Re: [ccp4bb] Problem with making PDB from Coot
Seconday structure assignement by Pymol is poor and unreliable to say the least. This behavior is very common. Best is to assign secondary structure using other software and then tell Pymol explicitely from where to where the starnds and helices run Remy Loris Vriej universiteit Brussel On 23/07/12 23:46, meisam nosrati wrote: Dear CCP4ers It seems like the text has not showed up, but I have a problem with making pdbs from coot. As I refine my structure ( with MR solution ) the beta sheets become loops while H-bondings are still there. I am not sure, if the problem is originating from making PDBs from coot. I will appriciate your help Meisam On Mon, Jul 23, 2012 at 5:31 PM, Meisam Nosrati meisam.nosr...@gmail.com mailto:meisam.nosr...@gmail.com wrote:
Re: [ccp4bb] Problem with making PDB from Coot
You should type Dss into pymol and this will assign more appropriate secondary structure From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of meisam nosrati Sent: Tuesday, 24 July 2012 9:47 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problem with making PDB from Coot Dear CCP4ers It seems like the text has not showed up, but I have a problem with making pdbs from coot. As I refine my structure ( with MR solution ) the beta sheets become loops while H-bondings are still there. I am not sure, if the problem is originating from making PDBs from coot. I will appriciate your help Meisam On Mon, Jul 23, 2012 at 5:31 PM, Meisam Nosrati meisam.nosr...@gmail.commailto:meisam.nosr...@gmail.com wrote:
Re: [ccp4bb] Problem with making PDB from Coot
Dear CCP4ers It seems like the text has not showed up, but I have a problem with making pdbs from coot. As I refine my structure ( with MR solution ) the beta sheets become loops while H-bondings are still there. I am not sure, if the problem is originating from making PDBs from coot. I will appriciate your help Meisam On Mon, Jul 23, 2012 at 5:31 PM, Meisam Nosrati meisam.nosr...@gmail.comwrote:
Re: [ccp4bb] Problem with making PDB from Coot
On 23/07/12 22:46, meisam nosrati wrote: Dear CCP4ers It seems like the text has not showed up, but I have a problem with making pdbs from coot. As I refine my structure ( with MR solution ) the beta sheets become loops while H-bondings are still there. I am not sure, if the problem is originating from making PDBs from coot. I will appriciate your help It is not clear to me what the problem is or if there is a problem with Coot at all. If you read in the model and write it out again are the beta sheets still present? You say refine - do you mean you refine with Coot? Let's presume that you do. So my guess is that you move the atoms so that they better fit the density and (quite probably) don't have beta sheet restraints. Thus the atoms have moved sufficiently so that DSSP (or whatever algorithm you use to detect SS) no longer recognises those residues as beta strands... OK... You want secondary structure to be preserved when you refine with Coot? Try adding beta strand restraints or initial position restraints or user-defined inter-strand restraints or use ProSMART's additional bond restraints. Paul.
