Re: [PyMOL] effect of number of pixels on ray image quality

Thanks very much to all who answered, for the detailed and helpful responses to my questions. Yvonne

Re: [PyMOL] selection help + align question

Thanks for that one; it works as advertised. Another question: if I have 10 different structures read into PyMOL, what is the best (most accurate) method for aligning the structures as an ensemble? Currently, I'm aligning all to the first structure read in (i.e. 2>1, 3>1, etc.) using a for l

RE: [PyMOL] selection help

Doug, Setwise logical ANDs and ORs are tricky at first. In this case, you want to create a new set that contains atoms in a1 *or* a2. There aren't any atoms that are in both a1 and a2 which is why you're ending up with an empty object. create one, a1 or a2 Cheers, Warren -- Warren L. DeLa

[PyMOL] electrostatics in MacPyMol

Thanks to all for the help on recent topics. I'm now making beautiful movies (my eye being that of the beholder), and learning a lot more about the protein I study. I'm using MacPyMol and can't find a replacement for the Windows "generate vacuum electrostatics" command. Apparently I can't insta

[PyMOL] selection help

Hi All- I'm having some problems with selection syntax w/ multiple objects. I've loaded four different PDB files (in sequence & structure): load 1.pdb, a1 load 2.pdb, a2 load 3.pdb, b1 load 4.pdb, b2 I wanted to create two new selections: one = a1 & a2 two = b1 & b2 I've

Re: [PyMOL] effect of number of pixels on ray image quality

On Thursday 20 January 2005 15:37, yvonne leduc wrote: > [snip] > And the reason for all this is ... > ... is a *.png image created with ray 1000,750 going to be good enough > for publication standards? Is there much benefit in going higher? what > causes the limits, if any? Journals typically d

Re: [PyMOL] effect of number of pixels on ray image quality

yvonne leduc wrote: I would like some confirmation or explanation about the differences I see, and the way I understand it. Hello Yvonne, The command "ray" does not care about the size of your display, it may even be used in batch mode on a computer that does not have a monitor attached to it

[PyMOL] how do I color specific residues

Hello, I am trying to learn PyMOL and doesn't know any programming. I am working with a file from pdb (1HPV). I would like to color specific residues. Basically I have trouble picking residues (there are two chains and a ligand in the asymmetric unit). How do I choose a specific residue/atom? Pleas

[PyMOL] effect of number of pixels on ray image quality

Hi everyone, I would like some confirmation or explanation about the differences I see, and the way I understand it. I was comparing the quality of images with different numbers of pixels along the length and width, e.g. ray 1000,750 I used the above command initially, because the highest

[PyMOL] Monitors

I can highly recommend the price awarded Iiyama HM204DT 22" 140KHz TCO99 Vision Master Pro 514. It has the same specs as the NEC monitor with a similar price tag. The Dell P1130 is also not bad at all with 130KHz (Iiyama technology!?) Also, the Nuvision glases are certenly not low cost and offer