Re: [PyMOL] PyMol Question

Mohsen– set transparency , .5, sele Cheers, Spencer On Tue, Nov 3, 2015 at 3:18 AM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi there, > > > > I was wondering how I can make the surface of a selected part of a protein > transparent?

[PyMOL] PyMol Question

Hi there, I was wondering how I can make the surface of a selected part of a protein transparent? I tried transparency command, but, I came up with a message that "transparency" was not found. Thank you --

Re: [PyMOL] pymol question

Hi, You can draw a CGO circle in the yz plane using: x1,y1,z1 = -0.1, 0, 0 # start point r1,g1,b1 = 1,0,0 # color (red) x2,y2,z2 = 0.1, 0, 0 # end point r2,g2,b2 = 1,1,0 # color (yellow) radius = 10 cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], cylinder1 ) To

[PyMOL] pymol question

Does anyone know how to draw a circle with a given radius in pymol? I have a distance that I want to use to see what residues lie on the end of that radius, but I have no idea how to write the command to draw the circle. Could someone help me please?

Re: [PyMOL] pymol question

I'm sure there's a way to actually draw a circle, but for your particular use it might be better to use a sphere. If you're comfortable with python scripting, you can use CGO objects. If not, you might do something like this: fetch 1hhp create thing, resi 24 and name ca # create a new object from

Re: [PyMOL] PyMol question?

Hi, You can do this using alter_state: alter_state 1,selection,(x,y,z) = (a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2, a31*x+a32*y+a33*z+d3) where a11-a33 are the matrix elements (check whether they have to be transposed) and d1-d3 are the elements of the shift vector. It may

Re: [PyMOL] PyMol question?

Hi Mark: Most likely there is, but I don't know the answer to your question. I'm posting this to the pymol users list (via cc) so hopefully someone else will know the answer. I trust all is going well for you. Bill On Jun 30, 2006, at 8:19 AM, Mark Collins wrote: Hi Bill, I've been

Re: [PyMOL] PyMol question?

The easiest way I'm aware of to do this would be to use the ccp4 program pdbset, but there are numerous other ways/programs that will do this (if pymol has this capacity, I'm not aware of it; but someone else will correct me). Pete snip I've been looking through the PyMol reference and wiki

[PyMOL] PyMOL] question about electrostatic maps

Hi Qun, And here is some more useful information. http://www-personal.umich.edu/~mlerner/Pymol/ Ciao, Scott On Aug 4, 2004, at 8:55 AM, Qun Wan wrote: Hi, I want to get electrostatic map of my protein, which need APBS installation. However, I have a PC with platform of windows XP and a mac