Re: [PyMOL] Pseudoatom for a cavity

[kanika sharma]

​Hey Tsjerk!
So good to connect again here!
​I will look up Mole plugin for possible channels, come back and write here
again and a script would of course be very nice to have.

Thanks for the help.
Kanika

On Thu, Jan 26, 2017 at 10:39 PM, Tsjerk Wassenaar 
wrote:

> Hi Kanika,
>
> That's been quite a while! Nice to see you again and to see you're still
> your determined self, still a bit impatient, reposting a message within a
> day :)
>
> The issue with the second question is not about center_of_mass, but about
> center_of_no_mass, which is a bit harder (and I don't think there's an
> import for that). You can have a look at hollow.sourceforge.net or so. If
> they're channels, connected to the surface of the protein, you can also
> have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
> some bits of code that could be forged together to get something similar
> and which would allow for getting a center_of_no_mass, but I probably won't
> be able to do the forging before next week.
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel 
> wrote:
>
>> Hi,
>>
>> For your 2nd question:
>> You can make pseudoatom at Center of mass or center of geometry (for an
>> object or probably selection too) using the following script:
>> https://pymolwiki.org/index.php/Center_of_mass
>>
>> In your case you mat try:
>>
>> import center_of_mass
>>
>> com SelectionObjectName, state=1#Create a pseudoatom representing the Object 
>> COG and store it as "SelectionObjectName_COM"
>>
>>
>>
>> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma 
>> wrote:
>>
>>> Dear PyMol Users,
>>>
>>> I am struggling here two things.
>>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>>> residue, like arginine.
>>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>>> in the protein? I am thinking how can I define the co ordinates of the
>>> position where I wan t to place the pseudoatom?
>>>
>>> ​Thanks ​
>>>
>>> --
>>> *Best,*
>>>
>>> *Kanika*
>>>
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot__
>>> _
>>> 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
>>
>> --
>> Regards,
>>
>> Dr. Hitesh Patel
>> Post-Doctoral Fellow,
>> CADD Group,
>> Building 376, Room: 205A
>> Chemical Biology laboratory,
>> Center for Cancer Research,
>> National Cancer Institute,
>> Frederick, MD-21702
>>
>> Work: +1 301 846 5993 <(301)%20846-5993>
>> Mob.: +1 240 367 5208 <(240)%20367-5208>
>> Website: http://www.hiteshpatel379.com/
>> Email: hitesh.pa...@nih.gov
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> 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
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
>


-- 
*Best,*

*Kanika Sharma*
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Re: [PyMOL] Pseudoatom for a cavity

[kanika sharma]

Is there a way to calculate COM for a tunnel?

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel 
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object 
> COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma 
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot__
>> _
>> 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
>
> --
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> CADD Group,
> Building 376, Room: 205A
> Chemical Biology laboratory,
> Center for Cancer Research,
> National Cancer Institute,
> Frederick, MD-21702
>
> Work: +1 301 846 5993 <+1%20301-846-5993>
> Mob.: +1 240 367 5208 <+1%20240-367-5208>
> Website: http://www.hiteshpatel379.com/
> Email: hitesh.pa...@nih.gov
>



-- 
*Best,*

*Kanika Sharma*
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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Re: [PyMOL] Pseudoatom for a cavity

[kanika sharma]

Thanks Jared.

First part, is perfect. So pseudo atom lies between nitrogen atoms.
Second part, I don't have specific xyz coordinates because it is centre of
a tunnel in the protein and that's the struggle.

On Thu, Jan 26, 2017 at 10:01 PM, Sampson, Jared M. <
jms2...@cumc.columbia.edu> wrote:

> Hi Kanika -
>
> You can get more information on the wiki: https://pymolwiki.org/
> index.php/Pseudoatom.
>
> To answer your specific questions, to make a pseudoatom between the two
> terminal Ns of Arg 100 on chain A of myobj:
>
> ```
> pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
> ```
>
> and to place a pseudoatom at a specific XYZ coordinate, pass the `pos`
> parameter with a 3-tuple of floats:
>
> ```
> pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
> ```
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
> On Jan 26, 2017, at 8:58 AM, kanika sharma  wrote:
>
>
>
> Dear PyMol Users,
>
> ​I asked this question but no body replied so I am trying again. ​
>
> I am struggling here two things.
> 1). I want to place a pseudo
> ​ ​
> atom in the charge centre of a non aromatic residue, like arginine.
> 2). Is it possible to place
> ​a
>  pseudo
> ​ ​
> atom in the centre of a cavity in the protein? I am thinking how can I
> define the co ordinates of the position where I wan t to place the pseudo
> ​ ​
> atom?
>
> ​Thanks ​
>
> --
> *Best,*
>
> *Kanika*
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot__
> _
> 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
>
>
>


-- 
*Best,*

*Kanika Sharma*
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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

Re: [PyMOL] Pseudoatom for a cavity

[Tsjerk Wassenaar]

Hi Kanika,

That's been quite a while! Nice to see you again and to see you're still
your determined self, still a bit impatient, reposting a message within a
day :)

The issue with the second question is not about center_of_mass, but about
center_of_no_mass, which is a bit harder (and I don't think there's an
import for that). You can have a look at hollow.sourceforge.net or so. If
they're channels, connected to the surface of the protein, you can also
have a look at the Mole plugin on the Pymol wiki. Alternatively, I have
some bits of code that could be forged together to get something similar
and which would allow for getting a center_of_no_mass, but I probably won't
be able to do the forging before next week.

Hope it helps,

Tsjerk

On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel 
wrote:

> Hi,
>
> For your 2nd question:
> You can make pseudoatom at Center of mass or center of geometry (for an
> object or probably selection too) using the following script:
> https://pymolwiki.org/index.php/Center_of_mass
>
> In your case you mat try:
>
> import center_of_mass
>
> com SelectionObjectName, state=1#Create a pseudoatom representing the Object 
> COG and store it as "SelectionObjectName_COM"
>
>
>
> On Thu, Jan 26, 2017 at 4:52 AM kanika sharma 
> wrote:
>
>> Dear PyMol Users,
>>
>> I am struggling here two things.
>> 1). I want to place a pseudoatom in the charge centre of a non aromatic
>> residue, like arginine.
>> 2). Is it possible to place another pseudoatom in the centre of a cavity
>> in the protein? I am thinking how can I define the co ordinates of the
>> position where I wan t to place the pseudoatom?
>>
>> ​Thanks ​
>>
>> --
>> *Best,*
>>
>> *Kanika*
>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot__
>> _
>> 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
>
> --
> Regards,
>
> Dr. Hitesh Patel
> Post-Doctoral Fellow,
> CADD Group,
> Building 376, Room: 205A
> Chemical Biology laboratory,
> Center for Cancer Research,
> National Cancer Institute,
> Frederick, MD-21702
>
> Work: +1 301 846 5993 <(301)%20846-5993>
> Mob.: +1 240 367 5208 <(240)%20367-5208>
> Website: http://www.hiteshpatel379.com/
> Email: hitesh.pa...@nih.gov
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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

Re: [PyMOL] Pseudoatom for a cavity

[Hitesh Patel]

Hi,

For your 2nd question:
You can make pseudoatom at Center of mass or center of geometry (for an
object or probably selection too) using the following script:
https://pymolwiki.org/index.php/Center_of_mass

In your case you mat try:

import center_of_mass

com SelectionObjectName, state=1#Create a pseudoatom representing the
Object COG and store it as "SelectionObjectName_COM"



On Thu, Jan 26, 2017 at 4:52 AM kanika sharma  wrote:

> Dear PyMol Users,
>
> I am struggling here two things.
> 1). I want to place a pseudoatom in the charge centre of a non aromatic
> residue, like arginine.
> 2). Is it possible to place another pseudoatom in the centre of a cavity
> in the protein? I am thinking how can I define the co ordinates of the
> position where I wan t to place the pseudoatom?
>
> ​Thanks ​
>
> --
> *Best,*
>
> *Kanika*
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> 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

-- 
Regards,

Dr. Hitesh Patel
Post-Doctoral Fellow,
CADD Group,
Building 376, Room: 205A
Chemical Biology laboratory,
Center for Cancer Research,
National Cancer Institute,
Frederick, MD-21702

Work: +1 301 846 5993
Mob.: +1 240 367 5208
Website: http://www.hiteshpatel379.com/
Email: hitesh.pa...@nih.gov
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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

Re: [PyMOL] Pseudoatom for a cavity

[Sampson, Jared M.]

Hi Kanika -

You can get more information on the wiki: 
https://pymolwiki.org/index.php/Pseudoatom.

To answer your specific questions, to make a pseudoatom between the two 
terminal Ns of Arg 100 on chain A of myobj:

```
pseudoatom my_ps1, myobj and chain A and resi 100 and name NH1+NH2
```

and to place a pseudoatom at a specific XYZ coordinate, pass the `pos` 
parameter with a 3-tuple of floats:

```
pseudoatom my_ps2, pos=[1.0, 2.0, 3.0]
```

Hope that helps.

Cheers,
Jared


On Jan 26, 2017, at 8:58 AM, kanika sharma 
> wrote:



Dear PyMol Users,

​I asked this question but no body replied so I am trying again. ​

I am struggling here two things.
1). I want to place a pseudo
​ ​
atom in the charge centre of a non aromatic residue, like arginine.
2). Is it possible to place
​a
 pseudo
​ ​
atom in the centre of a cavity in the protein? I am thinking how can I define 
the co ordinates of the position where I wan t to place the pseudo
​ ​
atom?

​Thanks ​

--
Best,

Kanika
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! 
http://sdm.link/slashdot___
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(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

--
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[PyMOL] Pseudoatom for a cavity

[kanika sharma]

Dear PyMol Users,

I am struggling here two things.
1). I want to place a pseudoatom in the charge centre of a non aromatic
residue, like arginine.
2). Is it possible to place another pseudoatom in the centre of a cavity in
the protein? I am thinking how can I define the co ordinates of the
position where I wan t to place the pseudoatom?

​Thanks ​

-- 
*Best,*

*Kanika*
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
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