Protonation of selected atoms ?
Dear all, I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer. I tried Structure "Editing -> Add hydrogens" but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation. So is there any way how to protonate only selected N atoms ? If not would be a good idea to add this possibility into Add Hydrogens panel (function). Thank you, Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, Sorry, the hydrogens are added to the whole model. The whole structure is used to calculate the hydrogen locations (hydrogens from different parts may sterically clash or H-bond with one another). However, you can delete all the hydrogens you don't want after addition. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 27, 2013, at 7:24 AM, Marek Maly wrote:
Dear all,
I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer.
I tried Structure "Editing -> Add hydrogens"
but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation.
So is there any way how to protonate only selected N atoms ?
If not would be a good idea to add this possibility into Add Hydrogens panel (function).
Thank you, Best wishes, Marek
Let me rephrase that: obviously hydrogens don't H-bond with one another, but the placement of one hydrogen affects how a nearby hydrogen should be placed within a network of H-bonding functional groups. Elaine On Nov 27, 2013, at 9:56 AM, Elaine Meng wrote:
Hi Marek, Sorry, the hydrogens are added to the whole model. The whole structure is used to calculate the hydrogen locations (hydrogens from different parts may sterically clash or H-bond with one another). However, you can delete all the hydrogens you don't want after addition. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#deletion> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2013, at 7:24 AM, Marek Maly wrote:
Dear all,
I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer.
I tried Structure "Editing -> Add hydrogens"
but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation.
So is there any way how to protonate only selected N atoms ?
If not would be a good idea to add this possibility into Add Hydrogens panel (function).
Thank you, Best wishes, Marek
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Marek, You can do this with Build Structure. With the nitrogens selected, go to that tool's "Modify Structure" tab and do the following: 1) Change element to N 2) Change geometry to tetrahedral if it isn't already 3) Change bonds to 4 4) Change "Residue Name" option to "Leave unchanged" 5) Click Apply Normally using Build Structure would be suboptimal since hydrogen placement would not consider H-bonding interactions, but for protonating tertiary amines that consideration is moot. --Eric Eric Pettersen UCSF Computer Graphics Lab On Nov 27, 2013, at 7:24 AM, "Marek Maly" <marek.maly@ujep.cz> wrote:
Dear all,
I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer.
I tried Structure "Editing -> Add hydrogens"
but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation.
So is there any way how to protonate only selected N atoms ?
If not would be a good idea to add this possibility into Add Hydrogens panel (function).
Thank you,
Best wishes,
Marek
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Eric and Elaine, thank you very much for your help ! My request comes from the fact that depending e.g. on pH in general just the certain percentage of protonable groups is really protonated. This for sure holds for "synthetic" polymers but perhaps also for proteins. To adjust protonation states on proteins I am using H++ server ( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated software e.g. to calculate ionic state of the protonable groups taking here in account pH, dielectric constants (internal/external), micro-environment of the protonable groups etc. Unfortunately this tool seems to works "just" for the proteins (not for example for synthetic polymers or other molecules). So I appreciated the possibility to add hydrogens to the molecular structure in Chimera. Both advices (Elain's and Eric's) might be used to achieve desired partial protonation of the molecular structure using actual chimera possibilities however depending on the size of the structure and depending on the percentage of the protonation and depending on the eventual additional requirements regrading distribution of the protons between different molecular residues (e.g. those containing primary amines, those containing secondary amines those containing tertiary amines ...) it might be still more or less "dirty" manual work. So if may I suggest something for the future Chimera development, it would be perhaps the possibility to protonate just the given percentage (e.g. with random distribution) of certain kind of protonable atoms (e.g. primary, secondary, tertiary amines , O atoms on COO groups ) which moreover belongs just to actually selected molecular part. Of course that regarding "steric clashes" etc. also the "non-selected" parts of the structure should be always considered in the process of protonation of the actually selected parts. Best wishes, Marek Dne Wed, 27 Nov 2013 20:18:58 +0100 Eric Pettersen <pett@cgl.ucsf.edu> napsal/-a:
Hi Marek, You can do this with Build Structure. With the nitrogens selected, go to that tool's "Modify Structure" tab and do the following:
1) Change element to N 2) Change geometry to tetrahedral if it isn't already 3) Change bonds to 4 4) Change "Residue Name" option to "Leave unchanged" 5) Click Apply
Normally using Build Structure would be suboptimal since hydrogen placement would not consider H-bonding interactions, but for protonating tertiary amines that consideration is moot.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Nov 27, 2013, at 7:24 AM, "Marek Maly" <marek.maly@ujep.cz> wrote:
Dear all,
I would like to protonate just several nitrogen atoms (tertiary amines) of my hyperbranched polymer.
I tried Structure "Editing -> Add hydrogens"
but it protonised all my tertiary amines in the structure ignoring the fact that only few of them were selected and considered for protonation.
So is there any way how to protonate only selected N atoms ?
If not would be a good idea to add this possibility into Add Hydrogens panel (function).
Thank you,
Best wishes,
Marek
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, You might also want to take a look at PROPKA, developed by the Jensen group, University of Copenhagen: <http://propka.ki.ku.dk/> Although developed originally for proteins, it looks like it has been extended to "ligands" as well. I haven't tried it on nonproteins, but there are some literature references on that page that discuss the method and how it has been extended. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Nov 28, 2013, at 5:44 AM, Marek Maly wrote:
Dear Eric and Elaine,
thank you very much for your help !
My request comes from the fact that depending e.g. on pH in general just the certain percentage of protonable groups is really protonated. This for sure holds for "synthetic" polymers but perhaps also for proteins.
To adjust protonation states on proteins I am using H++ server ( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated software e.g. to calculate ionic state of the protonable groups taking here in account pH, dielectric constants (internal/external), micro-environment of the protonable groups etc. Unfortunately this tool seems to works "just" for the proteins (not for example for synthetic polymers or other molecules).
So I appreciated the possibility to add hydrogens to the molecular structure in Chimera.
Both advices (Elain's and Eric's) might be used to achieve desired partial protonation of the molecular structure using actual chimera possibilities however depending on the size of the structure and depending on the percentage of the protonation and depending on the eventual additional requirements regrading distribution of the protons between different molecular residues (e.g. those containing primary amines, those containing secondary amines those containing tertiary amines ...) it might be still more or less "dirty" manual work.
So if may I suggest something for the future Chimera development, it would be perhaps the possibility to protonate just the given percentage (e.g. with random distribution) of certain kind of protonable atoms (e.g. primary, secondary, tertiary amines , O atoms on COO groups ) which moreover belongs just to actually selected molecular part. Of course that regarding "steric clashes" etc. also the "non-selected" parts of the structure should be always considered in the process of protonation of the actually selected parts.
Best wishes, Marek
Dear Elaine, thanks for PROPKA advice, but it seems that PPI dendrimer is still too "exotic" structure for this software - see the attached results. Anyway after the short experiment with "tutorial" 1hpx structure I am not sure that this software physically adds/deletes hydrogen atoms to/from the molecular structure, taking in account calculated pKa values and the desired pH value. In fact it seems to me that there is no chance to provide pH value of the interest here as the important input value for estimating the ionic states of the protonable residues. Best wishes, Marek Dne Thu, 28 Nov 2013 16:32:50 +0100 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, You might also want to take a look at PROPKA, developed by the Jensen group, University of Copenhagen: <http://propka.ki.ku.dk/>
Although developed originally for proteins, it looks like it has been extended to "ligands" as well. I haven't tried it on nonproteins, but there are some literature references on that page that discuss the method and how it has been extended. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 28, 2013, at 5:44 AM, Marek Maly wrote:
Dear Eric and Elaine,
thank you very much for your help !
My request comes from the fact that depending e.g. on pH in general just the certain percentage of protonable groups is really protonated. This for sure holds for "synthetic" polymers but perhaps also for proteins.
To adjust protonation states on proteins I am using H++ server ( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated software e.g. to calculate ionic state of the protonable groups taking here in account pH, dielectric constants (internal/external), micro-environment of the protonable groups etc. Unfortunately this tool seems to works "just" for the proteins (not for example for synthetic polymers or other molecules).
So I appreciated the possibility to add hydrogens to the molecular structure in Chimera.
Both advices (Elain's and Eric's) might be used to achieve desired partial protonation of the molecular structure using actual chimera possibilities however depending on the size of the structure and depending on the percentage of the protonation and depending on the eventual additional requirements regrading distribution of the protons between different molecular residues (e.g. those containing primary amines, those containing secondary amines those containing tertiary amines ...) it might be still more or less "dirty" manual work.
So if may I suggest something for the future Chimera development, it would be perhaps the possibility to protonate just the given percentage (e.g. with random distribution) of certain kind of protonable atoms (e.g. primary, secondary, tertiary amines , O atoms on COO groups ) which moreover belongs just to actually selected molecular part. Of course that regarding "steric clashes" etc. also the "non-selected" parts of the structure should be always considered in the process of protonation of the actually selected parts.
Best wishes, Marek
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
participants (3)
-
Elaine Meng -
Eric Pettersen -
Marek Maly