From: James S. <jms...@gm...> - 2012-01-20 06:02:50
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Dear PyMol users! I've decided create new topic about representation of the protein-ligand interactions via Pymol because of alot of questions wich have been emerged during last month. Commonly I use the PyMol built-in command a-> present->ligands sites-> cartoon for the representation of the polar contacts between protein and ligand 1- Some of my proteins consist of ligand wich include some of amino acids from sequence of my protein ( e.g fluorophores in GFP). So I'd like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly motif in GFP). How I could do it? 2- In some cases there are relatively long distances between polar ligand groups and protein's polar residues where H-bond must be formed ( eg in some cases up to 3.5-3.7 A ). So the default a-> present->ligands sites-> cartoon does not recognize that long H-bonds. How I could set the H-bond cutoff distance in the above method? 3- Is there any way to represent tight packing contacts beetween non-polar groups in my protein (or protein\ ligand sites) besides common representation of the Vdv radii ? Thank for help, James |
From: Thomas H. <sp...@us...> - 2012-01-20 12:06:18
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Hi James, > 1- Some of my proteins consist of ligand wich include some of amino > acids from sequence of my protein ( e.g fluorophores in GFP). So I'd > like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly > motif in GFP). How I could do it? The preset selects hetatoms as ligands, so you could do: select motif, (pepseq SYG) and not (name C+N+O) alter motif, type="HETATM" > 2- In some cases there are relatively long distances between polar > ligand groups and protein's polar residues where H-bond must be formed ( > eg in some cases up to 3.5-3.7 A ). So the default a-> present->ligands > sites-> cartoon does not recognize that long H-bonds. How I could set > the H-bond cutoff distance in the above method? there are several h_bond_* settings that control this. (I recommend http://pymolwiki.org/index.php/Grepset to find settings) For example: set h_bond_cutoff_center, 5.0 set h_bond_cutoff_edge, 4.0 Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-01-23 07:00:25
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Thanks Thomas I've just one extra question about ligand sites. As I've said previously I can obtain information about polar contacts between ligand and its surrounding residues via Present- ligand sites. On the next step I mask all other non relevant parts of the protein ( wich are represented as the cartoon) by hide cartoon so as the consequence I have only ligand and its environment ( other residues and some water) How I could select all this visible (relevant) part and save it in the separate pdb? I've not found such simple selection by the visible part in the selection algebra :( James 2012/1/20 Thomas Holder <sp...@us...> > Hi James, > > > 1- Some of my proteins consist of ligand wich include some of amino >> acids from sequence of my protein ( e.g fluorophores in GFP). So I'd >> like to assign some residue motif as the ligand group ( e.g Ser Tyr Gly >> motif in GFP). How I could do it? >> > > The preset selects hetatoms as ligands, so you could do: > > select motif, (pepseq SYG) and not (name C+N+O) > alter motif, type="HETATM" > > > 2- In some cases there are relatively long distances between polar >> ligand groups and protein's polar residues where H-bond must be formed ( >> eg in some cases up to 3.5-3.7 A ). So the default a-> present->ligands >> sites-> cartoon does not recognize that long H-bonds. How I could set >> the H-bond cutoff distance in the above method? >> > > there are several h_bond_* settings that control this. (I recommend > http://pymolwiki.org/index.**php/Grepset<http://pymolwiki.org/index.php/Grepset>to find settings) For example: > > set h_bond_cutoff_center, 5.0 > set h_bond_cutoff_edge, 4.0 > > > Cheers, > Thomas > > -- > Thomas Holder > MPI for Developmental Biology > Spemannstr. 35 > D-72076 Tübingen > |
From: Thomas H. <sp...@us...> - 2012-01-23 08:31:57
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Hi James, > How I could select all this visible (relevant) part and save it in the > separate pdb? > I've not found such simple selection by the visible part in the > selection algebra :( use the "visible" single-word selector :) http://pymolwiki.org/index.php/Single-word_Selectors save onlyvisible.pdb, visible Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-01-23 09:32:11
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Thomas, thanks again! I want to recall to the ligand assignment via select motif, (pepseq TYG) and not (name C+N+O) alter motif, type="HETATM" I have no problems with the representation of the assigned ligand with its environment but when I save this as new pdb via save test.pdb, visible my output pdb contains some errors like missing bonds between HETATM residues ( ligand ) etc. Also I've checked this new pdb and find alot of TER strings between each of residues. I've tried to remove this TER strings and renamed HETATOMS to ATOMS but this didnt help :( I suppose that error might be due to the HETATM ussage because when I check sequence of my structure I'vee found many repeates of the assigned residues like THR-THR-THR-THR-TYR-TYR-TYR-TYR-TYR-GLY-GLY-GLY instead of simple THR-TYR-GLY triplet What should I do? 2012/1/23 James Starlight <jms...@gm...> > Thomas, thanks again! > > > > I want to recall to the ligand assignment via > > > select motif, (pepseq TYG) and not (name C+N+O) > alter motif, type="HETATM" > > I have no problems with the representation of the assigned ligand with its > environment but when I save this as new pdb via > > > save test.pdb, visible > > my output pdb contains some errors like missing bonds between HETATM > residues ( ligand ) etc. Also I've checked this new pdb and find alot of > TER strings between each of residues. > > I've tried to remove this TER strings and renamed HETATOMS to ATOMS but > this didnt help :( > > What should I do? > > > James > > > 2012/1/23 Thomas Holder <sp...@us...> > >> Hi James, >> >> >> How I could select all this visible (relevant) part and save it in the >>> separate pdb? >>> I've not found such simple selection by the visible part in the >>> selection algebra :( >>> >> >> use the "visible" single-word selector :) >> >> http://pymolwiki.org/index.**php/Single-word_Selectors<http://pymolwiki.org/index.php/Single-word_Selectors> >> >> save onlyvisible.pdb, visible >> >> >> Cheers, >> Thomas >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > |
From: Thomas H. <sp...@us...> - 2012-01-23 10:34:32
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Hi James, > I have no problems with the representation of the assigned ligand with > its environment but when I save this as new pdb via > > save test.pdb, visible > > my output pdb contains some errors like missing bonds between HETATM > residues ( ligand ) etc. maybe this trick was too dirty... change the type back to ATOM before saving: select motif, (pepseq TYG) and not (name C+N+O) alter motif, type="HETATM" preset.ligand_cartoon("all") alter motif, type="ATOM" > Also I've checked this new pdb and find alot of > TER strings between each of residues. This is because you only selected the local environment which has only short pieces of the polymer. PyMOL sees chain breaks there. You can suppress TER records by: unset pdb_use_ter_records Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |
From: James S. <jms...@gm...> - 2012-01-25 19:17:13
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In addition I'd like to know more about possible flexibility in the representation of the protein-ligand contacts by means of the present-> ligand site option. For instance sometimes I have ligand group situated in the some distance from the interiour group. So this space forms empty cavity around ligand. So if I use present- ligand sites by default pymol didnt see the interiour residues due to its remoteness from ligand. But could I vary some cutoff distance to represent POSSIBLE polar and packing contacts like as this interiour would be in the contact with the ligand? I'd like to use this for better prediction of the mutations wich will change the shape and geometry of the ligand binding pockets in the above cases. \ Thanks again, James 2012/1/23 James Starlight <jms...@gm...> > Thanks Thomas > > The reversible convertion indeed solved problem. > > James > > > 2012/1/23 Thomas Holder <sp...@us...> > >> Hi James, >> >> >> I have no problems with the representation of the assigned ligand with >>> its environment but when I save this as new pdb via >>> >>> save test.pdb, visible >>> >>> my output pdb contains some errors like missing bonds between HETATM >>> residues ( ligand ) etc. >>> >> >> maybe this trick was too dirty... change the type back to ATOM before >> saving: >> >> >> select motif, (pepseq TYG) and not (name C+N+O) >> alter motif, type="HETATM" >> preset.ligand_cartoon("all") >> alter motif, type="ATOM" >> >> >> Also I've checked this new pdb and find alot of >>> TER strings between each of residues. >>> >> >> This is because you only selected the local environment which has only >> short pieces of the polymer. PyMOL sees chain breaks there. You can >> suppress TER records by: >> >> unset pdb_use_ter_records >> >> >> Cheers, >> Thomas >> >> -- >> Thomas Holder >> MPI for Developmental Biology >> Spemannstr. 35 >> D-72076 Tübingen >> > > |
From: Xiaoshan M. <xs...@ya...> - 2012-02-03 22:02:38
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Hi Pymoler, I want to present a structure to non-structural biologist. They want to visualize the change of surface charge at different pH. For example, Histidine will have different protonation state at pH 7.5 and 5. What would be the best way to visualize this? I know an accurate calculation probably is too hard, but would like to know if there is a clever way of approximation. Thanks a lot. Xiaoshan |
From: Troels E. L. <tl...@gm...> - 2012-02-04 13:23:11
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How about using the APBS plugin? http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol The plugin that is shipped with Pymol as standard http://www.pymolwiki.org/index.php/APBS The same plugin, but in the Pymol-script-repo<http://www.pymolwiki.org/index.php/Git_intro> . Here the plugin is setup to find the included (psize.py) and (pdb2pqr.py) http://www.pymolwiki.org/index.php/Apbsplugin And calculate the PQR at different pH? http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr Server http://kryptonite.nbcr.net/pdb2pqr/ In the "Main" tab, in the APBS pymol plugin. Select: "Choose Externally generated PQR". Or use this: python pdb2pqr.py --ff=AMBER --with-ph=5 As far as I know, pdb2pqr, uses PROPKA 1.0 to get the pKa. There has been a large development to PROPKA since then. Version 3.1 is available at homepage: http://propka.ki.ku.dk/ If you want to visualize the pKa, try this Pymol script. http://www.pymolwiki.org/index.php/Propka Troels Emtekær Linnet Lyongade 24. 4.mf, 2300 København S Mobil: +45 60210234 2012/2/3 Xiaoshan Min <xs...@ya...> > Hi Pymoler, > > I want to present a structure to non-structural biologist. They want to > visualize the change of surface charge at different pH. For example, > Histidine will have different protonation state at pH 7.5 and 5. What > would be the best way to visualize this? I know an accurate calculation > probably is too hard, but would like to know if there is a clever way of > approximation. > > Thanks a lot. > > Xiaoshan > > > > ------------------------------------------------------------------------------ > Try before you buy = See our experts in action! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-dev2 > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |