Re: [ccp4bb] visualizing G310 helices in PYMOL
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Faisal, none of the secondary structure prediction programs are perfect (although dssp is pretty good). This means you should always check the predictions yourself, at least at the boundaries of helices and beta-strands and then fine-tune the graphics programs. Best, Tim On 09/26/2013 10:02 PM, Faisal Tarique wrote: > Dear all > > Sorry for the off topic question. > > My protein has few G310 helices. It is clearly visible through > STRIDE or DSSP, but when i open the structure in PYMOL it didnt > show it. Other visualization graphics like CHIMERA and VMD are > able to pick few of them but not all the G310 helices..For > manuscript preparation i have drawn the topology diagram taking the > output from STRIDE and DSSP while the overall 3D structure is from > PYMOL..Will it be O.K to show some helices missing from the output > of pymol while they are present in the toplogy diagrma ? or the > reviewer will raise the issue? hope you are able to understand what > i mean to say. > > Please suggest me > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFSRKTKUxlJ7aRr7hoRAllFAJ0Sr7afo0Aqr2CgC2NttSnvpSLczgCg1zSg lHem+ve2eguHUlEHx+TgEQo= =734N -END PGP SIGNATURE-
Re: [ccp4bb] visualizing G310 helices in PYMOL
Thanx to all Your suggestions really worked and solved my problem. regards Faisal On Fri, Sep 27, 2013 at 2:08 AM, Parthasarathy Sampathkumar < spart...@gmail.com> wrote: > Hi Faisal, > > you could run dssp2pdb by James Stroud ( > http://www.jamesstroud.com/software/dssp2pdb/ ) to convert dssp output > into PDB readable format as part of the header. When you open resultant PDB > in PyMOL, secondary structure as defined by dssp would be displayed. > > OR > > one could also define secondary structure in PyMOL manually (see at the > end of this link: > http://pymol.sourceforge.net/newman/user/S0260cartoons.html) > > HTH, > Partha > > > On Thu, Sep 26, 2013 at 4:02 PM, Faisal Tarique > wrote: > >> >> Dear all >> >> Sorry for the off topic question. >> >> My protein has few G310 helices. It is clearly visible through STRIDE or >> DSSP, but when i open the structure in PYMOL it didnt show it. Other >> visualization graphics like CHIMERA and VMD are able to pick few of them >> but not all the G310 helices..For manuscript preparation i have drawn the >> topology diagram taking the output from STRIDE and DSSP while the overall >> 3D structure is from PYMOL..Will it be O.K to show some helices missing >> from the output of pymol while they are present in the toplogy diagrma ? or >> the reviewer will raise the issue? hope you are able to understand what i >> mean to say. >> >> Please suggest me >> >> -- >> Regards >> >> Faisal >> School of Life Sciences >> JNU >> > > -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] visualizing G310 helices in PYMOL
Hi Faisal, you could run dssp2pdb by James Stroud ( http://www.jamesstroud.com/software/dssp2pdb/ ) to convert dssp output into PDB readable format as part of the header. When you open resultant PDB in PyMOL, secondary structure as defined by dssp would be displayed. OR one could also define secondary structure in PyMOL manually (see at the end of this link: http://pymol.sourceforge.net/newman/user/S0260cartoons.html) HTH, Partha On Thu, Sep 26, 2013 at 4:02 PM, Faisal Tarique wrote: > > Dear all > > Sorry for the off topic question. > > My protein has few G310 helices. It is clearly visible through STRIDE or > DSSP, but when i open the structure in PYMOL it didnt show it. Other > visualization graphics like CHIMERA and VMD are able to pick few of them > but not all the G310 helices..For manuscript preparation i have drawn the > topology diagram taking the output from STRIDE and DSSP while the overall > 3D structure is from PYMOL..Will it be O.K to show some helices missing > from the output of pymol while they are present in the toplogy diagrma ? or > the reviewer will raise the issue? hope you are able to understand what i > mean to say. > > Please suggest me > > -- > Regards > > Faisal > School of Life Sciences > JNU >
Re: [ccp4bb] visualizing G310 helices in PYMOL
Dear Faisal, I usually assign in PYMOL the secondary structure generally obeying DSSP output. You have to use the alter command. eg: alter myprotein and resi 103:106, ss='H' Bytheway, pymol swaps inside and outside color on left handed helices, wich you might also have. Hope this helps, Matthias - Dr. Matthias Zebisch Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK Phone (+44) 1865 287549; Fax (+44) 1865 287547 Email matth...@strubi.ox.ac.uk Website http://www.strubi.ox.ac.uk - On 9/26/2013 9:02 PM, Faisal Tarique wrote: Dear all Sorry for the off topic question. My protein has few G310 helices. It is clearly visible through STRIDE or DSSP, but when i open the structure in PYMOL it didnt show it. Other visualization graphics like CHIMERA and VMD are able to pick few of them but not all the G310 helices..For manuscript preparation i have drawn the topology diagram taking the output from STRIDE and DSSP while the overall 3D structure is from PYMOL..Will it be O.K to show some helices missing from the output of pymol while they are present in the toplogy diagrma ? or the reviewer will raise the issue? hope you are able to understand what i mean to say. Please suggest me -- Regards Faisal School of Life Sciences JNU
[ccp4bb] visualizing G310 helices in PYMOL
Dear all Sorry for the off topic question. My protein has few G310 helices. It is clearly visible through STRIDE or DSSP, but when i open the structure in PYMOL it didnt show it. Other visualization graphics like CHIMERA and VMD are able to pick few of them but not all the G310 helices..For manuscript preparation i have drawn the topology diagram taking the output from STRIDE and DSSP while the overall 3D structure is from PYMOL..Will it be O.K to show some helices missing from the output of pymol while they are present in the toplogy diagrma ? or the reviewer will raise the issue? hope you are able to understand what i mean to say. Please suggest me -- Regards Faisal School of Life Sciences JNU
