Error reading PubChem3D SDF Files
I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug? Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!' Many thanks in advance, Jon http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=23853897707157... You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Hmm. The link below returns a page with the error message "invalid input type". Going to the PubChem/Pub3D URL returns a page with the error message "Not Found [MAIN PAGE]". Perhaps there's something going on with the PubChem server? I'll try checking on it again later. Conrad On 5/14/2013 1:19 AM, Jon Fuller wrote:
I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug?
Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!'
Many thanks in advance,
Jon
http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=23853897707157...
You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
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Hi Conrad, I guess that was a bad link for me to post and something has expired. This link should give the required file: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=71739&disopt=3DSaveS... Best, Jon On 14 May 2013 18:37, Conrad Huang <conrad@cgl.ucsf.edu> wrote:
Hmm. The link below returns a page with the error message "invalid input type". Going to the PubChem/Pub3D URL returns a page with the error message "Not Found [MAIN PAGE]". Perhaps there's something going on with the PubChem server? I'll try checking on it again later.
Conrad
On 5/14/2013 1:19 AM, Jon Fuller wrote:
I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug?
Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!'
Many thanks in advance,
Jon
http://pubchem.ncbi.nlm.nih.**gov/vw3d/vw3d.cgi?cmd=crtvw&** reqid=238538977071577164<http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=23853897707157...>
You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.**sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.**sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.**sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
______________________________**_________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users<http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Jon, I do get the error with the downloaded SDF, but if I fetch directly in Chimera it works fine for me. I tried your compound (71739) and the example compound (12123). The difference is possibly that Chimera's fetch goes through an intermediate web service (Pub3D, described in Chimera's Fetch By ID help page) that undoubtedly doesn't contain the problematic section of the SDF file. How about you try the direct fetch again, but check the "Ignore any cached data" button at the bottom of the fetch dialog and see what happens. In the interim, I will try to get Chimera to handle the downloaded version also. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On May 14, 2013, at 1:19 AM, Jon Fuller <jonathan.fuller@gmail.com> wrote:
I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug?
Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!'
Many thanks in advance,
Jon
http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=23853897707157...
You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The next release candidate and daily builds will handle the new format for charges that PubChem is using. This only affects files directly downloaded from PubChem and then opened in Chimera. Files fetched by Chimera directly don't have a charges section and therefore work and continue to work. It seems that the intermediate web service (Pub3D) may have been down when you reported the problem initially -- it seems to be up now. --Eric On May 15, 2013, at 2:21 PM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Jon, I do get the error with the downloaded SDF, but if I fetch directly in Chimera it works fine for me. I tried your compound (71739) and the example compound (12123). The difference is possibly that Chimera's fetch goes through an intermediate web service (Pub3D, described in Chimera's Fetch By ID help page) that undoubtedly doesn't contain the problematic section of the SDF file. How about you try the direct fetch again, but check the "Ignore any cached data" button at the bottom of the fetch dialog and see what happens. In the interim, I will try to get Chimera to handle the downloaded version also.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On May 14, 2013, at 1:19 AM, Jon Fuller <jonathan.fuller@gmail.com> wrote:
I tried to read an SDF file directly downloaded from pubchem into Chimera. However, I ran into the following problem (link to example file used, and reply log below). Is this expected behaviour, or a bug?
Additionally I tried to import the pubchem CID 71739 (same compound) from the fetch structure by ID tab, and got the error message: Unexpected end of file (parser state: counts) in MOL/SDF file 'FILEPATH HERE!'
Many thanks in advance,
Jon
http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=23853897707157...
You are now running Chimera version 1.8 (build 38642). Your previous version was 1.5 (build 32133). Check the release notes for new features and other info. (To access the release notes, use the Help menu to bring up the User's Guide. Then click the 'Documentation index' link and you will then see a link for the release notes.) Error while processing CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_3672_e5800000001_conf.sdf: Non-numeric charge (1 -0.65) in PUBCHEM_MMFF94_PARTIAL_CHARGES data
Error reading CID_71739_1183b00000003_conf.sdf: Non-numeric charge (1 -0.36) in PUBCHEM_MMFF94_PARTIAL_CHARGES data _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Conrad Huang -
Eric Pettersen -
Jon Fuller