From: James S. <jms...@gm...> - 2012-06-11 08:33:45
|
Dear PyMol Users! I'm performing visualisation of the results of my MD simulation- protein-ligand system in water. 1) I want to visualise individual water mollecules wich have moved to the protein interiour during my MD run. How I could hide all solvent water and visualise only those water wich are within defined cutoff distance from the protein ? 2) I've compared electrostatic protein- ligand contacts by means of PyMol's present- ligand sites option. As I've noticed the polar contacts are visualised as the different object. It's very uncomfortable in case when I want to compare protein-ligand interactions in two conformations of my protein by means of GRID mode because the polar interactions from both conformations as the different objects. So as the result I obtain 4 objects ( 2 of proteins +2 of polar contacts as the simple distances ) instead of 2 conformations with the polar distances. Is there any possible way to merge polar interactions with the protein structures to one object ? Thanks for help, James S. |
From: Jason V. <jas...@sc...> - 2012-06-11 16:46:36
|
James, > 1) I want to visualise individual water mollecules wich have moved to the > protein interiour during my MD run. How I could hide all solvent water and > visualise only those water wich are within defined cutoff distance from the > protein ? You can find buried waters with this script: http://www.pymolwiki.org/index.php/Find_buried_waters. It doesn't select waters within a cutoff of the protein, but by each water's solvent accessibility. > 2) I've compared electrostatic protein- ligand contacts by means of PyMol's > present- ligand sites option. As I've noticed the polar contacts are > visualised as the different object. It's very uncomfortable in case when I > want to compare protein-ligand interactions in two conformations of my > protein by means of GRID mode because the polar interactions from both > conformations as the different objects. So as the result I obtain 4 objects > ( 2 of proteins +2 of polar contacts as the simple distances ) instead of 2 > conformations with the polar distances. Is there any possible way to merge > polar interactions with the protein structures to one object ? No. In PyMOL, the underlying representations of molecules are distances are completely different. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: Thomas H. <sp...@us...> - 2012-06-11 20:20:59
|
Hi James, > [...] Is there any possible way to merge polar interactions > with the protein structures to one object ? yes, you can put them in the same "group" object. This will show them in the same slot in group mode. http://pymolwiki.org/index.php/Group Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-06-15 06:25:57
|
Thomas, thanks this works perfect. Jason, I've tested this script on my system ( this is the membrane protein inserted in the bilayer surrounded by two water layers ( up and down ). During simulation individual water mollecules move into the protein interiour ( in that case protein like a water pore althought it's the receptor ) so I want to visualise only that buried water. I've tried to do it via find_buried_waters script both via ASA as well as in case when I've used small cutoffs ( 0.1) but the script selected too many waters ( e.g virtually all waters from up and down layers have been selected ). How I could specify this selection more carefully ? find_buried_waters 1, 0.1 James 2012/6/12 Thomas Holder <sp...@us...> > This will show them in the same slot in group mode. >> > > sorry, not "group mode" but "grid mode" of course. > > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: James S. <jms...@gm...> - 2012-06-26 06:07:17
|
By the way in some papers I've seen 2D schematic diagrams of the protein-ligand interactions. The exapmle of such maps could be found here http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-gr4.jpg Could you tell me examples of software wich could produce such maps? Thanks James 2012/6/15 James Starlight <jms...@gm...> > Thomas, thanks this works perfect. > > > Jason, I've tested this script on my system ( this is the membrane > protein inserted in the bilayer surrounded by two water layers ( up and > down ). During simulation individual water mollecules move into the protein > interiour ( in that case protein like a water pore althought it's the > receptor ) so I want to visualise only that buried water. > > I've tried to do it via find_buried_waters script both via ASA as well as > in case when I've used small cutoffs ( 0.1) but the script selected too > many waters ( e.g virtually all waters from up and down layers have been > selected ). How I could specify this selection more carefully ? > > find_buried_waters 1, 0.1 > > > James > > > 2012/6/12 Thomas Holder <sp...@us...> > >> This will show them in the same slot in group mode. >>> >> >> sorry, not "group mode" but "grid mode" of course. >> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > |
From: Christian R. <chr...@bb...> - 2012-06-26 06:20:27
|
Hi James, the program you can use for this is ligplot from Roman Laskowski at the EBI. the solvent accessability shading is done with the help of naccess. Best Regards Christian Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie: > By the way > > in some papers I've seen 2D schematic diagrams of the protein-ligand > interactions. > The exapmle of such maps could be found here > http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-g > r4.jpg > > Could you tell me examples of software wich could produce such maps? > > > Thanks > > James > > 2012/6/15 James Starlight <jms...@gm...> > > > Thomas, thanks this works perfect. > > > > > > Jason, I've tested this script on my system ( this is the membrane > > protein inserted in the bilayer surrounded by two water layers ( up and > > down ). During simulation individual water mollecules move into the > > protein interiour ( in that case protein like a water pore althought it's > > the receptor ) so I want to visualise only that buried water. > > > > I've tried to do it via find_buried_waters script both via ASA as well as > > in case when I've used small cutoffs ( 0.1) but the script selected too > > many waters ( e.g virtually all waters from up and down layers have been > > selected ). How I could specify this selection more carefully ? > > > > find_buried_waters 1, 0.1 > > > > > > James > > > > > > 2012/6/12 Thomas Holder <sp...@us...> > > > >> This will show them in the same slot in group mode. > >> > >> > >> sorry, not "group mode" but "grid mode" of course. > >> > >> > >> -- > >> Thomas Holder > >> MPI for Developmental Biology > >> Spemannstr. 35 > >> D-72076 Tübingen > |
From: James S. <jms...@gm...> - 2012-06-26 06:30:25
|
Hi Christian! As I understood that LigPlot is not free for accademical ussage isnt? By the way in that paper http://onlinelibrary.wiley.com.sci-hub.org/doi/10.1002/minf.201000167/pdf there is exhaustive comparison of three different packages for such 2D diagram generation. Have anybody used such software else ? James 2012/6/26 Christian Roth <chr...@bb...> > Hi James, > > the program you can use for this is ligplot from Roman Laskowski at the > EBI. > the solvent accessability shading is done with the help of naccess. > > > Best Regards > > Christian > Am Dienstag 26 Juni 2012 08:07:07 schrieben Sie: > > By the way > > > > in some papers I've seen 2D schematic diagrams of the protein-ligand > > interactions. > > The exapmle of such maps could be found here > > > http://ars.els-cdn.com.sci-hub.org/content/image/1-s2.0-S0005273610001707-g > > r4.jpg > > > > Could you tell me examples of software wich could produce such maps? > > > > > > Thanks > > > > James > > > > 2012/6/15 James Starlight <jms...@gm...> > > > > > Thomas, thanks this works perfect. > > > > > > > > > Jason, I've tested this script on my system ( this is the membrane > > > protein inserted in the bilayer surrounded by two water layers ( up and > > > down ). During simulation individual water mollecules move into the > > > protein interiour ( in that case protein like a water pore althought > it's > > > the receptor ) so I want to visualise only that buried water. > > > > > > I've tried to do it via find_buried_waters script both via ASA as well > as > > > in case when I've used small cutoffs ( 0.1) but the script selected too > > > many waters ( e.g virtually all waters from up and down layers have > been > > > selected ). How I could specify this selection more carefully ? > > > > > > find_buried_waters 1, 0.1 > > > > > > > > > James > > > > > > > > > 2012/6/12 Thomas Holder <sp...@us...> > > > > > >> This will show them in the same slot in group mode. > > >> > > >> > > >> sorry, not "group mode" but "grid mode" of course. > > >> > > >> > > >> -- > > >> Thomas Holder > > >> MPI for Developmental Biology > > >> Spemannstr. 35 > > >> D-72076 Tübingen > > > > > |
From: Christian R. <chr...@bb...> - 2012-06-26 07:36:28
|
Hi James, LigPlot is free for academic users. You just have to verify that you are a academic user. MOE does a simimlar representiation but is definitely not free. Christian |
From: James S. <jms...@gm...> - 2012-06-26 08:14:01
|
Christian, Also I've found the same software- pose view (in that article I've also found link on it). Its very friendly but I've noticed some erorrs during representation of the non-covalent contacts partly in case of the vdw interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some crussial interactions could not be visualized) And the main disadvantage of that software is that it does not take into account burrial water and it's h-bond networks within protein. I've ordered free license on the lig prot and hope that this software will be better ;) James 2012/6/26 Christian Roth <chr...@bb...> > Hi James, > > LigPlot is free for academic users. You just have to verify that you are a > academic user. MOE does a simimlar representiation but is definitely not > free. > > Christian > |
From: Thomas H. <sp...@us...> - 2012-06-26 13:24:13
|
Hi all, I thought it would be nice to run such tools directly from PyMOL. So there is a PoseView wrapper on the PyMOLWiki now: http://pymolwiki.org/index.php/PoseView A LigPlot wrapper may follow... Cheers, Thomas On 06/26/2012 10:13 AM, James Starlight wrote: > Christian, > Also I've found the same software- pose view (in that article I've also > found link on it). Its very friendly but I've noticed some erorrs during > representation of the non-covalent contacts partly in case of the vdw > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some > crussial interactions could not be visualized) > And the main disadvantage of that software is that it does not take into > account burrial water and it's h-bond networks within protein. > I've ordered free license on the lig prot and hope that this software > will be better ;) > James > 2012/6/26 Christian Roth <chr...@bb... > <mailto:chr...@bb...>> > > Hi James, > > LigPlot is free for academic users. You just have to verify that you > are a > academic user. MOE does a simimlar representiation but is definitely > not free. > > Christian -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-06-26 15:11:48
|
Thomas, Its really great ) Could you tell me if you find a possible way to take into account burried water from the protein interiour in the Pose View protein-ligand interaction 2D plots ? Most of my proteins consist of such internal water ( like a het atoms in the protein.pdb ) but pose view didnt take this mollecules into account so the final plot lack of many crussial h_bonds between ligand and protein itself. James 2012/6/26 Thomas Holder <sp...@us...> > Hi all, > > I thought it would be nice to run such tools directly from PyMOL. So > there is a PoseView wrapper on the PyMOLWiki now: > > http://pymolwiki.org/index.php/PoseView > > A LigPlot wrapper may follow... > > Cheers, > Thomas > > On 06/26/2012 10:13 AM, James Starlight wrote: > > Christian, > > Also I've found the same software- pose view (in that article I've also > > found link on it). Its very friendly but I've noticed some erorrs during > > representation of the non-covalent contacts partly in case of the vdw > > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw but some > > crussial interactions could not be visualized) > > And the main disadvantage of that software is that it does not take into > > account burrial water and it's h-bond networks within protein. > > I've ordered free license on the lig prot and hope that this software > > will be better ;) > > James > > 2012/6/26 Christian Roth <chr...@bb... > > <mailto:chr...@bb...>> > > > > Hi James, > > > > LigPlot is free for academic users. You just have to verify that you > > are a > > academic user. MOE does a simimlar representiation but is definitely > > not free. > > > > Christian > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: Thomas H. <sp...@us...> - 2012-06-26 16:23:46
|
Hi James, hm, looks like PoseView ignores all water molecules :( Have you tried LigPlot? It has a "-w" option to include waters. Cheers, Thomas On 06/26/2012 05:11 PM, James Starlight wrote: > Thomas, > Its really great ) > Could you tell me if you find a possible way to take into account > burried water from the protein interiour in the Pose View protein-ligand > interaction 2D plots ? > Most of my proteins consist of such internal water ( like a het atoms in > the protein.pdb ) but pose view didnt take this mollecules into account > so the final plot lack of many crussial h_bonds between ligand and > protein itself. > James > 2012/6/26 Thomas Holder <sp...@us... > <mailto:sp...@us...>> > > Hi all, > > I thought it would be nice to run such tools directly from PyMOL. So > there is a PoseView wrapper on the PyMOLWiki now: > > http://pymolwiki.org/index.php/PoseView > > A LigPlot wrapper may follow... > > Cheers, > Thomas > > On 06/26/2012 10:13 AM, James Starlight wrote: > > Christian, > > Also I've found the same software- pose view (in that article > I've also > > found link on it). Its very friendly but I've noticed some erorrs > during > > representation of the non-covalent contacts partly in case of the vdw > > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw > but some > > crussial interactions could not be visualized) > > And the main disadvantage of that software is that it does not > take into > > account burrial water and it's h-bond networks within protein. > > I've ordered free license on the lig prot and hope that this software > > will be better ;) > > James > > 2012/6/26 Christian Roth <chr...@bb... > <mailto:chr...@bb...> > > <mailto:chr...@bb... > <mailto:chr...@bb...>>> > > > > Hi James, > > > > LigPlot is free for academic users. You just have to verify > that you > > are a > > academic user. MOE does a simimlar representiation but is > definitely > > not free. > > > > Christian -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-06-26 18:23:03
|
I'm still waiting for accademical license on lig prot. By the way it's very strange that PoseView have not been accompanied with 'internal water detector' ;) i've sent the letter to developers with this question and hope they can help James 2012/6/26 Thomas Holder <sp...@us...> > Hi James, > > hm, looks like PoseView ignores all water molecules :( > > Have you tried LigPlot? It has a "-w" option to include waters. > > Cheers, > Thomas > > > On 06/26/2012 05:11 PM, James Starlight wrote: > >> Thomas, >> Its really great ) >> Could you tell me if you find a possible way to take into account >> burried water from the protein interiour in the Pose View protein-ligand >> interaction 2D plots ? >> Most of my proteins consist of such internal water ( like a het atoms in >> the protein.pdb ) but pose view didnt take this mollecules into account >> so the final plot lack of many crussial h_bonds between ligand and >> protein itself. >> James >> 2012/6/26 Thomas Holder <sp...@us... >> <mailto:speleo3@users.**sourceforge.net <sp...@us...>>> >> >> >> >> Hi all, >> >> I thought it would be nice to run such tools directly from PyMOL. So >> there is a PoseView wrapper on the PyMOLWiki now: >> >> http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.php/PoseView> >> >> A LigPlot wrapper may follow... >> >> Cheers, >> Thomas >> >> On 06/26/2012 10:13 AM, James Starlight wrote: >> > Christian, >> > Also I've found the same software- pose view (in that article >> I've also >> > found link on it). Its very friendly but I've noticed some erorrs >> during >> > representation of the non-covalent contacts partly in case of the >> vdw >> > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw >> but some >> > crussial interactions could not be visualized) >> > And the main disadvantage of that software is that it does not >> take into >> > account burrial water and it's h-bond networks within protein. >> > I've ordered free license on the lig prot and hope that this >> software >> > will be better ;) >> > James >> > 2012/6/26 Christian Roth <christian.roth@bbz.uni-**leipzig.de<chr...@bb...> >> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >> > >> > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >> >> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >> >>> >> > >> > Hi James, >> > >> > LigPlot is free for academic users. You just have to verify >> that you >> > are a >> > academic user. MOE does a simimlar representiation but is >> definitely >> > not free. >> > >> > Christian >> > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Martin H. <ma...@bl...> - 2012-06-27 10:01:07
|
Dear PyMOL users Does anybody know a script to verify that a file contains valid a valid PDB formatted structure? The file extension alone obviously does not provide sufficient validation. Thanks for any feedback. Martin |
From: Joel T. <joe...@ot...> - 2012-06-27 21:42:52
|
Hi Martin, I might be missing something but a little more information might help as to what you want to do. agreed, a file extension can be changed to anything but viewing the text file should tell you the type (of coordinate file). If you are doing this in batch mode then I guess a script would help! Joel -----Original Message----- From: Martin Hediger [mailto:ma...@bl...] Sent: Wednesday, 27 June 2012 10:01 p.m. To: pym...@li... Subject: [PyMOL] Verify PDB format Dear PyMOL users Does anybody know a script to verify that a file contains valid a valid PDB formatted structure? The file extension alone obviously does not provide sufficient validation. Thanks for any feedback. Martin ------------------------------------------------------------------------------ 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 (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: Jason V. <jas...@sc...> - 2012-06-27 22:24:57
|
Martin, Are you looking for a structure validator or a PDB file format validator? Cheers, -- Jason On Wed, Jun 27, 2012 at 6:00 AM, Martin Hediger <ma...@bl...> wrote: > Dear PyMOL users > Does anybody know a script to verify that a file contains valid a valid > PDB formatted structure? > The file extension alone obviously does not provide sufficient validation. > > Thanks for any feedback. > Martin > > ------------------------------------------------------------------------------ > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Jason Vertrees, PhD PyMOL Product Manager Schrödinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |
From: James S. <jms...@gm...> - 2012-06-28 05:53:38
|
I've obtained accademical licence on LigProt and I found that this softwatre is most handfull in the 2d analysis of protein-ligand interactions. Is it possible to integrate it into pymol what have been done in case of Pose view ? ) By the way does anybody know any another intresting software or pymol modules for the analysis of protein-ligand interactions. In particular I'd like to obtain 3d surfaces of vdw as well as electrosctatics profiles of the active sites of my proteins as well as analysing of H-bonds ? James 2012/6/26 James Starlight <jms...@gm...> > I'm still waiting for accademical license on lig prot. By the way it's > very strange that PoseView have not been accompanied with 'internal water > detector' ;) i've sent the letter to developers with this question and > hope they can help > > James > > 2012/6/26 Thomas Holder <sp...@us...> > >> Hi James, >> >> hm, looks like PoseView ignores all water molecules :( >> >> Have you tried LigPlot? It has a "-w" option to include waters. >> >> Cheers, >> Thomas >> >> >> On 06/26/2012 05:11 PM, James Starlight wrote: >> >>> Thomas, >>> Its really great ) >>> Could you tell me if you find a possible way to take into account >>> burried water from the protein interiour in the Pose View protein-ligand >>> interaction 2D plots ? >>> Most of my proteins consist of such internal water ( like a het atoms in >>> the protein.pdb ) but pose view didnt take this mollecules into account >>> so the final plot lack of many crussial h_bonds between ligand and >>> protein itself. >>> James >>> 2012/6/26 Thomas Holder <sp...@us... >>> <mailto:speleo3@users.**sourceforge.net <sp...@us...>>> >>> >>> >>> >>> Hi all, >>> >>> I thought it would be nice to run such tools directly from PyMOL. So >>> there is a PoseView wrapper on the PyMOLWiki now: >>> >>> http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.php/PoseView> >>> >>> A LigPlot wrapper may follow... >>> >>> Cheers, >>> Thomas >>> >>> On 06/26/2012 10:13 AM, James Starlight wrote: >>> > Christian, >>> > Also I've found the same software- pose view (in that article >>> I've also >>> > found link on it). Its very friendly but I've noticed some erorrs >>> during >>> > representation of the non-covalent contacts partly in case of the >>> vdw >>> > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw >>> but some >>> > crussial interactions could not be visualized) >>> > And the main disadvantage of that software is that it does not >>> take into >>> > account burrial water and it's h-bond networks within protein. >>> > I've ordered free license on the lig prot and hope that this >>> software >>> > will be better ;) >>> > James >>> > 2012/6/26 Christian Roth <christian.roth@bbz.uni-**leipzig.de<chr...@bb...> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >>> > >>> > <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >>> >>> <mailto:christian.roth@bbz.**uni-leipzig.de<chr...@bb...> >>> >>> >>> > >>> > Hi James, >>> > >>> > LigPlot is free for academic users. You just have to verify >>> that you >>> > are a >>> > academic user. MOE does a simimlar representiation but is >>> definitely >>> > not free. >>> > >>> > Christian >>> >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > |
From: Christian R. <chr...@bb...> - 2012-06-28 06:14:32
|
Dear James. I found the hollow script and/or Castp quite useful for this. There exist also a program called surfplot, from Roman Laskowski again. It is integrated in the pdbsum interface and creates ther surfaces. You may look there for examples. Another possibility is Voidoo from Uppsala. By the way, there are already comments about the internal waters from the pose-view group? Best Regards Christian Am Donnerstag 28 Juni 2012 07:53:31 schrieb James Starlight: > I've obtained accademical licence on LigProt and I found that this > softwatre is most handfull in the 2d analysis of protein-ligand > interactions. Is it possible to integrate it into pymol what have been > done in case of Pose view ? ) > > By the way does anybody know any another intresting software or pymol > modules for the analysis of protein-ligand interactions. In particular I'd > like to obtain 3d surfaces of vdw as well as electrosctatics profiles of > the active sites of my proteins as well as analysing of H-bonds ? > > > James > > 2012/6/26 James Starlight <jms...@gm...> > > > I'm still waiting for accademical license on lig prot. By the way it's > > very strange that PoseView have not been accompanied with 'internal water > > detector' ;) i've sent the letter to developers with this question and > > hope they can help > > > > James > > > > 2012/6/26 Thomas Holder <sp...@us...> > > > >> Hi James, > >> > >> hm, looks like PoseView ignores all water molecules :( > >> > >> Have you tried LigPlot? It has a "-w" option to include waters. > >> > >> Cheers, > >> Thomas > >> > >> On 06/26/2012 05:11 PM, James Starlight wrote: > >>> Thomas, > >>> Its really great ) > >>> Could you tell me if you find a possible way to take into account > >>> burried water from the protein interiour in the Pose View > >>> protein-ligand interaction 2D plots ? > >>> Most of my proteins consist of such internal water ( like a het atoms > >>> in the protein.pdb ) but pose view didnt take this mollecules into > >>> account so the final plot lack of many crussial h_bonds between ligand > >>> and protein itself. > >>> James > >>> 2012/6/26 Thomas Holder <sp...@us... > >>> <mailto:speleo3@users.**sourceforge.net > >>> <sp...@us...>>> > >>> > >>> > >>> > >>> Hi all, > >>> > >>> I thought it would be nice to run such tools directly from PyMOL. So > >>> there is a PoseView wrapper on the PyMOLWiki now: > >>> > >>> > >>> http://pymolwiki.org/index.**php/PoseView<http://pymolwiki.org/index.ph > >>>p/PoseView> > >>> > >>> A LigPlot wrapper may follow... > >>> > >>> Cheers, > >>> Thomas > >>> > >>> On 06/26/2012 10:13 AM, James Starlight wrote: > >>> > Christian, > >>> > Also I've found the same software- pose view (in that article > >>> > >>> I've also > >>> > >>> > found link on it). Its very friendly but I've noticed some erorrs > >>> > >>> during > >>> > >>> > representation of the non-covalent contacts partly in case of the > >>> > >>> vdw > >>> > >>> > interactions ( e,g i've change cutof from 0.8 to 1.2 nm for vdw > >>> > >>> but some > >>> > >>> > crussial interactions could not be visualized) > >>> > And the main disadvantage of that software is that it does not > >>> > >>> take into > >>> > >>> > account burrial water and it's h-bond networks within protein. > >>> > I've ordered free license on the lig prot and hope that this > >>> > >>> software > >>> > >>> > will be better ;) > >>> > James > >>> > 2012/6/26 Christian Roth > >>> > <christian.roth@bbz.uni-**leipzig.de<christian.roth@bbz.uni-leipz > >>> >ig.de> > >>> > >>> > >>> <mailto:christian.roth@bbz.**uni-leipzig.de<christian.roth@bbz.uni-leip > >>>zig.de> > >>> > >>> > <mailto:christian.roth@bbz.**uni-leipzig.de<christian.roth@bbz.un > >>> >i-leipzig.de> > >>> > >>> > >>> <mailto:christian.roth@bbz.**uni-leipzig.de<christian.roth@bbz.uni-leip > >>>zig.de> > >>> > >>> > Hi James, > >>> > > >>> > LigPlot is free for academic users. You just have to verify > >>> > >>> that you > >>> > >>> > are a > >>> > academic user. MOE does a simimlar representiation but is > >>> > >>> definitely > >>> > >>> > not free. > >>> > > >>> > Christian > >> > >> -- > >> Thomas Holder > >> MPI for Developmental Biology > >> Spemannstr. 35 > >> D-72076 Tübingen > -- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319 |
From: James S. <jms...@gm...> - 2012-06-28 06:52:21
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Dear Christian, thank you for infromation- I'll examine this software. In particular I'm looking for possible modules for pymol because as I've found previously it's a good visualisation of the surfaces wich have been already included in PyMol. 2012/6/28 Christian Roth <chr...@bb...> > > > By the way, there are already comments about the internal waters from the > pose-view group? > yes, I've told with the pose view developers and they said that there have no options to include buried water yet. So the LigProt software is the best sollution for 2D diaagrams as yet. |