Re: [ccp4bb] secondary structure assignment to sequence

vember 13, 2024 16:23 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] secondary structure assignment to sequence > > > > Presumably DSSP is still available - > > > > https://swift.cmbi.umcn.nl/gv/dssp/ > > > > Harry > > > >

Re: [ccp4bb] secondary structure assignment to sequence

@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] secondary structure assignment to sequence > > Presumably DSSP is still available - > > https://swift.cmbi.umcn.nl/gv/dssp/ > > Harry > > > On 13 Nov 2024, at 12:18, Marc Graille > wrote: > > > > Dear Vitali

Re: [ccp4bb] secondary structure assignment to sequence

Presumably DSSP is still available - https://swift.cmbi.umcn.nl/gv/dssp/ Harry > On 13 Nov 2024, at 12:18, Marc Graille wrote: > > Dear Vitali, > > I used to do it with Stride server. > > Stride > wzw.tum.de > > > > Hope this helps, > > Best wishes, > > Marc > > > — > Marc GR

Re: [ccp4bb] secondary structure assignment to sequence

Dear Vitali, I used to do it with Stride server. https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py Hope this helps, Best wishes, Marc https://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py — Marc GRAILLE, PhD DR1-CNRS Head of the team: “Translation and degradation of eukaryotic mR

[ccp4bb] secondary structure assignment to sequence

Dear User, Is there any tool that can assign the secondary structure to the sequence of protein in the PDB. In the past I have used a 2Struc: the secondary structure server, but it's not available any more. Is there any easy way to list the sequence and ss below the sequence of provided PDB models

Re: [ccp4bb] !SPAM: [ccp4bb] secondary structure assignment to PDB file

As I understood the problem, it is that automatic assignment comes out differently for different structures of the same protein or proteins so close that they should have the same secondary structure, due to differences in quality of the structures. The question then is not how to determine sec

Re: [ccp4bb] !SPAM: [ccp4bb] secondary structure assignment to PDB file

Dear J. Vitali, there are tools that have been mentioned by others, that assist with the assignment. The final decision depends on you as researcher. You should visually check the hydrogen bonding whether the boundaries are consistent with the automated assignment. People often seem to think t

Re: [ccp4bb] secondary structure assignment to PDB file

*Sent:* 29 January 2017 10:41 *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:* [ccp4bb] secondary structure assignment to PDB file Hi Is there any tool that can assign secondary structure to the PDB file. The problem is if I used different modelling tools,

Re: [ccp4bb] secondary structure assignment to PDB file

-- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of chemocev > marker [jirivit...@gmail.com] > *Sent:* 29 January 2017 10:41 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] secondary structure assignment to PDB file > > Hi > Is there any t

Re: [ccp4bb] secondary structure assignment to PDB file

anuary 2017 10:41 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] secondary structure assignment to PDB file Hi Is there any tool that can assign secondary structure to the PDB file. The problem is if I used different modelling tools, there are regions in the protein which does not remain consi

[ccp4bb] secondary structure assignment to PDB file

Hi Is there any tool that can assign secondary structure to the PDB file. The problem is if I used different modelling tools, there are regions in the protein which does not remain consistent and looks different in different application. best J. Vitali

[ccp4bb] Secondary structure assignment

When I was checking a structure and preparing figures for an upcoming article, I found out that Procheck and Pymol use different criteria to assign secondary structure for residues in a PDB (i.e.: some residues that appeared as loops in the cartoon representation in pymol were assigned as beta-stra