[PyMOL] RMSD between two ligands

2008-02-21 Thread Horacio Emilio Pérez Sánchez
Hi, I need to calculate the RMSD between two ligands (around 50 atoms). For proteins works very well but it seems that for small molecules it gives errors. I looked through the forum and I did not find any useful info. I tried rms , rms_cur and so between the atoms selections but I get errors

[PyMOL] Align output

2008-02-21 Thread Sadler, Evan
I know in the past this question was to be addressed in a future version. Anyway, after aligning two structures, is there a way to dump out the sequence alignment (i.e., as a msf file) or is the alignment display onscreen the only way to see it? Evan Sadler -- J. Evan Sadler, M.D., Ph.D. Howard

[PyMOL] Importing pymol modules into python

2008-02-21 Thread Shatadal Ghosh
Hi All, I am using MacPyMOL 0.99rc6 on Mac OS X leopard (10.5.1). I wanted to import the pymol modules into python. As suggested by MacPyMOL.app/pymol/modules/pymol/__init__.py I set the following environment variables: export PYMOL_PATH=$PYMOL_PATH:/Volumes/Home/shatadal/Programs/MacPyMOL.app/p

Re: [PyMOL] RMSD between two ligands

2008-02-21 Thread DeLano Scientific
Horacio, PyMOL cannot currently superimpose small molecules unless: 1. either the identifiers match between the two molecules (fit commmand) or 2. the pairwise correspondance between the two is explicitly specified (pair_fit command or pair fitting wizard) Cheers, Warren -- DeLano Scientific

Re: [PyMOL] Align output

2008-02-21 Thread DeLano Scientific
Evan, You can save the "alignment" object resulting from an align command to an aln file: align sele1, sele2, object=aln_obj save alignment.aln, aln_obj Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info > -Original Message- > From: pymol-u

Re: [PyMOL] Importing pymol modules into python

2008-02-21 Thread DeLano Scientific
Unfortunately, this cannot work since MacPyMOL embeds Python directly. Your choices are as follows: 1. run your Python scripts from within MacPyMOL 2. launch PyMOL in command-line mode with your script /Applications/MacPyMOL.app/Contents/MacOS/MacPyMOL -qc script.py or 3. compile the open-sou

Re: [PyMOL] scenes and animate versus frames mdo

2008-02-21 Thread DeLano Scientific
Richard, It is fair to say that scenes and mdo commands are effectively distinct through the PyMOL 1.0x releases. One can either program movies manually (via mdo, mview, scene, movie.rock, movie.roll, etc.), or one can deliver presentations live from within PyMOL using scenes (stored in sessions)

[PyMOL] load cgo into existing pymol session

2008-02-21 Thread hari jayaram
Hi I have a running pymol session with nothing loaded. I now want to load a cgo object into this session. When I read in the cgo file using either command line (load /Users/hari/Desktop/test.cgo , test ) or the GUI menu , I get an object entry on the side panel but nothing shows up in the viewing

[PyMOL] Isotropic thermal ellipsoids

2008-02-21 Thread Thomas Stout
Hi All -- Yes, I know I want to do something silly here, but does anyone know of a "jiffy" that will generate anisotropic thermal parameters for an isotropic atom? My end goal is to create a figure showing a ligand as ball-and-stick where the spheres are scaled by the B-factor. Since I'm not d