>>> plt.figure(figsize=(10,8)) # make a large figure so that you can see

>>> labels = ['1XXX', '2YYY', ...] # len of labels must be equal to len of
ensemble
>>> for i, conf in enumerate(ensemble):
>>>    showProjection(conf, pca[:2])
>>>    xy = calcProjection(conf, pca[:2])[0]
>>>    plt.text(xy[0], xy[1], labels[i])

On Sun, Oct 9, 2011 at 10:22 PM, Shanu <shaher...@gmail.com> wrote:
> Dear Ahmet,

> I'm using Prody to create a projection of the ensemble onto PC1 and
> PC2 for my analysis:

> plt.figure(figsize=(5,4))
> showProjection(ensemble, pca[:2])
> plt.show ()

> Can you suggest me on how to label each marker point. I want to check
> which point represent which protein. Is it possible to plot the string
> label (PDB ID) besides each point?

> Thanks in advance.

> Regards,
> Shaherin Basith.

On Mon, Oct 10, 2011 at 12:15 PM, Ahmet Bakan <lordn...@gmail.com> wrote:
> Hi Shaherin,

> You can do it as follows:

> >>> plt.figure(figsize=(10,8)) # make a large figure so that you can see
> labels clearly when you have a large ensemble
> >>> labels = ['1XXX', '2YYY', ...] # len of labels must be equal to len of
> ensemble
> >>> for i, conf in enumerate(ensemble):
> >>>    showProjection(conf, pca[:2])
> >>>    xy = calcProjection(conf, pca[:2])[0]
> >>>    plt.text(xy[0], xy[1], labels[i])

> This is something I just figure looking examples in
> http://matplotlib.sourceforge.net/gallery.html and picking the one
> that looks like what I want to do. It maybe helpful to make other
> adjustments in your figures.

> Best,
> Ahmet

> On Sun, Oct 9, 2011 at 10:22 PM, Shanu <shaher...@gmail.com> wrote:

>> Dear Ahmet,

>> I'm using Prody to create a projection of the ensemble onto PC1 and
>> PC2 for my analysis:

>> plt.figure(figsize=(5,4))
>> showProjection(ensemble, pca[:2])
>> plt.show ()

>> Can you suggest me on how to label each marker point. I want to check
>> which point represent which protein. Is it possible to plot the string
>> label (PDB ID) besides each point?

>> Thanks in advance.

>> Regards,
>> Shaherin Basith.

> Dear Ahmet,

> The length of the PDB files for the query sequence obtained is 38. However,
> the length of ensemble obtained is 76 [len (pdbfiles) is not equal to
> len(ensemble)]. In this case, please suggest me how to label each marker
> point inorder to check which point represent which protein.

> Thanking you in advance.

> Regards,
> --
> Shaherin Basith
> Phd Student
> Systems Biology lab
> Ajou University
> Suwon
> South Korea
> e-mail: shaher...@ajou.ac.kr
> Mobile: 010-6873-1033

> On Mon, Oct 10, 2011 at 12:15 PM, Ahmet Bakan <lordn...@gmail.com> wrote:

>> Hi Shaherin,

>> You can do it as follows:

>> >>> plt.figure(figsize=(10,8)) # make a large figure so that you can see
>> labels clearly when you have a large ensemble
>> >>> labels = ['1XXX', '2YYY', ...] # len of labels must be equal to len of
>> ensemble
>> >>> for i, conf in enumerate(ensemble):
>> >>>    showProjection(conf, pca[:2])
>> >>>    xy = calcProjection(conf, pca[:2])[0]
>> >>>    plt.text(xy[0], xy[1], labels[i])

>> This is something I just figure looking examples in
>> http://matplotlib.sourceforge.net/gallery.html and picking the one
>> that looks like what I want to do. It maybe helpful to make other
>> adjustments in your figures.

>> Best,
>> Ahmet

>> On Sun, Oct 9, 2011 at 10:22 PM, Shanu <shaher...@gmail.com> wrote:

>>> Dear Ahmet,

>>> I'm using Prody to create a projection of the ensemble onto PC1 and
>>> PC2 for my analysis:

>>> plt.figure(figsize=(5,4))
>>> showProjection(ensemble, pca[:2])
>>> plt.show ()

>>> Can you suggest me on how to label each marker point. I want to check
>>> which point represent which protein. Is it possible to plot the string
>>> label (PDB ID) besides each point?

>>> Thanks in advance.

>>> Regards,
>>> Shaherin Basith.