[PyMOL] non-pdb coordinate help

I have several txt files of coordinates (mostly heme type compounds) that I'd like to format correctly for pymol to be able to read. I've tried several things looking at PDBs with hemes, but can't figure it out. Will someone with more experience please show me how this should be formatted for

[PyMOL] distance from plane

Hi Pymolers! Is there a way for me to define a plane of atoms say 4 Nitrogens in a heme complex and then determine how far out-of-plane the Fe atom is? If so either in Pymol or another program I'd love to know the secret. Thanks, Kristl kri...@physics.purdue.edu

[PyMOL] cartoon transparent?

It there a way to make the cartoon round helixes transparent? The transparency command doesn't seem to work on cartoon. Thanks, Kristl kri...@physics.purdue.edu

[PyMOL] PDB SS Question

Following question concerns Secondary Structure of hemoglobin pdb 1BZ0 If the PDB comes with HELIX information do I still need to add the secondary structure from the web (http://www.mbfys.lu.se/Services/SecStr/)? They are different, especially at the ends of the helixes ... the web SS seems to h

[PyMOL] bond cut-off

Anyone know how to increase the bond drawing cut-off? I'm trying to get Pymol to draw bonds from the Fe to the N atoms in a heme group. Thanks in advance, Kristl kri...@physics.purdue.edu

Re: [PyMOL] Setting light direction in ray traced images

You can go to Settings - Edit all and change the vetor of the light ... you may also want to increase direct -- light coming from camera shot or ambient light. Check out pg 32 and 33 in the online manual (Ray-Tracing section). Do you know if I can add an additional light and how to do that? Thank

[PyMOL] Poyray / windows

Is it possible to output a Pymol file that Povray can read using windows? Also is it possible to add lights into a Pymol file? Thanks, Kristl

[PyMOL] settings of ribbons and cartoons

Where can I find a list of what I can set with regard to ribbons and cartoons. Currently the cartoons command just shows a thin round tube and the ribbons command shows just a thin line. I'd ideally like to have cartoonishly round ribbons with some of the residues on them drawn in sticks. I'm a

[PyMOL] moving/fitting

I'd like to fit the porphyrin of the alpha subunit of Hemoglobin on top of the porphyrin of myoglobin ( in order to compare the heme pockets ). I am a new user of Pymol and have been fiddling with it to become familiar, but am having no luck in this area. Please send any useful hints my way. Tha