From: Rene F. <ren...@gm...> - 2017-03-03 16:03:25
|
Hi All, I have been working on a python code that i am running in pymol. This code takes in two files, one of which is a multi-model ligand pdb file that has already been run through autodock vina. Therefore, each model within the pdb file has a remark saying: "REMARK VINA RESULT:" followed by the binding energy and RMSD values. The goal of my code is to iterate through the atoms within different states of the ligand and run some calculations--which is currently working very well. However, i would like to add some other capabilities to the code, including being able to take the autodock vina binding energy result into account. Due to the ability of iterating through the states of the pdb file as well as running other pymol commands on these files, i am using the pymol command 'cmd.load()' to import the files instead of the python command of 'open()'. Looking through pymol archives i saw a brief mention that when opening a pdb file with cmd.load(), it ignores and thus does not store any line that starts with "REMARK"... is this always the case? or is there an option that allows the user to store the information that is in the remarks? The few solutions i have found online regarding being able to access the information in a REMARK statement all take in the file with open(), and proceed to look if the line has a certain string. This seems very cumbersome, as the files i am working with will have anywhere from 20 to 100 models and i would have to go about a very convoluted process to get each state's binding energy. Also, as far as my understanding goes, if you use open() to read the file, you will not be able to run other pymol commands on the file (such as cmd.iterate_state, cmd.pseudoatom, etc) which are vital for my code. So i am currently at a standstill when it comes to reading and storing the binding affinities for each state of the multi-model pdb file. It would be great if i could just create a list that contained all of the binding affinities. Are there any ideas out there to help remedy this problem? Thanks very much, Rene -- *Rene Francolini* Carnegie Mellon University M.S. Computational Biology 2016 B.S. Biological Sciences 2015 ------ LinkedIn: www.linkedin.com/in/rfrancolini Email: ren...@gm... Phone: (973) 303-5203 |