[PyMOL] CEalign parameter d0 and d1

2013-04-17 Thread QT
Dear all, I have a question regarding CEalign d0 and d1 parameter. What exactly are their functions? I don't know enough C++ to decipher the algorithm but they are used findPath() in ccealignmodule.cpp. It seems that that d0 controls a similarity matrix and d1 the path length. A d1 below a

Re: [PyMOL] CEalign parameter d0 and d1

2013-04-17 Thread Jason Vertrees
Hi Quyen, It's been a few years since I wrote that but here is what I recall: D0 is a constant cutoff that represents the upper bound of dissimilarity for the difference of two distance matrices A_i and B_j, rooted at subsequences i to i+8 and j to j+8, respectively. Raising this value allows

[PyMOL] Fwd: Translate command seems to translate along an arbitrary axis

2013-04-17 Thread Kyle Sutherland-Cash
Hello everyone, I've been trying to write a script to orient two particular molecules with respect to one another. I do this by calculating a translation vector between the two and then using cmd.translate to move the second object to the desired location. However, this didn't seem to have the

Re: [PyMOL] Fwd: Translate command seems to translate along an arbitrary axis

2013-04-17 Thread Thomas Holder
Hi Kyle, the translate command has a camera argument, which controls whether the vector is in camera space (default) or in model space. You want model space, so you need: PyMOLtranslate [1, 0, 0], glycan*, camera=0 Cheers, Thomas Kyle Sutherland-Cash wrote, On 04/17/13 19:47: Hello