Re: [PyMOL] using a pseudoatom for distance measurement

[M. Faridounnia]

Hi there,

This works perfect. Indeed, I was wondering how to extract position data.
This is very useful.

Thanks a million!


On Tue, May 6, 2014 at 7:58 PM, Sampson, Jared wrote:

>  Hi Mary -
>
>  If you already know which state has the conformation you want to use for
> your measurement, or if you want to create a pseudoatom for each state, you
> can do so by passing the `state` keyword to pseudoatom:
>
>  set state, 1   # or 2, 3, etc.
> pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue, state=1  # or 2, 3, etc.
>
>  You also may be interested in the iterate_state function.
>
>  Cheers,
> Jared
>
>   --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On May 6, 2014, at 9:32 AM, M. Faridounnia  wrote:
>
>Thanks a lot for the tip and explaining the whole thing, Jared. I
> learned a lot from that. It worked but here is why I had a problem at the
> beginning (and tried the command I emailed), still same problem persists.
>
>  I had tried similar command on one of the models after splitting the pdb
> file (split_states pdbfile, ) and it was not working.
> >split_states pdbfile,
> >pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>
>
> Now, I tried exactly what you mentioned. After splitting the states it
> doesn't work, but when I don't do split_states, the same command works and
> creates a pseudoatom. The problem is that the NMR structure I have been
> doing split_states on is an average structure of 20 models. So, I need to
> create the pseudoatom on one of the 20 structure models ( the closest to
> the average or the lowest energy). It is not a big deal for now because for
> these two residues all the 20 structure are very similar but I still wonder
> why isn't it possible!
>
>  I mean it would make more sense that the command doesn't work on the
> average structure, because it doesn't refer to a real coordinate in the
> file and it can take any of the twenty models, but when it knows which
> model to take, it is more probable to work because it refers to the right
> coordinates. Any comments on that?
>
>  Cheers
>  Mary
>
>
> On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared wrote:
>
>> Hi Mary -
>>
>>  There are a couple problems here.  First, you’re giving the pseudoatom
>> command a positional argument out-of-order (and after keyword parameters).
>>  Keyword parameters can appear in any order, but only if you use the
>> keyword.  Otherwise, you must list them in the order specified by the
>> function.  So, you either need to use the keyword and enclose the selection
>> in quotes (selection=“n. …”) or simply move it to its proper position, like
>> this:
>>
>>  pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue
>>
>>
>>  For the full order of arguments, see
>> http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom`
>> on the PyMOL command line.
>>
>>  Second, your current selection is going to use any atom named
>> cg+cd1…etc. in the entire session, not just in your single Phe residue.
>>  This is because the resi=100 and color=tv_blue are used to determine the
>> properties of the new pseudoatom, and not to determine or refine the
>> selection.  If you want to use the ring of Phe 100 only, the selection
>> argument needs to include that information.  If you have more than one
>> object or chain that includes resi 100, you will also need to specify that.
>>
>>  So I’m guessing what you probably want is something along the lines of
>> (replacing “myobject” and “A” with appropriate values):
>>
>>  pseudoatom test, myobject and chain A and resi 100 and n.
>> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>>
>>
>>  which will create a tv_blue-colored pseudoatom in the center of the
>> ring of residue 100.
>>
>>  Hope that helps.
>>
>>  Cheers,
>> Jared
>>
>>  --
>> Jared Sampson
>> Xiangpeng Kong Lab
>> NYU Langone Medical Center
>> http://kong.med.nyu.edu/
>>
>>
>>
>> On May 4, 2014, at 2:12 PM, M. Faridounnia  wrote:
>>
>>Hi there,
>>
>> I want to measure the distance and angle between an aromatic ring
>> (phenylalanin and a residue backbone) like this:
>> http://www.pymolwiki.org/index.php/File:Pseu1.png
>>
>>  I learned from here that I need to make a pseudoatom but I cannot make
>> it work.
>>
>>  I tried
>> pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2
>>
>>  and some other ways! I don't know how should I choose the write atoms
>> and make the pseudoatom. After this probably distance and angle measurement
>> would be straightforward.
>>
>>  Best regards
>> Mary
>>
>> --
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
>> unparalleled scalability from the best Selenium testing platform
>> available.
>> Simple to use. Noth

Re: [PyMOL] using a pseudoatom for distance measurement

[Sampson, Jared]

Hi Mary -

If you already know which state has the conformation you want to use for your 
measurement, or if you want to create a pseudoatom for each state, you can do 
so by passing the `state` keyword to pseudoatom:

set state, 1   # or 2, 3, etc.
pseudoatom test, pdbfile_0001 and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue, state=1  # or 2, 3, etc.

You also may be interested in the iterate_state function.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On May 6, 2014, at 9:32 AM, M. Faridounnia 
mailto:faridoun...@gmail.com>> wrote:

Thanks a lot for the tip and explaining the whole thing, Jared. I learned a lot 
from that. It worked but here is why I had a problem at the beginning (and 
tried the command I emailed), still same problem persists.

I had tried similar command on one of the models after splitting the pdb file 
(split_states pdbfile, ) and it was not working.
>split_states pdbfile,
>pseudoatom test, pdbfile_0001 and chain A and resi 100 and n. 
>cg+cd1+ce1+cz+ce2+cd2, color=tv_blue


Now, I tried exactly what you mentioned. After splitting the states it doesn't 
work, but when I don't do split_states, the same command works and creates a 
pseudoatom. The problem is that the NMR structure I have been doing 
split_states on is an average structure of 20 models. So, I need to create the 
pseudoatom on one of the 20 structure models ( the closest to the average or 
the lowest energy). It is not a big deal for now because for these two residues 
all the 20 structure are very similar but I still wonder why isn't it possible!

I mean it would make more sense that the command doesn't work on the average 
structure, because it doesn't refer to a real coordinate in the file and it can 
take any of the twenty models, but when it knows which model to take, it is 
more probable to work because it refers to the right coordinates. Any comments 
on that?

Cheers
Mary


On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared 
mailto:jared.samp...@nyumc.org>> wrote:
Hi Mary -

There are a couple problems here.  First, you’re giving the pseudoatom command 
a positional argument out-of-order (and after keyword parameters).  Keyword 
parameters can appear in any order, but only if you use the keyword.  
Otherwise, you must list them in the order specified by the function.  So, you 
either need to use the keyword and enclose the selection in quotes 
(selection=“n. …”) or simply move it to its proper position, like this:

pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue

For the full order of arguments, see 
http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom` on the 
PyMOL command line.

Second, your current selection is going to use any atom named cg+cd1…etc. in 
the entire session, not just in your single Phe residue.  This is because the 
resi=100 and color=tv_blue are used to determine the properties of the new 
pseudoatom, and not to determine or refine the selection.  If you want to use 
the ring of Phe 100 only, the selection argument needs to include that 
information.  If you have more than one object or chain that includes resi 100, 
you will also need to specify that.

So I’m guessing what you probably want is something along the lines of 
(replacing “myobject” and “A” with appropriate values):

pseudoatom test, myobject and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue

which will create a tv_blue-colored pseudoatom in the center of the ring of 
residue 100.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/



On May 4, 2014, at 2:12 PM, M. Faridounnia 
mailto:faridoun...@gmail.com>> wrote:

Hi there,

I want to measure the distance and angle between an aromatic ring (phenylalanin 
and a residue backbone) like this: 
http://www.pymolwiki.org/index.php/File:Pseu1.png

I learned from here that I need to make a pseudoatom but I cannot make it work.

I tried
pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2

and some other ways! I don't know how should I choose the write atoms and make 
the pseudoatom. After this probably distance and angle measurement would be 
straightforward.

Best regards
Mary
--
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Re: [PyMOL] using a pseudoatom for distance measurement

[M. Faridounnia]

Thanks a lot for the tip and explaining the whole thing, Jared. I learned a
lot from that. It worked but here is why I had a problem at the beginning
(and tried the command I emailed), still same problem persists.

I had tried similar command on one of the models after splitting the pdb
file (split_states pdbfile, ) and it was not working.
>split_states pdbfile,
>pseudoatom test, pdbfile_0001 and chain A and resi 100 and n.
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue


Now, I tried exactly what you mentioned. After splitting the states it
doesn't work, but when I don't do split_states, the same command works and
creates a pseudoatom. The problem is that the NMR structure I have been
doing split_states on is an average structure of 20 models. So, I need to
create the pseudoatom on one of the 20 structure models ( the closest to
the average or the lowest energy). It is not a big deal for now because for
these two residues all the 20 structure are very similar but I still wonder
why isn't it possible!

I mean it would make more sense that the command doesn't work on the
average structure, because it doesn't refer to a real coordinate in the
file and it can take any of the twenty models, but when it knows which
model to take, it is more probable to work because it refers to the right
coordinates. Any comments on that?

Cheers
Mary


On Mon, May 5, 2014 at 4:17 PM, Sampson, Jared wrote:

>  Hi Mary -
>
>  There are a couple problems here.  First, you’re giving the pseudoatom
> command a positional argument out-of-order (and after keyword parameters).
>  Keyword parameters can appear in any order, but only if you use the
> keyword.  Otherwise, you must list them in the order specified by the
> function.  So, you either need to use the keyword and enclose the selection
> in quotes (selection=“n. …”) or simply move it to its proper position, like
> this:
>
>  pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue
>
>
>  For the full order of arguments, see
> http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom`
> on the PyMOL command line.
>
>  Second, your current selection is going to use any atom named
> cg+cd1…etc. in the entire session, not just in your single Phe residue.
>  This is because the resi=100 and color=tv_blue are used to determine the
> properties of the new pseudoatom, and not to determine or refine the
> selection.  If you want to use the ring of Phe 100 only, the selection
> argument needs to include that information.  If you have more than one
> object or chain that includes resi 100, you will also need to specify that.
>
>  So I’m guessing what you probably want is something along the lines of
> (replacing “myobject” and “A” with appropriate values):
>
>  pseudoatom test, myobject and chain A and resi 100 and n.
> cg+cd1+ce1+cz+ce2+cd2, color=tv_blue
>
>
>  which will create a tv_blue-colored pseudoatom in the center of the ring
> of residue 100.
>
>  Hope that helps.
>
>  Cheers,
> Jared
>
>  --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
> On May 4, 2014, at 2:12 PM, M. Faridounnia  wrote:
>
>   Hi there,
>
> I want to measure the distance and angle between an aromatic ring
> (phenylalanin and a residue backbone) like this:
> http://www.pymolwiki.org/index.php/File:Pseu1.png
>
>  I learned from here that I need to make a pseudoatom but I cannot make it
> work.
>
>  I tried
> pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2
>
>  and some other ways! I don't know how should I choose the write atoms
> and make the pseudoatom. After this probably distance and angle measurement
> would be straightforward.
>
>  Best regards
> Mary
>
> --
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos.  Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
>
> http://p.sf.net/sfu/SauceLabs___
> 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
>
>
>  
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caus

Re: [PyMOL] using a pseudoatom for distance measurement

[Sampson, Jared]

Hi Mary -

There are a couple problems here.  First, you’re giving the pseudoatom command 
a positional argument out-of-order (and after keyword parameters).  Keyword 
parameters can appear in any order, but only if you use the keyword.  
Otherwise, you must list them in the order specified by the function.  So, you 
either need to use the keyword and enclose the selection in quotes 
(selection=“n. …”) or simply move it to its proper position, like this:

pseudoatom test, n. cg+cd1+ce1+cz+ce2+cd2, resi=100, color=tv_blue

For the full order of arguments, see 
http://www.pymolwiki.org/index.php/Pseudoatom or type `help pseudoatom` on the 
PyMOL command line.

Second, your current selection is going to use any atom named cg+cd1…etc. in 
the entire session, not just in your single Phe residue.  This is because the 
resi=100 and color=tv_blue are used to determine the properties of the new 
pseudoatom, and not to determine or refine the selection.  If you want to use 
the ring of Phe 100 only, the selection argument needs to include that 
information.  If you have more than one object or chain that includes resi 100, 
you will also need to specify that.

So I’m guessing what you probably want is something along the lines of 
(replacing “myobject” and “A” with appropriate values):

pseudoatom test, myobject and chain A and resi 100 and n. 
cg+cd1+ce1+cz+ce2+cd2, color=tv_blue

which will create a tv_blue-colored pseudoatom in the center of the ring of 
residue 100.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/


On May 4, 2014, at 2:12 PM, M. Faridounnia  wrote:

Hi there,

I want to measure the distance and angle between an aromatic ring (phenylalanin 
and a residue backbone) like this: 
http://www.pymolwiki.org/index.php/File:Pseu1.png

I learned from here that I need to make a pseudoatom but I cannot make it work.

I tried
pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2

and some other ways! I don't know how should I choose the write atoms and make 
the pseudoatom. After this probably distance and angle measurement would be 
straightforward.

Best regards
Mary
--
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[PyMOL] using a pseudoatom for distance measurement

[M. Faridounnia]

Hi there,

I want to measure the distance and angle between an aromatic ring
(phenylalanin and a residue backbone) like this:
http://www.pymolwiki.org/index.php/File:Pseu1.png

I learned from here that I need to make a pseudoatom but I cannot make it
work.

I tried
pseudoatom test, resi=100, color=tv_blue, n. cg+cd1+ce1+cz+ce2+cd2

and some other ways! I don't know how should I choose the write atoms and
make the pseudoatom. After this probably distance and angle measurement
would be straightforward.

Best regards
Mary
--
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get 
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs___
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