[PyMOL] loading StringIO

Dear All, I was wondering if there was a way to load a PDB file stored in memory instead of disk, i. e., a memory file, defined through StringIO or tempfile.SpooledTemporaryFile. Is there a variant of cmd.load that could handle an open file instead of a file? Thanks, Albert -- --

Re: [PyMOL] loading StringIO

Probably could use load_object instead. def load_object(type,object,name,state=0,finish=1,discrete=0, quiet=1,zoom=-1,_self=cmd): ''' DESCRIPTION "load_object" is a general developer function for loading Python objects into PyMOL. > On Oct 26, 2016, at

Re: [PyMOL] loading StringIO

Hi Jordan, I still don't figure out how to do that with "load_object". What is the "type" for a file handler? Would be "object" the file handler itself? Albert On 10/26/2016 10:58 AM, Jordan Willis wrote: > Probably could use load_object instead. > > >def load_object(type,object,name,state=0

Re: [PyMOL] loading StringIO

https://pymolwiki.org/index.php/Read_Pdbstr -David > On Oct 26, 2016, at 3:55 AM, Albert Solernou wrote: > > Dear All, > I was wondering if there was a way to load a PDB file stored in memory > instead of disk, i. e., a memory file, defined through StringIO or > tempfile.SpooledTemporaryFile.

Re: [PyMOL] loading StringIO

That's lovely, David. Thanks, Albert On 10/26/2016 11:56 AM, David Hall wrote: > https://pymolwiki.org/index.php/Read_Pdbstr > > -David > > On Oct 26, 2016, at 3:55 AM, Albert Solernou > wrote: > >> Dear All, >> I was wondering if there was a way to load a PDB file

[PyMOL] PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol

PDB entry 3B5D is a low resolution (3.8 Å) structure that contains only C alpha coordinates (chain trace, no side chains) in the original pdb file. There are servers that will generate full backbone and side chain coordinates, e.g.  SABBAC (http://bioserv.rpbs.univ-paris-diderot.fr/services/SABBA

[PyMOL] Opening large trajectories

Dear all, I am trying to open a large trajectory file from a NAMD MD simulation on a Windows machine running Pymol 1.7.2.. In order to do this, I tried two things (both with defer_builds_mode 3): - Opening the .dcd file using load_traj, I was able to load most of it (400 frames); however, if