Hi Pius - There are MD-specific analysis packages out there (mdtraj, mdanalysis, bio3d), but if you want to do this using "standard" structural software you can also do it fairly easily in PyMOL with two selections for your intra/extracellular residues and using get_area <https://pymolwiki.org/index.php/Get_area> in a loop:
``` # Load the topology and trajectory # Here I used a Desmond trajectory with interval=20 for speed. # (see https://pymolwiki.org/index.php/Load_traj for other examples) load mytraj-out.cms, trj load_traj mytraj.xtc, trj, interval=20 # Basic visualization as cartoon util.cbc # Define selections however you like select sel1, chain A+B select sel2, chain C deselect # Calculate areas in a python block python from pymol import cmd from pymol import stored num_states = cmd.count_states("trj") stored.areas1 = [] stored.areas2 = [] for i in range(1, num_states + 1): stored.areas1.append(cmd.get_area("sel1", state=i)) stored.areas2.append(cmd.get_area("sel2", state=i)) python end # Print the areas print("Areas for sel1:", stored.areas1) print("Areas for sel2:", stored.areas2) ``` For me this prints: ``` PyMOL>print("Areas for sel1:", stored.areas1) Areas for sel1: [25629.009765625, 25627.626953125, 25662.083984375, 25626.73046875, 25641.3828125, 25555.92578125, 25612.93359375, 25500.0390625, 25533.642578125, 25599.818359375, 25593.6015625, 25637.169921875, 25606.119140625, 25645.43359375, 25632.478515625, 25702.109375, 25608.13671875, 25593.099609375, 25552.3671875, 25626.318359375] PyMOL>print("Areas for sel2:", stored.areas2) Areas for sel2: [14734.4228515625, 14847.4892578125, 14760.9716796875, 14728.2529296875, 14763.095703125, 14770.4052734375, 14753.7646484375, 14762.462890625, 14868.7685546875, 14861.6240234375, 14819.146484375, 14758.13671875, 14779.591796875, 14767.9990234375, 14729.06640625, 14761.2568359375, 14832.7705078125, 14782.37890625, 14781.837890625, 14838.466796875] ``` You can also write them to a file, etc. Hope that helps! Cheers, Jared On Mon, Apr 14, 2025 at 3:32 PM Pius Padayatti <ppadaya...@gmail.com> wrote: > Hi All Have several intermediary states of a receptor-ligand structure > simulated over several nanoseconds and have done such calculations for > around 500 + complexes. I want to ask this forum about ways to > calculate the surface changes on extracellular and > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > > ZjQcmQRYFpfptBannerEnd > Hi All > Have several intermediary states of a receptor-ligand structure > simulated over several nanoseconds and have done such calculations for > around 500 + complexes. I want to ask this forum about ways to > calculate the surface changes on extracellular and > intracellular surfaces of the receptor protein for simulated intermediate > structures. The initial input for all the simulations is > experimental crystal structures obtained from PDB. > Thanks all in advance > Padayatti > *Pius Padayatti* > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=009klHSCxuh5AI1vNQzSO0KGjl4nbi2Q0M1QLJX9BeE&r=eJsmGe6bhczRCKHT7i2qBzpnItn7ySMphie0EUWajIc&m=Gx3SXpgnHXr5fLQTi7LdB7kn_Xpt9Sip_2Tuj5XwxaYMmue6XWkB09rB9sSjt-97&s=wPwUcXpUrlRYFcP-M0irCYr2AWFqxcqb5xjSi5o64mk&e=> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
