[PyMOL] question about domain movement

Hi, I have built two models from one protein molecule with the different nucleotides bound: one is ATP, one is ADP. Their overall structures are similar except that a few secondary structure domains shift. For example, alpha4 helix has move left for about 1.2Å and rotate about 4º. Could I use pymo

[PyMOL] Question about rotation

1.When I want to get the exact rotation of my current view, I did as the following instruction, but Pymol programe says: invalid syntax. I do not know why that happens. Could you figure it out for me? Getting the right view in the script: When creating the script, it is nice to have the view come

[PyMOL] Questions about rotation view

1.When I want to get the exact rotation of my current view, I did as the following instruction, but Pymol programe says: invalid syntax. I do not know why that happens. Could you figure it out for me? Getting the right view in the script: When creating the script, it is nice to have the view come

[PyMOL] question about superposition

Hi, If I want to insert ATP molecule into a molecule which contains ADP to see how the extra gamma phosphate contact with it possible neighbors, can I use pair_fit to superimpose ATP with ADP? How? Thanks!

[PyMOL] questions about electrostatics

Hi, I want to show the electrostatics of my protein. However, when I click electrostatics from the Demo menu, the molecule shown in electrostatics is not what I want. Does any one know what is wrong? Meanwhile, I want to show my protein according to its B-factor. When I label it in color from t

[PyMOL] how to cancel the showing up

Dear all: When I have shown a representation of one residue and found I want to cancel it, how can I do since there is no undo function in my MacPymol? In other words, how can I just disable the representation of only one residue? Thanks!

[PyMOL] question about electrostatic maps

Hi, I want to get electrostatic map of my protein, which need APBS installation. However, I have a PC with platform of windows XP and a mac with platform of OSX.2.8. I do not know if they are they OK for APBS installation and running? And how? Thanks!

[PyMOL] questions about PQR visualization

Hi, guys: I have a confusion about PQR file visualization. Since my computer is Mac G4, I think I may not be able to use the new version of mac pymol 0.97 for the APBS plugin. I converted my pdb file to PQR from the serve: https://gridport.npaci.edu/apbs/. However, when I want to visualize the

[PyMOL] question about superimpose

Hi, I have a question about superimpose. When I make superimpose about two molecules, I want to get the pdb file of the rotated molecule. Does anyone know how can I get it? Your help is greatly appreciated!

[PyMOL] question about loading a xplor map

Hi, everyone: I have a simple question about loading the electron density map. I have generated x-plor format map and try to load it into pymol. However, pymol only shows me the unit cell, not the map. Does anyone know how can I "see" the map, not just the unit cell? Thanks!

[PyMOL] question abut loading xplor map

Hi, everyone: I have a simple question about loading the electron density map. I have generated x-plor format map and try to load it into pymol. However, pymol only shows me the unit cell, not the map. Does anyone know how can I "see" the map, not just the unit cell? Thanks!

[PyMOL] question about selecting multiple residues

Hi, everyone: If I want to select every cystein residues in my molecules, can I select them based on their name, not their id number? It will be easier than searching the sequence first and select them according to their sequence ID. Thank