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 Company 180

Re: [PyMOL] Strange pattern on the cartoon representation

) 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 Message- From: Tsjerk Wassenaar

Re: [PyMOL] Principal Axes of Rotation

-- 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 Confidentiality Note: This e-mail, and any attachment to it, contains privileged

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

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 Confidentiality Note: This e-mail, and any attachment to it, contains privileged

Re: [PyMOL] rotating maps ??

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 intended only

Re: [PyMOL] Sequence Viewer Details

, 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, NY 10014 phone:(917)606-4116 fax:(212)645-2054

Re: [PyMOL] Transparent cartoon disapearing with ray trace

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 New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any

Re: [PyMOL] Surface Edge

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, and any attachment to it, contains privileged and confidential information

Re: [PyMOL] Depth buffer and close surfaces

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 floor New York, NY 10014 Confidentiality Note: This e-mail, and any

Re: [PyMOL] run out of memory problem

to Quality. You may be able to reduce the quality a bit without noticeably affecting the image and it should reduce memory usage. Reducing the size of the raytraced image will also reduce memory usage, but of course your image will be smaller... Hope these suggestions help, Matt -- Matthew

Re: [PyMOL] resize viewing window

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 similar.) - Matt -- Matthew Franklin phone:(917)606-4116

Re: [PyMOL] Atom type selection with the *

* 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 atom C5* but not C5M. Thanks, Matt -- Matthew Franklin phone:(917)606-4116 Senior Scientist, ImClone

Re: [PyMOL] selection disordered

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 Note: This e-mail, and any attachment to it, contains privileged

Re: [PyMOL] Ray, 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 Franklin phone:(917)606-4116 Senior Scientist, ImClone Systems fax:(212)645-2054 180 Varick

Re: [PyMOL] Setting sphere_transparency for individual selections

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 fax:(212)645-2054 180 Varick Street, 6th