[ccp4bb] how to improve experimental phase by combining partial homology models

2013-09-26 Thread LISA
Dear all, I am now working on a very low resolution phase determination (around 4.5A with hg anomalous signal around 5.5 A). I can find the Hg sites and get the phase, but the density map is not so good. Two components of my protein complex (about 1/3) has a homologue model which is also can not

Re: [ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Tim Gruene
-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 gra

Re: [ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Faisal Tarique
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 ds

Re: [ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Parthasarathy Sampathkumar
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 sec

Re: [ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Matthias Zebisch
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, Ma

[ccp4bb] visualizing G310 helices in PYMOL

2013-09-26 Thread Faisal Tarique
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 manu

Re: [ccp4bb] Off-topic, visualization

2013-09-26 Thread Peter Artymiuk
Rasmol has always done this. Just use slab … best wishes Pete On 5 Sep 2013, at 21:30, Arthur Glasfeld wrote: > I am hoping to create some images of protein cross-sections where the atoms > are depicted as spheres, and the spheres that are "cut" by the slab are shown > as solids with the s