Re: [PyMOL] Deleting and Loading multiple SDF files

Hi Renuka,

Please keep all PyMOL-related correspondence on the mailing list. That way,
other people can find the answers by reading the mailing list or searching
the web.

Your task is now getting a little more complicated. I think you'll probably
want to define some Python functions and use them. It's useful to know that
using the distance command with mode=2 will show polar contacts. Also,
distance objects with names starting with an underscore won't show up in the
GUI.


I'd do something like this:

1. Define some functions in a Python file that you can use via "run" (or
perhaps in your .pymolrc). [see
http://www.pymolwiki.org/index.php/Python_Integration and
http://www.pymolwiki.org/index.php/Script_Tutorial]. You'll need to pass the
name of your protein to these functions.

import os
from pymol import cmd

def loadclust(filename,protname):
    cmd.load(filename)
    dir,fname = os.path.split(filename)
    # PyMOL automatically names the object by the filename
    fname,extension = os.path.splitext(fname)
    # cluster_4 --> 4
    custernum = fname.split('_')[1]
    # hidden from GUI display because it starts with _
    polarname = '_polar_'+clusternum
    cmd.dist(polarname,fname,protname,mode=2)
cmd.extend('loadclust',loadclust)
def delclust(filename):
    dir,fname = os.path.split(filename)
    # PyMOL automatically names the object by the filename
    fname,extension = os.path.splitext(fname)
    # cluster_4 --> 4
    custernum = fname.split('_')[1]
    # hidden from GUI display because it starts with _
    polarname = '_polar_'+clusternum
    cmd.delete(fname)
    cmd.delete(polarname)
cmd.extend('delclust',delclust)

2. Then you should be able to use a similar procedure to
before. Remember that you now need to delete things and pass the name of
your protein to the functions so that polar contacts can be displayed
correctly:

for i in glob.glob("Model_1/cluster_*.sdf"): loadclust(i,myprotein)

<analyze things>

for i in glob.glob("Model_1/cluster_*.sdf"): delclust(i,myprotein)

for i in glob.glob("Model_2/cluster_*.sdf"): loadclust(i,myprotein)

Unfortunately, I don't have any SD files on hand, so I haven't tested these!
Some modification may be necessary. You should also check out the script
that Jason linked.

Cheers,

-Michael

On Wed, Sep 22, 2010 at 11:52 AM, Renuka Robert <ren...@ym...>wrote:

> Dear Michael
> Thanks for your detailed reply. This is what exactly i needed. Now i want
> to find the hydrogen bonding between each cluster files and the protein. So
> i do the following step
>
> cd /home/user
>
> import glob
>
>
>  then I load the Model_1 files with
>
>
>  for i in glob.glob("Model_1/cluster_*.sdf"): cmd.load(i)
>
>
>  Now hydrogen bond should be displayed between protein and
> Model_1/cluster_*.sdf. Polar contacts in different colors would be more
> appreciated.
>
>
>  Could you please attach your script in the above command, so that all the
> cluster_*.sdf is loaded and its polar contacts is displayed in one press.
>
>
>  Thanks in advance
>
> Renuka.
>
>
> --- On *Wed, 22/9/10, Michael Lerner <mgl...@gm...<mglerner%2Bs...@gm...>
> >* wrote:
>
>
> From: Michael Lerner <mgl...@gm...<mglerner%2Bs...@gm...>
> >
> Subject: Re: [PyMOL] Deleting and Loading multiple SDF files
> To: "Renuka Robert" <ren...@ym...>
> Cc: PyM...@li...
> Date: Wednesday, 22 September, 2010, 1:46 PM
>
>
> Hi Renuka,
>
> If I understand correctly, this is what you want to do:
>
> 1. Load up all of the cluster*.sdf files in Model_1.
> 2. Analyze them
> 3. Delete them
> 4. Load up all of the cluster*.sdf files in Model_2.
> 5. Analyze them
> 6. Delete them
> etc.
>
> If that's right, I think the easiest thing is just to change to the
> directory that contains your Model_N subdirectories. In your example, that
> would be:
>
> cd /home/user
> import glob
>
> then load the Model_1 files with
>
> for i in glob.glob("Model_1/cluster_*.sdf"): cmd.load(i)
>
> then analyze them. It sounds like you're analyzing them by hand; if you're
> analyzing them by running some scripts, we can probably help to automate
> that process as well.
>
> After analyzing them, (and saving your results!), you'll want to delete the
> current batch of cluster files and load the new ones:
>
> delete cluster_*
> for i in glob.glob("Model_2/cluster_*.sdf"): cmd.load(i)
>
> Note that you only have to type "import glob" once.
>
> Hope that helps,
>
> -Michael
>
> On Wed, Sep 22, 2010 at 9:12 AM, Renuka Robert <ren...@ym...<http://mc/compose?to=...@ym...>
> > wrote:
>
>  Dear Pymol users
>
>
>  I have to do TWO jobs simultaneously in PYMOL.
>
>
>  JOB 1: Load multiple *sdf files
>
>
>  I have set of ligand files in *.sdf format as follows:
>
>
>  /home/user/Model_1/cluster_1.sdf
>
> /home/user/Model_1/cluster_2.sdf
>
> /home/user/Model_1/cluster_3.sdf
>
>
>  /home/user/Model_2/cluster_1.sdf
>
> /home/user/Model_2/cluster_2.sdf
>
> /home/user/Model_2/cluster_3.sdf
>
>
>  /home/user/Model_3/cluster_1.sdf
>
> /home/user/Model_3/cluster_2.sdf
>
> /home/user/Model_3/cluster_3.sdf
>
>
>  I've got an answer from one of the PYMOL user as:
>
>
>  PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  But this command works only in the present working directory. For the
> next try I have to change my directory every time. Like:
>
>
>  cd /home/user/Model_1/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  cd /home/user/Model_2/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  cd /home/user/Model_3/
>
> PyMOL>import glob
>
> PyMOL>for i in glob.glob("cluster_*.sdf"): cmd.load(i)
>
>
>  Could you please tell me how to load these multiple *.sdf files in one
> command without changing the directory?
>
>
>  JOB2: Delete multiple *.sdf files
>
>
>  I have to analyze cluster_*.sdf files of several 100 directories.
>
>
> So when I load cluster_*.sdf files from directory Model_2, the already
> loaded cluster:*.sdf files from Model_1 should be deleted.
>
> Like wise when I load cluster_*.sdf files from directory Model_3, the
> already loaded cluster:*.sdf files from Model_2 should be deleted.
>
>
> I am not good in programming. Could anybody help me in scripting to sort
> out this problem?
>
>
>  Thanks in advance.
>
> Regards
>
> Renuka
>
>
>
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>
> --
> Michael Lerner, Ph.D.
> IRTA Postdoctoral Fellow
> Laboratory of Computational Biology NIH/NHLBI
> 5635 Fishers Lane, Room T909, MSC 9314
> Rockville, MD 20852 (UPS/FedEx/Reality)
> Bethesda MD 20892-9314 (USPS)
>
>
>


-- 
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)