Re: [PyMOL] Coordinates of an atom
Dear Mohsen, when I Google "pymol coordinates atom", the top hit is this: https://pymolwiki.org/index.php/Get_Coordinates_I Worth a try. All best. Andreas On Thu, Dec 1, 2016 at 2:19 PM, Mohsen Chitsaz < mohsen.chit...@flinders.edu.au> wrote: > Hi all, > > > > Can anyone please help me in how to get coordinates of a selected atom or > residue? > > > > Thank you > > > > Mohsen > > > -- > > ___ > 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 > -- ___ 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
[PyMOL] Coordinates of an atom
Hi all, Can anyone please help me in how to get coordinates of a selected atom or residue? Thank you Mohsen -- ___ 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
[PyMOL] Coordinates of ligand-binding site
Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sites ( e.g if i visualize ligand binding site by means of Pymol itself ). Thx for help James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
I'm thinking a good work around is simply this. Select the binding site of the amino acids and ligand in pymol. Then copy those selected aa's and atoms to another object: save - model - copied_object as output.pdb output.pdb will then contain all the x,y,z coordinates of only what was selected. Then just get those columns and upload them to swiss dock. Jordan On Jul 18, 2012, at 2:23 AM, James Starlight wrote: Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sites ( e.g if i visualize ligand binding site by means of Pymol itself ). Thx for help James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
Jordan, Thank you for advise. I've tried to do the same already but 1- In Resulted pbd file ( with ligand and surrounded residues only) the coordinates of ligand and residues have been changed in comparison to the initial pdb/ How to prevent it? 2- The resulted pdb consist of coordinates of each atoms but how to define the proper coordinates of ligand-binding BOX based on that point coordinates? James 2012/7/18 Jordan Willis jwillis0...@gmail.com: I'm thinking a good work around is simply this. Select the binding site of the amino acids and ligand in pymol. Then copy those selected aa's and atoms to another object: save - model - copied_object as output.pdb output.pdb will then contain all the x,y,z coordinates of only what was selected. Then just get those columns and upload them to swiss dock. Jordan On Jul 18, 2012, at 2:23 AM, James Starlight wrote: Dear PyMol users! Some of docking servers (e.g swiss dock) which I'm using need in explicit definition of the coordinates (in XYZ) of the docking region as well as coordinates of its COM. How I could obtain such coordinates of intrested pdb file based on the knowing protein-ligand interaction sites ( e.g if i visualize ligand binding site by means of Pymol itself ). Thx for help James -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ 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] Coordinates of ligand-binding site
Hi James,
the get_extent command in PyMOL will give you the corners of the
selected region, from which you easily can calculate center and edge
lengths.
http://pymolwiki.org/index.php/Get_extent
Example:
box = cmd.get_extent('sele')
print 'Center:', [(a+b)/2.0 for (a,b) in zip(*box)]
print 'Size:', [(b-a) for (a,b) in zip(*box)]
Regarding your issue (1-): Coordinates should not change unless you
align to some other molecule.
Cheers,
Thomas
On 07/18/2012 09:37 AM, James Starlight wrote:
Jordan,
Thank you for advise.
I've tried to do the same already but
1- In Resulted pbd file ( with ligand and surrounded residues only)
the coordinates of ligand and residues have been changed in
comparison to the initial pdb/ How to prevent it?
2- The resulted pdb consist of coordinates of each atoms but how to
define the proper coordinates of ligand-binding BOX based on that
point coordinates?
James
2012/7/18 Jordan Willis jwillis0...@gmail.com:
I'm thinking a good work around is simply this.
Select the binding site of the amino acids and ligand in pymol.
Then copy those selected aa's and atoms to another object:
save - model - copied_object as output.pdb
output.pdb will then contain all the x,y,z coordinates of only what was
selected.
Then just get those columns and upload them to swiss dock.
Jordan
On Jul 18, 2012, at 2:23 AM, James Starlight wrote:
Dear PyMol users!
Some of docking servers (e.g swiss dock) which I'm using need in
explicit definition of the coordinates (in XYZ) of the docking region
as well as coordinates of its COM. How I could obtain such coordinates
of intrested pdb file based on the knowing protein-ligand interaction
sites ( e.g if i visualize ligand binding site by means of Pymol
itself ).
Thx for help
James
--
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[PyMOL] Coordinates of a mesh
Hi, I actual try to get the coordinates of the mesh from a protein/selection. At first I run the following command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) There I get points shifted by one axis or something like that. Then somebody here from the mailinglist tells me that I have to use cmd.get_object_matrix. I read in the Wiki how to use this command. (http://www.pymolwiki.org/index.php/Get_object_matrix) But when I try to run the example with my points and the protein I always get an error. Can sombody help me, or tell me what I do wrong?? Thanks in advance, Björn -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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] Coordinates of a mesh
Check this, and tell if it works. http://pymolwiki.org/index.php/Matrix_Copy Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/ 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/25 Bjoern-oliver Gohlke bjoern-oliver.goh...@student.uni-tuebingen.de The error I get is from the following command: super 1A9U, mesh ExecutiveAlign: invalid selections for alignment. I think that the problem is that I try to align the mesh points with an protein. In my understanding, I need this one to run the get_object matrix command. Or do I understand something in the wrong manner?? Zitat von Troels Emtekær Linnet tlin...@gmail.com: Can you provide the error message? 2011/8/25 Bjoern-oliver Gohlke bjoern-oliver.gohlke@student.**uni-tuebingen.debjoern-oliver.goh...@student.uni-tuebingen.de Hi, I actual try to get the coordinates of the mesh from a protein/selection. At first I run the following command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) There I get points shifted by one axis or something like that. Then somebody here from the mailinglist tells me that I have to use cmd.get_object_matrix. I read in the Wiki how to use this command. (http://www.pymolwiki.org/**index.php/Get_object_matrixhttp://www.pymolwiki.org/index.php/Get_object_matrix ) But when I try to run the example with my points and the protein I always get an error. Can sombody help me, or tell me what I do wrong?? Thanks in advance, Björn --**--** -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-**dev2devhttp://p.sf.net/sfu/emc-vnx-dev2dev __**_ PyMOL-users mailing list (PyMOL-users@lists.**sourceforge.netPyMOL-users@lists.sourceforge.net ) Info Page: https://lists.sourceforge.net/**lists/listinfo/pymol-usershttps://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/**pymol-users@lists.sourceforge.** net http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev___ 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] Coordinates of a mesh
Hi Bjoern, Please do also give a more explicit account of what you want to achieve in the end and what you've tried to get there, including the commands used. Cheers, Tsjerk 2011/8/25 Troels Emtekær Linnet tlin...@gmail.com: Check this, and tell if it works. http://pymolwiki.org/index.php/Matrix_Copy Troels Emtekær Linnet Karl-Liebknecht-Straße 53, 2 RE 04107 Leipzig, Tyskland Mobil: +49 1577-8944752 2011/8/25 Bjoern-oliver Gohlke bjoern-oliver.goh...@student.uni-tuebingen.de The error I get is from the following command: super 1A9U, mesh ExecutiveAlign: invalid selections for alignment. I think that the problem is that I try to align the mesh points with an protein. In my understanding, I need this one to run the get_object matrix command. Or do I understand something in the wrong manner?? Zitat von Troels Emtekær Linnet tlin...@gmail.com: Can you provide the error message? 2011/8/25 Bjoern-oliver Gohlke bjoern-oliver.goh...@student.uni-tuebingen.de Hi, I actual try to get the coordinates of the mesh from a protein/selection. At first I run the following command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) There I get points shifted by one axis or something like that. Then somebody here from the mailinglist tells me that I have to use cmd.get_object_matrix. I read in the Wiki how to use this command. (http://www.pymolwiki.org/index.php/Get_object_matrix) But when I try to run the example with my points and the protein I always get an error. Can sombody help me, or tell me what I do wrong?? Thanks in advance, Björn -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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 -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev ___ 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
[PyMOL] Coordinates of the mesh-points
Hey, I have a little problem to get the points/coordinates of a mesh. I know he command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) But when I run this command, the coordinates of these spheres are not equal to these of the mesh. For example, if a generate the mesh for a protein and run this command, the coordinates of the generated spheres are shifted by an axis I think. So my question is, is there a function where I can get the coordinates of the SES-mesh in an easier way?? Or do sombody know what my fault is, by running the above command? Thanks in advance, Björn -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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] Coordinates of the mesh-points
Hey Björn, The mesh will be in Pymol camera coordinates, not in PDB coordinates. You'll have to take the object_matrix (cmd.get_object_matrix) and apply it to the protein to convert it to the same space if you are to use it outside of Pymol. Hope it helps, Tsjerk On Mon, Aug 22, 2011 at 8:12 PM, björn bjoern-oliver.goh...@student.uni-tuebingen.de wrote: Hey, I have a little problem to get the points/coordinates of a mesh. I know he command: open(pymol.mesh,w).write( cmd.get_povray()[1] ) But when I run this command, the coordinates of these spheres are not equal to these of the mesh. For example, if a generate the mesh for a protein and run this command, the coordinates of the generated spheres are shifted by an axis I think. So my question is, is there a function where I can get the coordinates of the SES-mesh in an easier way?? Or do sombody know what my fault is, by running the above command? Thanks in advance, Björn -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-dev2dev ___ 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
[PyMOL] coordinates
hi all: could any one tell me how to get the coordinates for a specific atom in a particular amino acid using pymol commands is their a commant with can list the coordinates for each aminoacid in a protein molecule?? \ kindly clarify, thanking you in advance. - mohan -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev___ 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] coordinates
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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proactively, and fine-tune applications for parallel performance.
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Re: [PyMOL] coordinates
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
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Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
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Re: [PyMOL] coordinates
Of course, you could just use the .pdb file as a text file:
grep CA .pdb | cut -f 2,4,7,8,9
will get you the amino acid number, the amino acid identity, and x,y,z
coordinates for the CA.
Jed
Jason Vertrees wrote:
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given selection. The
.atom property is the list of atoms. If you want to know what else is
possible you might want to have a look at the
properties/attributes/methods defined:
for i in dir(cmd.get_model('n. ca').atom[0]): print i
Hope it helps,
Tsjerk
Of course neither way would restrict you to plotting...
On Mon, Mar 22, 2010 at 1:38 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
could any one tell me how to get the coordinates for a specific atom in
a particular amino acid using pymol commands
is their a commant with can list the coordinates for each aminoacid in
a protein molecule?? \
kindly clarify, thanking you in advance.
- mohan
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
--
Download Intel#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
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Phone: 508-289-4823
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Re: [PyMOL] coordinates
Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
Of course you're all correct - Thierry Fischmann already emailed me to correct me :) I hadn't actually tested anything (mea culpa). I was just trying to point out for those of us less familiar with python that there were alternatives to doing this relatively simple thing outside of pymol. Apologies to the list, Jed Robert Campbell wrote: Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. Cheers, Rob -- Jed Goldstone Research Specialist Woods Hole Oceanographic Institution Redfield 3-52 MS#32 Woods Hole, MA 02543 http://www.whoi.edu/hpb/Site.do?id=481 Phone: 508-289-4823 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] coordinates
But it is very doable using grep/cut, you'll just have to use the -b flag that allows you to cut columns: grep CA .pdb | cut -b 13-26,30-54 Cheers, Tsjerk On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Jed, On Mon, 22 Mar 2010 10:23:34 -0400 Jed Goldstone jgoldst...@whoi.edu wrote: Of course, you could just use the .pdb file as a text file: grep CA .pdb | cut -f 2,4,7,8,9 will get you the amino acid number, the amino acid identity, and x,y,z coordinates for the CA. Often this will work, but unfortunately it is not fool proof. If there is no chain ID, if the residue numbers are greater than 999 or if there are alternate position characters present on the atom names, then your field counts in your cut command will be off. The PDB file is very strict about which character columns contain which information and there is no requirement for spaces between those data columns. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] Coordinates for End Groups
Ramon, Though PyMOL's molecular editor is extensible in this way, there are some pieces missing when it comes to adding new fragments into the mix. What you hope to do will require general design improvements followed by some Python development. For example, one of the problems with the peptide builder right now is that it it is relying on naming conventions that are valid for the limited subset of groups it knows, but wouldn't be in general. Thus, it might make sense to use a tool other than PyMOL for the time being... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Dr. Ramón Garduño-Juárez Sent: Tuesday, February 08, 2005 1:02 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Coordinates for End Groups Dear Pymol-users: We are working on an interface between PYMOL and ECEPP/3 inorder to perform a conformational search in small peptides. We have done most of the dirty work, but still can not figure out how to include coordinates for End Groups other than the ones given in the modules/chempy subdirectory. To make myself clear, I want to be able to build peptides that would contain the following amino and carboxyl end groups: AMINO-H2 AMINO-H3+ AMINO-CH3 AMINO-COCH3 FORMYL CARBOXYL-COOH CARBOXYL-O CARBOXYL-CH3 CARBOXYL-NHCH3 METHYL-ESTER ETHYL-ESTER Any help surely will be appreciated. Thank you all in advance. Cheers,
