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 them ?
When you load fileXYZ.pdb into PyMOL, the PyMOL object will be
called fileXYZ--we just cut off the .pdb when making the object
name. So, in your example above
cmd.load(pdb%04d.pdb%ener1)
cmd.load(pdb%04d.pdb%ener2)
will create two new objects, one called pdb0001 and pdb0002 and
the rms command would be:
cmd.rms(pdb0001 and name CA, pdb0002 and name CA);
If you're scripting this, then you can write the RMS command like this:
cmd.rms( pdb%04d and name CA % ener1, pdb%04d and name CA % ener2 )
When and How do I do the import like from pymol import cmd,stored ?
Where do I place them in my Python script ?
Create a script called myRMSScript.py with all the Python/PyMOL
commands in it. At the top of that file put:
import pymol
from pymol import cmd
To run the script just type run ./path/to/myRMSScript.py and PyMOL
will run the script.
Any other function other than FIT like rms_cur,rms, allign that I could use
to get rmsd between these PDBS
both my pdbs are of the same protein
Please read the help I suggested earlier. If you type help fit you
will see that there are lots of alignment and fitting commands in
PyMOL, including: align, super, pair_fit, rms, rms_cur, intra_fit,
intra_rms, and intra_rms_cur--and each of those commands has
corresponding help documentation and PyMOLWiki page.
Cheers,
-- Jason
Please advise
Best
On Wed, Jun 15, 2011 at 2:58 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
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 given command. You can also
type help to get general help. Next, we have a community-editable
wiki, the PyMOLWiki (http://pymolwiki.org) that has thousands of pages
of information to get you up to speed.
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 written till now
[codes are in bold]
from pymol import cmd
cmd.load(pdb%04d.pdb%ener1)
cmd.load(pdb%04d.pdb%ener2)
This I believe should just load in the PDBs through PYMOL [both these
pdbs
are in the same directory]
rms=cmd.fit(pdb ) so I do not know how to get the RMSD using
this
function ( I need for CA atoms only)
Here, cmd.fit is expecting two protein selections to fit. So, we can
give it something like:
# fit protein pdb0001 to pdb0002
v = cmd.fit(pdb0001, pdb0002)
# print the RMS
print v
But as you stated you only want alpha carbons you can restrict the
selection of each protein to just alpha carbons using the selection
syntax name CA:
v = cmd.fit(pdb0001 and name CA, pdb0002 and name CA)
print v
To learn more about PyMOL selections please see
(http://www.pymolwiki.org/index.php/Category:Selecting).
This is the only part where I am getting jammed . I only need the RMSD
values between the structures(without any changes to the structures)
If you want PyMOL to do the calculation, but leave the structures
untouched use cmd.rms instead of cmd.fit. They both have a
similar syntax.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
--
EditLive Enterprise is the world's most technically advanced content
authoring tool. Experience the power of Track Changes, Inline Image
Editing and ensure content is compliant with Accessibility Checking.
http://p.sf.net/sfu/ephox-dev2dev
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
