[PyMOL] Need help in calculating buried surface area

2023-08-24 Thread Mukhopadhyay, Shreya via PyMOL-users
Hello Everyone, I am trying to find a way to calculate the buried surface area in a complex with 2 molecules using pymol. Can anyone direct me to the correct way to do it? I am currently trying out the following method, and I need to find out if there is anything else I need to do to do this

Re: [PyMOL] Need help to get SASA for individual Amino Acids

2015-08-24 Thread Vinod Devaraji
Thanks Osvaldo for your suggestion . I will work it out and let you know if any issues raises . Regards On Mon, Aug 24, 2015 at 5:17 PM, Osvaldo Martin aloctavo...@gmail.com wrote: Dear Vinod, One option is to call PyMOL function from Python script. import __main__ __main__.pymol_argv

[PyMOL] Need help to get SASA for individual Amino Acids

2015-08-24 Thread Vinod Devaraji
Hi All I doing one task with pymol where I need to calculate Solvent Accessible Surface Area for individual residues numbers. I tried with get_area command but little confused on how to put it for individual residues . Could any one please suggest command or script to do it ? Any

Re: [PyMOL] Need help to get SASA for individual Amino Acids

2015-08-24 Thread Osvaldo Martin
Dear Vinod, One option is to call PyMOL function from Python script. import __main__ __main__.pymol_argv = ['pymol','-qc'] import pymol from pymol import cmd, stored pymol.finish_launching() cmd.set('dot_solvent', 1) cmd.set('dot_density', 3) cmd.load('pdb.file') # use the name of your pdb

[PyMOL] need help

2014-09-09 Thread Vic Pinas
Dear all, I need help. I just start using Pymol in Ubuntu, this was advised to me since windows give a lot of trouble. I install pymol already on ubuntu, but I need an manual how to transport the data from the pdb to ubuntu pymol. I can enter pdb nicely but after I dowload the files I cannot

Re: [PyMOL] need help

2014-09-09 Thread David Hall
I am very unsure of your question, but I believe you're asking if you have a PDB id, how to load that into pymol. For that, you can use the fetch command ( http://www.pymolwiki.org/index.php/Fetch ) You type: fetch 1acb into the pymol interface and it will download pdb id 1acb and load it into

[PyMOL] Need help with RMSD ( I am a member of this community now , yayy)

2011-06-15 Thread Babban Mia
Hello Pymol Users I am quite new to python and more specifically to PYTHON ,PYMOL interface hence I urgently need a help from you. I simple need to calculate the RMSD between two pdb files and use that rmsd for further programming but somehow I can not figure how to do it This is what I have

Re: [PyMOL] Need help with RMSD ( I am a member of this community now , yayy)

2011-06-15 Thread Jason Vertrees
Hello, I am quite new to python and more specifically to PYTHON ,PYMOL interface hence I urgently need a help from you. Welcome! This list has about 1500 people on it and is accepting of new users. A couple hints to get you started. First, you can type help commandName in PyMOL to help on a

Re: [PyMOL] Need help with RMSD ( I am a member of this community now , yayy)

2011-06-15 Thread Jason Vertrees
Hi, Just a small doubt cmd.load(pdb%04d.pdb%ener1) cmd.load(pdb%04d.pdb%ener2) so   if ener1 =0001 ener2 =0002 The program will understand  the pdb0001 and pdb0002 in v = cmd.fit(pdb0001 and name CA, pdb0002 and name CA)  or not ? or would I need to assign them some names while loading

[PyMOL] Need Help with Stereo L/R Confusion

2005-09-29 Thread Warren DeLano
Folks, We are trying to track down and hopefully resolve a problem with the left and right images getting confused in stereo mode with PyMOL. I think this problem is limited to nVidia Quadro cards, but need more info. So... If (and only if) you use PyMOL in hardware stereo mode (with shutter