Re: [ccp4bb] Off-topic, visualization
Rasmol has always done this. Just use slab … best wishes Pete On 5 Sep 2013, at 21:30, Arthur Glasfeld glasf...@reed.edu 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 same color as the surface. An example of what I'm after can be found here: people.reed.edu/~glasfeld/xsection.jpg Does anyone know of any software that can produce similar images? Thanks, Arthur Glasfeld Reed College Portland, OR Prof Peter Artymiuk Krebs Institute Department of Molecular Biology Biotechnology University of Sheffield Sheffield S10 2TN ENGLAND
[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
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
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 faisaltari...@gmail.comwrote: 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
[ccp4bb] how to improve experimental phase by combining partial homology models
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 be found using Phaser. My native data is 3.5 A. Can I combine the experimental phase and homology model to improve electron density? Is there anybody can help find which program can work on this? Thank you. Lisa
