[PyMOL] arranging atom records in pdb file by resid

Dear PyMOL users/developers, Is there any way to rearrange the atom records in a .pdb file according to their residue ID? I have run Vina with flexible sidechains and then concatenated the rigid receptor part with the sidechain conformations for each pose. That resulted to .pdb files where the

Re: [PyMOL] arranging atom records in pdb file by resid

Hi Thomas, Probably something like this should do something close to what you need: sed -n '/^\(ATOM\|HETATM\)/s/^.\{16\}\(.\{10\}\)/\1 \0/p' file.pdb | sort -n -k 3 | cut -b 11- Hope it helps, Tsjerk On Thu, May 30, 2013 at 10:21 AM, Thomas Evangelidis teva...@gmail.comwrote: Dear PyMOL

[PyMOL] how to get cealign outputs for mulitple structures

Hi all, can anyone suggest a straightforward way of collecting the cealign output in bulk, (RMS, #atoms compared), using alignto doesn't even print this to screen (I tried adjusting quiet=, to no avail). thanks in advance jacob

Re: [PyMOL] how to get cealign outputs for mulitple structures

Hi Jacob, Use the result from cmd.cealign and an alignment object. Here's an example: # fetch two proteins fetch 1cll 1ggz, async=0 # use a python block python # cealign the two structures and create a corresponding alignment object result = cmd.cealign(1cll, 1ggz, object=aln) # print out