Re: [PyMOL] stick transparency

(I'm putting this back on-list) That's too bad. It worked for me: PyMOL 1.2r2, Windows XP. Can you set other properties of this object: color, stick_radius, etc.? - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly &am

Re: [PyMOL] Strange pattern on the cartoon representation

turned on and with colors different enough that you can see the speckling. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 From: Af

Re: [PyMOL] Strange pattern on the cartoon representation

yMOL viewer) and the effect should go away. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 > -Original

Re: [PyMOL] Smooth fading of surface in movie?

you'll have a series of image files showing the fade. I recommend using Quicktime Pro to fuse them into a movie - it only costs $30, and it's easy to use for this purpose. Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidi

Re: [PyMOL] Principal Axes of Rotation

thoscopic view". That should eliminate your "wobble effect". Hope that helps, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly & Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116

Re: [PyMOL] another odd PyMOL question....

e color name for the color you're looking at - maybe there's a way of getting the RGB values for an atom? - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiali

Re: [PyMOL] rotating "maps" ??

ng seems to move. HTH, Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intend

Re: [PyMOL] Sequence Viewer Details

of info for the sequence viewer, but the "red zeros" you're probably referring to are actually the letter O, and represent the oxygen of water molecules in the pdb file. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor New York, N

Re: [PyMOL] morphing between complexes

ovies in Pymol. For making movies in complicated situations like this, I've usually used script files to explicitly define each frame of the movie: load file1.pdb (rendering commands) ray 2400,2400 png frame1.png delete file1 load file2.pdb etc... You get a long script file, but you can use a te

Re: [PyMOL] Ligand Surface Representation

d. > > Simon > > > > > On Nov 2, 2006, at 3:53 PM, Nicholas Noinaj wrote: > > > can you get a surface for the protein-ligand complex? > > > > > > > > cheers, > > nick > > > > -- Matthew Franklin , Ph.D. Senior Scientist, ImClo

Re: [PyMOL] Transparent cartoon disapearing with ray trace

ust confirmed that this works. I find the results a bit busy, unless you're looking at just a small part of the protein. You may need to hide background details with the clipping planes. - Matt -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems 180 Varick Street, 6th floor

Re: [PyMOL] Surface Edge

your red triangles will fade into the semi-transparent gray surface. Hope that helps, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mail, an

Re: [PyMOL] Depth buffer and close surfaces

just produces mottled surfaces - one triangle of one color next to a triangle of the other color. Could you post a link to a picture of the artifacts? - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th f

Re: [PyMOL] run out of memory problem

memory usage, but of course your image will be smaller... Hope these suggestions help, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note: This e-mai

Re: [PyMOL] Atom type selection with the *

996 1.00 44.69 O HETATM 8027 C2* TTP 1 2.084 51.848 16.841 1.00 33.48 C HETATM 8028 C1* TTP 1 0.693 51.871 17.477 1.00 33.26 C So watch out! Warren - is there a way of escaping the "*" if you want to use it for selection? Let's say I wanted ato

Re: [PyMOL] resize viewing window

l image. This command behaves erratically if you try to draw the window larger than your screen will allow, and you can't save (in OpenGL mode) the parts of the image that are offscreen, so don't do that. (If you need a big image for publication, type 'ray 2000,2000' or something

Re: [PyMOL] ball-and-sticks, controlling bond color

d-stick of one chain where the balls are all green and the sticks are all gray. Modify as needed - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality Note:

Re: [PyMOL] selection disordered

esidues 429-430 in chain B are also occupancy 0 - what do you see if you run your script on chain B? - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick Street, 6th floor New York, NY 10014 Confidentiality

Re: [PyMOL] Ray, png

id - I usually just write a temporary png image to get the viewport dimensions, i.e. PyMOL>png junk.png ScenePNG: wrote 640x480 pixel image to file "junk.png". As long as you haven't just executed a raytracing, the png dimensions are the viewport dimensions. - Matt -- Matthew

Re: [PyMOL] Setting sphere_transparency for individual selections

ontaining only the atoms of interest and set sphere transparency on it, like so: PyMOL> load test.pdb PyMOL> create foo, HETATM and name COO PyMOL> set sphere_transparency,0.4,foo - Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems f