Usually externaly provided has pecedent over library routine .. you need to label any "amino-acid" as a peptide though to generate the required links in the protein chain. E
On Wed, 3 Apr 2019 at 16:09, <herman.schreu...@sanofi.com> wrote: > Dear Deniz, > > > > In the past, I had similar problems caused by the fact that when the > residue was “known” to ccp4, it would use the cif file from the ccp4 > library instead of the cif I had created myself. You could check if this > might be the case for you. You find the cif files under > $CCP4/lib/data/monomers in the subdirectory with the first letter of the > three-letter code of your ligand and check the CIF file with the same > three-letter code as you are using. > > However, it is possible that the ccp4 developers have resolved this issue > by letting an externally provided cif file override the internal cif file. > > > > Best, > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *"Deniz Üresin" > *Gesendet:* Mittwoch, 3. April 2019 13:15 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid > > > > Hello, > > I'm trying to refine the structure of a protein mutant that has an > unnatural amino acid in it. I created a restraint file for the AA and the > mutation worked fine in COOT. But when I use refmac5 for refinement, it > always changes the bond angle in the sidechain (an azide group, which > should have a bond angle of 180°). I set the SD of the angle to 0 but that > didn't help (the "refined" bond angle ends up somewhere between 120 and > 150°). > > Is there any other way to tell refmac5 to not alter that bond angle? > > Thanks in advance, > > Deniz Üresin > > > > _________ > > Deniz Üresin > > Institut für Biophysik > > Johann Wolfgang Goethe-Universität Frankfurt am Main > http://www.biophys.uni-frankfurt.de/~bredenbeck/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.biophys.uni-2Dfrankfurt.de_-7Ebredenbeck_&d=DwQBaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=VtXRbdKIg1WYPonFVekLyaS7tddwvCN3GUFjoukTqZQ&s=G3I19eTY_QBcb4mWr52acreOcEN42kvJGGwG5bK06hs&e=> > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMBaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=VtXRbdKIg1WYPonFVekLyaS7tddwvCN3GUFjoukTqZQ&s=vcOJNVs7sUJdzV2GEgVnQhdpOBeVAQHSPPA8XH7lP7A&e=> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
