[ccp4bb] engh huber
To what extent modern geometric restraints have been upgraded over original EnghHuber? And where I can find a consensus set of values (with variances)? For example, Fisher et al., Acta D68:800 discusses how histidine angles change with protonation, and refers to EnghHuber when it says that ND1-CE1-NE2 goes from 111.2 to 107.5 when histidine acquires positive charge (Fig.6). But angle table (Table 3) in original EnghHuber from 1991 does not have any 107.5 value and seems to suggest that the numbers should rather be 111.7+-1.3 and 108.4+-1.0, respectively. I understand that these values are derived from structural databases and thus can be frequently updated. Is there some resource where most current values would be listed? Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] engh huber
Hi Ed, Chapter 18.3 of international tables vol F includes values designated EH99 which are from a more recent CSD release than the original 1991 Engh Huber paper. R. A. Engh and R. Huber. Structure quality and target parameters. International Tables for Crystallography (2012). Vol. F, ch. 18.3, pp. 474-484 doi: 10.1107/9780955360206857 http://it.iucr.org/Fb/ch18o3v0001/ Also, the Buster groups' Grade server provides dynamic use of the CSD database to derive restraints. http://grade.globalphasing.org And the PURY restraint database has restraints derived from recent CSD releases. I belive it requires a current CSD license is required for use. http://pury.ijs.si/ Regards, Mitch -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed Pozharski Sent: Monday, January 14, 2013 9:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] engh huber To what extent modern geometric restraints have been upgraded over original EnghHuber? And where I can find a consensus set of values (with variances)? For example, Fisher et al., Acta D68:800 discusses how histidine angles change with protonation, and refers to EnghHuber when it says that ND1-CE1-NE2 goes from 111.2 to 107.5 when histidine acquires positive charge (Fig.6). But angle table (Table 3) in original EnghHuber from 1991 does not have any 107.5 value and seems to suggest that the numbers should rather be 111.7+-1.3 and 108.4+-1.0, respectively. I understand that these values are derived from structural databases and thus can be frequently updated. Is there some resource where most current values would be listed? Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] engh huber
There was an update by EH in 2001 in the International Tables Vol F. There are a small number of modifications to the 1991 values in the update as well as the addition of several conformational variabilities. If I understand correctly, Refmac and Phenix use the 2001 values, with the only conformational variability being some changes with cis-peptide bonds. Shelxl still uses EH 1991. Dale Tronrud On 01/14/13 09:54, Ed Pozharski wrote: To what extent modern geometric restraints have been upgraded over original EnghHuber? And where I can find a consensus set of values (with variances)? For example, Fisher et al., Acta D68:800 discusses how histidine angles change with protonation, and refers to EnghHuber when it says that ND1-CE1-NE2 goes from 111.2 to 107.5 when histidine acquires positive charge (Fig.6). But angle table (Table 3) in original EnghHuber from 1991 does not have any 107.5 value and seems to suggest that the numbers should rather be 111.7+-1.3 and 108.4+-1.0, respectively. I understand that these values are derived from structural databases and thus can be frequently updated. Is there some resource where most current values would be listed? Cheers, Ed.
Re: [ccp4bb] engh huber
Article in the Tables is the answer to my question about the latest EnghHuber parameters. These still don't match Fig.6 from Fisher, but I am OK with using Tables for my internal purposes. Thanks to Mitchell and Dale for prompt response. Cheers, Ed. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
