[ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jodie, except for the matter if there is 'right' and 'wrong' in science or rather 'good' and 'bad' models, Garib Murshudov maintains the cif-library and if you send him a compilation of possible fixes he would surely appreciate your input. Best, Tim On 10/29/2013 10:15 AM, Jodie Johnston wrote: Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ EfmUgIVb9xKGdzmxSaRsBbw= =7+vC -END PGP SIGNATURE-
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
There are errors in every branch of human endeavour I am sure! Please if you find something wrong. send your suggested correction to Garib Paul, and once there is a fix notify us all via the BB. CCP4 has always depended heavily on the users noticing the bugs Thank you for your observation. Eleanor On 29 October 2013 10:21, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jodie, except for the matter if there is 'right' and 'wrong' in science or rather 'good' and 'bad' models, Garib Murshudov maintains the cif-library and if you send him a compilation of possible fixes he would surely appreciate your input. Best, Tim On 10/29/2013 10:15 AM, Jodie Johnston wrote: Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ EfmUgIVb9xKGdzmxSaRsBbw= =7+vC -END PGP SIGNATURE-
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Thanks Jodie From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Tuesday, 29 October 2013 11:51 p.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ? There are errors in every branch of human endeavour I am sure! Please if you find something wrong. send your suggested correction to Garib Paul, and once there is a fix notify us all via the BB. CCP4 has always depended heavily on the users noticing the bugs Thank you for your observation. Eleanor On 29 October 2013 10:21, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Jodie, except for the matter if there is 'right' and 'wrong' in science or rather 'good' and 'bad' models, Garib Murshudov maintains the cif-library and if you send him a compilation of possible fixes he would surely appreciate your input. Best, Tim On 10/29/2013 10:15 AM, Jodie Johnston wrote: Hi I wanted to check is it possible that there could be errors in the library cif files associated with CCP4 and coot ? I have noticed a couple of potential errors in a ligand cif file from the CCP4 library. Perhaps it is my error - I shall need to triple check it again but, if it appears not to be, is it possible to talk to someone about correcting the cif file ? Many Thanks Jodie - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSb4wRUxlJ7aRr7hoRAu21AJ9u78CgI0EV2shsvQS7ghl1FbddxwCgjxfJ EfmUgIVb9xKGdzmxSaRsBbw= =7+vC -END PGP SIGNATURE-
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
On 29/10/13 06:54, Jodie Johnston wrote: Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Make suer that you are using the latest dictionary (of course) http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.html P.
Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ?
Can the fixes in the CCP4 dictionary be rolled out through the update system of CCP4? That way we can avoid (at least to some extent) that people keep working with erroneous restraint files. Some of these errors can really mess up your structure. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Emsley Sent: Tuesday, October 29, 2013 17:43 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Is it possible for a ligand cif file from the CCP4 library to contain errors ? On 29/10/13 06:54, Jodie Johnston wrote: Thanks Everyone for your input I shall triple check my reasoning tomorrow and email Garib if I do think there is an issue. Make suer that you are using the latest dictionary (of course) http://www2.mrc- lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/dictionary.ht ml P.
