When debugging, it is good to stop running pymol as a command line app and
just run your script in a pymol gui and see what it is going on.
In this case, you would find your selections have zero atoms. Why? Because
you are basing them on something like "resn 102" , which is using the
residue name selector with a residue number.
If you replace resn with resi , you should get nice pictures.
> 2) I still have no idea what the command cmd.get_pdbstr do
It returns a string in PDB format of the set of atoms in the selection. So,
the same string as would be in a file if you said save('xxx.pdb', 'sele')
On Tue, May 2, 2017 at 3:47 AM, Ahmad Abdelzaher <underoath...@gmail.com>
wrote:
> Thank you. I made a few mistakes in my code. I wasn't paying attention
> to the commented code because I was only trying stuff there. I still
> get:
>
> 1) a bunch of 3 kb black png's
> 2) I still have no idea what the command cmd.get_pdbstr do
> 3) can you give me a line using iterate to get the residue names and
> numbers?
>
>
> import __main__
> __main__.pymol_argv = ['pymol','-qc']
> import pymol
> from pymol import cmd, stored, util
>
> pymol.finish_launching()
>
> residues = {'3s4m.pdb': {'102': 'THR',
> '143': 'TYR',
> '158': 'SER',
> '166': 'TYR',
> '173': 'TRP',
> '181': 'SER',
> '183': 'HIS',
> '206': 'SER',
> '95': 'TYR'}}
>
> for name, data in residues.items():
> for resnumber, resname in data.items():
> cmd.delete('all')
> bare_name = name.split('.')[0]
> cmd.load(name, bare_name)
> cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> resn %s around 10' % resnumber)
> cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> resnumber),'all within 5 of %s_%s%s' % (bare_name, resname,
> resnumber), quiet=1,mode=2,label=0,reset=1)
> cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> util.cnc('%s_%s%s' % (bare_name, resname, resnumber))
> cmd.hide('everything', 'all and not %s_%s%s' % (bare_name,
> resname, resnumber))
> cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5)
> cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1)
>
>
>
> On Tue, May 2, 2017 at 7:14 AM, Jared Sampson
> <jared.samp...@columbia.edu> wrote:
> > Hi Ahmad - Please see below for some suggestions on getting your script
> to
> > do what I understand you would like to do.
> >
> > Cheers,
> > Jared
> >
> >
> > On May 1, 2017, at 4:54 PM, Ahmad Abdelzaher <underoath...@gmail.com>
> wrote:
> >
> > OK I finally tried some of Jared suggestions, I'm not sure why
> > util.cnc doesn't work I get "NameError: name 'util' is not defined",
> >
> >
> > You will need to import the `util` namespace. Try changing the pymol
> > submodule import line to:
> >
> > from pymol import cmd, stored, util
> >
> > Again, I want to color by element, second option from the gui. Also
> > the script outputs black screenshots, nothing is there, so there is a
> > bug somewhere! I attached the script and pdb below. I would appreciate
> > your help.
> >
> > import __main__
> > __main__.pymol_argv = ['pymol','-qc']
> > import pymol
> > from pymol import cmd, stored
> >
> > pymol.finish_launching()
> >
> > residues = {'3s4m.pdb': {'102': 'THR',
> > '143': 'TYR',
> > '158': 'SER',
> > '166': 'TYR',
> > '173': 'TRP',
> > '181': 'SER',
> > '183': 'HIS',
> > '206': 'SER',
> > '95': 'TYR'}}
> >
> > for name, data in residues.items():
> > for resnumber, resname in data.items():
> > cmd.delete('all')
> > cmd.load(name, name)
> >
> >
> > The load command here gives you an object called "3s4m.pdb" but you later
> > try to use a selection called only "3s4m" (`bare_name`). If you leave
> the
> > second argument off from cmd.load(), the .pdb extension will be stripped
> > automatically. Alternatively, you could assign `bare_name` first and
> give
> > that as the 2nd argument:
> >
> > bare_name = name.split('.')[0]
> > cmd.load(name, bare_name)
> >
> >
> > bare_name = name.split('.')[0]
> > cmd.select('%s_%s%s' % (bare_name, resname, resnumber), 'byres
> > resn %s around 3' % resnumber)
> > #selee = cmd.get_pdbstr('%s' % name.split('.')[0])
> >
> >
> > Since you've already assigned a variable for this, you can (and should!)
> use
> > `bare_name` instead of `name.split('.')[0]` wherever it occurs. Also,
> you
> > don't need to do "%"-style string formatting if your variable is a string
> > and comprises the entire argument string. Simply
> > `cmd.get_pdbstr(bare_name)`, for example, will work just fine.
> >
> > #print(selee)
> > cmd.dist('mysele_polar_conts','%s_%s%s' % (bare_name, resname,
> > resnumber),'all within 5 of %s_%s%s' % (name.split('.')[0], resname,
> > resnumber), quiet=1,mode=2,label=0,reset=1)
> > cmd.show_as('sticks', '%s_%s%s' % (bare_name, resname, resnumber))
> > #util.cnc('%s' % name.split('.')[0])
> > cmd.hide('everything', 'all and not %s_%s%s' % (bare_name,
> > resname, resnumber))
> > cmd.zoom('%s_%s%s' % (bare_name, resname, resnumber), 5)
> > cmd.png('%s_%s%s.png' % (bare_name, resname, resnumber), ray=1)
> >
> >
> > Also, to get information about residues in your selection as you asked in
> > your later message, have a look at cmd.iterate().
> > https://pymolwiki.org/index.php/Iterate
> >
> >
> > Hope that helps.
> >
> > Cheers,
> > Jared
> >
> >
> > On Sat, Apr 29, 2017 at 3:34 PM, Ahmad Abdelzaher
> > <underoath...@gmail.com> wrote:
> >
> > Thanks Jared. A lot of fantastic tips there. Much appreciated.
> >
> > Regards.
> >
> > On Sat, Apr 29, 2017 at 6:03 AM, Jared Sampson
> > <jared.samp...@columbia.edu> wrote:
> >
> > Hi Ahmad -
> >
> > Here are a few suggestions:
> >
> > I'm still a bit new to the API so I'm not sure which commands to use.
> > At least I know I will start with cmd.select(string name, string
> > selection).
> >
> > How can I tell Pymol to:
> >
> > 1) look within a certain radius distance, and return resi's within
> > that distacne.
> >
> >
> > cmd.select('mysele', 'byres all within 5 of sele')
> >
> > See https://pymolwiki.org/index.php/Selection_Algebra for more handy
> > operators (`beyond`, `around`, `expand`, etc.)
> >
> >
> > 2) find all polar interactions within a distance,
> >
> >
> > You can use cmd.distance (https://pymolwiki.org/index.php/Distance),
> e.g.
> > (as done in the GUI by [A] > find > polar contacts...)
> >
> > cmd.dist("mysele_polar_conts","mysele","all within 5 of
> > mysele",quiet=1,mode=2,label=0,reset=1)
> >
> > or for a list of atoms, check out https://pymolwiki.org/index.
> php/Polarpairs
> >
> >
> > use sticks,
> >
> >
> > cmd.show('sticks', 'mysele')
> >
> > or to hide all other representations,
> >
> > cmd.show_as('sticks', 'mysele')
> >
> >
> > color by atom
> >
> >
> > util.cnc('mysele')
> >
> > I use this one all the time ("cnc" == color non-carbon). There is also
> > `util.cbc` == color by chain.
> >
> >
> > hide everything else
> >
> >
> > cmd.hide('everything', 'all and not mysele')
> >
> >
> > and output an image of the selections and interactions around it.
> >
> >
> > cmd.zoom('mysele', 5)
> > cmd.png('mysele.png', ray=1)
> >
> >
> > Please feel free to throw in any useful commands that can you might
> think is
> > helpful.
> >
> >
> > One useful trick to learn new commands is to open a log file (via
> `log_open
> > log.pml` or the File menu) and then perform the desired action in the
> GUI.
> > The log file will show the API commands that are called from the GUI. It
> > doesn't work for everything (e.g. wizards), but for most basic actions,
> it
> > should be helpful. At least it will give you the right command to look
> up
> > on the PyMOL wiki!
> >
> > Hope that helps.
> >
> > Cheers,
> > Jared
> >
> >
> > Your help is greatly appreciated.
> >
> > Regards.
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
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> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> >
> >
> > <3s4m.pdb><pymol_png_test.py>
> >
> >
>
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