[ccp4bb] creat a model with insertion
Dear all, I have the wt protein structure that contains two domains. I want to creat a model with two glycerin inserted between the two domains. Which software or webserver could do this? Pls help. Qing Chen
Re: [ccp4bb] creat a model with insertion
use coot: calculate - model/fit/refine - add terminal residue. this will add alanines. you can change these to glycines with the simple mutate option in the same pop up menu. best, HErman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Qing Chen Sent: Thursday, January 13, 2011 11:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] creat a model with insertion Dear all, I have the wt protein structure that contains two domains. I want to creat a model with two glycerin inserted between the two domains. Which software or webserver could do this? Pls help. Qing Chen
Re: [ccp4bb] creat a model with insertion
Let's say I need to insert two G between resi 98 and 99. I tried in the way as Herman suggest: break the chain in the domain boundary, add terminal residues at the N-terminus of the 2nd domain. But then there is no space to accommodate the inserted residues, the two glycerin backbones overlap with resi 97 and 98. Is there a way to shift the whole 1st domain a bit ? On Thu, Jan 13, 2011 at 12:16 PM, wrote: > use coot: calculate - model/fit/refine - add terminal residue. > this will add alanines. you can change these to glycines with the simple > mutate option in the same pop up menu. > > best, > HErman > > -- > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Qing > Chen > *Sent:* Thursday, January 13, 2011 11:58 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] creat a model with insertion > > Dear all, > > I have the wt protein structure that contains two domains. I want to creat > a model with two glycerin inserted between the two domains. > Which software or webserver could do this? > Pls help. > > > Qing Chen > >
Re: [ccp4bb] creat a model with insertion
In that case, I would split your pdb file in two parts: Nterm to 101 and 99 to Cterm. With the rotate/translate zone option, you can move one complete domain to have residue 101 of the Nterm domain overlap with residue 99 of the Cterm domain. In a nex step you will have to delete residue 101 of the Nterm domain, which was only there as a help for the superposition, mutate residues 99 and 100 of the Nterm domain to glycine, renumber the Cterm to start at 101 and combine both pdb files again. Finally, you will have to regularize the link. Best, Herman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Qing Chen Sent: Thursday, January 13, 2011 12:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] creat a model with insertion Let's say I need to insert two G between resi 98 and 99. I tried in the way as Herman suggest: break the chain in the domain boundary, add terminal residues at the N-terminus of the 2nd domain. But then there is no space to accommodate the inserted residues, the two glycerin backbones overlap with resi 97 and 98. Is there a way to shift the whole 1st domain a bit ? On Thu, Jan 13, 2011 at 12:16 PM, wrote: use coot: calculate - model/fit/refine - add terminal residue. this will add alanines. you can change these to glycines with the simple mutate option in the same pop up menu. best, HErman From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Qing Chen Sent: Thursday, January 13, 2011 11:58 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] creat a model with insertion Dear all, I have the wt protein structure that contains two domains. I want to creat a model with two glycerin inserted between the two domains. Which software or webserver could do this? Pls help. Qing Chen
Re: [ccp4bb] creat a model with insertion
Hello Qing Chen, if by 'shift' you mean the actual coordinates you can do in coot as Herman describes. If you want to shift the sequence numbering: Coot also has an option to renumber a sequence by an offset and the offset can also be negative. Cheers, Tim On Thu, Jan 13, 2011 at 12:27:49PM +0100, Qing Chen wrote: > Let's say I need to insert two G between resi 98 and 99. I tried in the way > as Herman suggest: break the chain in the domain boundary, add terminal > residues at the N-terminus of the 2nd domain. But then there is no space to > accommodate the inserted residues, the two glycerin backbones overlap with > resi 97 and 98. Is there a way to shift the whole 1st domain a bit ? > > > > On Thu, Jan 13, 2011 at 12:16 PM, wrote: > > > use coot: calculate - model/fit/refine - add terminal residue. > > this will add alanines. you can change these to glycines with the simple > > mutate option in the same pop up menu. > > > > best, > > HErman > > > > -- > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > > *Qing > > Chen > > *Sent:* Thursday, January 13, 2011 11:58 AM > > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* [ccp4bb] creat a model with insertion > > > > Dear all, > > > > I have the wt protein structure that contains two domains. I want to creat > > a model with two glycerin inserted between the two domains. > > Which software or webserver could do this? > > Pls help. > > > > > > Qing Chen > > > > -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] creat a model with insertion
Hi Chen, Check SPDBViewer if it is of some help to you! Gauri On Thu, Jan 13, 2011 at 5:57 AM, Qing Chen wrote: > Dear all, > > I have the wt protein structure that contains two domains. I want to creat > a model with two glycerin inserted between the two domains. > Which software or webserver could do this? > Pls help. > > > Qing Chen >
