard" wrote:

...

Hi Darrell, Boaz,

I made a few improvement to the fetching of PDB biological unit files that will be in tonight¹s daily build.

1) Made fetching biounit give each assembly a separate top level model id number and separate color. Before all the assemblies were grouped together in Model Panel, and now each assembly is on a separate line in Model Panel.

2) Renamed biounit file type and prefix from pdbbuID to biounitID. So use Chimera command ³open biounitID:1hho².

3) Allowed specifing a specific biounit by number using pdb id plus "." followed by number, eg. 3fad.2. This works in the Fetch by Id dialog and on the command-line. Also to fetch a few different biounits you can use 3xyz.1.3.8 with each . specifying another assembly number. Used "." instead of comma since commas separate multiple identifiers in the fetch dialog.

Tom

On Jun 3, 2014, at 5:52 AM, Boaz Shaanan wrote:

...

Hi Tom,

This is a nice addition but can you ALSO give the option of fetching just one of the biological assemblies? It is my experience that biological assemblies for a particular pdb entry consist of one correct assembly, in the sense of biological function corresponding to the description given by the depositors and other assemblies. I usually flip between the assemblies on the RCSB website before deciding which one to fetch. With your new addition this of course can all be done now in Chimera but if possible, I'd rather not waste time and disk space with meaningless assemblies. What do you think?

Cheers,

Boaz