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From: kanika s. <ksh...@gm...> - 2017-01-26 09:51:39
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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* |
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From: kanika s. <ksh...@gm...> - 2017-01-26 13:58:43
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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* |
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From: Sampson, J. M. <jm...@cu...> - 2017-01-26 21:01:43
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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 <ksh...@gm...<mailto:ksh...@gm...>> 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://SlashDot.org>! http://sdm.link/slashdot_______________________________________________ PyMOL-users mailing list (PyM...@li...<mailto:PyM...@li...>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
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From: kanika s. <ksh...@gm...> - 2017-01-27 11:21:42
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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. < jm...@cu...> 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 <ksh...@gm...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > -- *Best,* *Kanika Sharma* |
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From: Hitesh P. <hit...@gm...> - 2017-01-26 21:14:56
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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 <ksh...@gm...> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- 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: hit...@ni... |
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From: kanika s. <ksh...@gm...> - 2017-01-27 11:22:23
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Is there a way to calculate COM for a tunnel? On Thu, Jan 26, 2017 at 10:14 PM, Hitesh Patel <hit...@gm...> 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 <ksh...@gm...> > 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > -- > 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: hit...@ni... > -- *Best,* *Kanika Sharma* |
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From: Tsjerk W. <ts...@gm...> - 2017-01-26 21:39:44
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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 <hit...@gm...> 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 <ksh...@gm...> > 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... > > -- > 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: hit...@ni... > > ------------------------------------------------------------ > ------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. |
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From: kanika s. <ksh...@gm...> - 2017-01-27 11:43:50
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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 <ts...@gm...> 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 <hit...@gm...> > 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 <ksh...@gm...> >> 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >> >> -- >> 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: hit...@ni... >> >> ------------------------------------------------------------ >> ------------------ >> 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > -- *Best,* *Kanika Sharma* |
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