Re: [phenixbb] phenix.ready_set hydrogens not compatable with coot library
Hi All, Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected] Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
Coming from using Refmac I'm slightly puzzled by the philosophy here. By default (I believe) Refmac always adds riding hydrogens for the refinement but doesn't output them in the refined PDB files. This seems to me to be the right thing to do. I don't see any reason for not including Hs in refinement since you know where most of them are relative to the heavy atoms, and they will (maybe marginally) improve things. On the other hand I don't normally want them cluttering up the display in Coot (maybe because I'm just not used to them), and I certainly don't want to include them in my PDB deposition, since I don't think they are an independent part of the model, and including them would imply I can see them. They are I suppose useful in bump checks, but I would just add them back for that purpose Phil On 23 Aug 2010, at 20:09, Joseph Noel wrote:
Hi All,
Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded.
Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA
Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected]
Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Phil,
By default in PHENIX hydrogens are treated as riding model, and as you
say they are important for preventing steric clashes from developing
during refinement. When used in refinement, however, it is very
important to include them in your deposition because how their
B-factor terms are specified and handled is essential to understanding
where the final model came from. Further, the final position of some
of the hydrogens is difficult to predict (such as a rotatable methyl
group), so knowing what the final positions are for such hydrogen
atoms is necessary to account for the deposited model and refinement
statistics. Without deposition atomic positions and B-factor
information for H atoms will be lost. I don't think that having them
in your model implies that you can see them necessarily, but rather
implies that you know with fairly high accuracy where they are
(assuming your heavy atom positions are correct) and thus used them to
arrive at your final model.
When using Coot from the PHENIX GUI, there is an option to turn the H
atoms off in the display if you do find them to clutter the screen too
much. Showing them in Coot can be useful, though, as Coot is able to
display Probe dots to help in guiding hand-correction of problem areas
in your model.
Jeff
On Mon, Aug 23, 2010 at 1:08 PM, Phil Evans
Coming from using Refmac I'm slightly puzzled by the philosophy here. By default (I believe) Refmac always adds riding hydrogens for the refinement but doesn't output them in the refined PDB files. This seems to me to be the right thing to do. I don't see any reason for not including Hs in refinement since you know where most of them are relative to the heavy atoms, and they will (maybe marginally) improve things. On the other hand I don't normally want them cluttering up the display in Coot (maybe because I'm just not used to them), and I certainly don't want to include them in my PDB deposition, since I don't think they are an independent part of the model, and including them would imply I can see them. They are I suppose useful in bump checks, but I would just add them back for that purpose
Phil
On 23 Aug 2010, at 20:09, Joseph Noel wrote:
Hi All,
Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded.
Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA
Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: [email protected]
Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Hi Phil, each program handles hydrogen atoms slightly different: - B-factors of hydrogen atoms may be simply inherited from the parent atoms (atom X in X-H bond) or they may be multiplied by a factor 1.0...1.5. These B-factors may be set once at the beginning of refinement run or they may be updated during refinement; - Different X-H bond lengths may be used: shorter distances (corresponding to electron cloud; as described in Shelxl) or longer "neutron distances" (corresponding to nuclear position). Even within one library you can observe some mixtures: for example, in Monomer library shorter distances are used for amino-acids and longer distances are used for some other compounds; - Programs may or may not account for H atom scattering (they may only use hydrogens in geometry restraints). This all makes it not very straightforward to restore hydrogen atoms the same way they were in original structure, which means that the reported statistics may not be exactly reproducible. This is illustrated in our recent paper: Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J. Appl. Cryst. 2010, 43, 669-67 Finally, removing hydrogens is a matter of a simple command, for example: phenix.reduce model.pdb -trim > model_no_H.pdb while restoring H atoms the exact same way they were originally is much less straightforward. All the best! Pavel. On 8/23/10 1:08 PM, Phil Evans wrote:
Coming from using Refmac I'm slightly puzzled by the philosophy here. By default (I believe) Refmac always adds riding hydrogens for the refinement but doesn't output them in the refined PDB files. This seems to me to be the right thing to do. I don't see any reason for not including Hs in refinement since you know where most of them are relative to the heavy atoms, and they will (maybe marginally) improve things. On the other hand I don't normally want them cluttering up the display in Coot (maybe because I'm just not used to them), and I certainly don't want to include them in my PDB deposition, since I don't think they are an independent part of the model, and including them would imply I can see them. They are I suppose useful in bump checks, but I would just add them back for that purpose
Phil
On Aug 23, 2010, at 9:09 PM, Joseph Noel wrote:
Hi All,
Indeed even the latest COOT still relies on the old PDB format and hydrogens fly. Its probably not prudent to use hydrogens in refinement then remove them and add back each time. Kind of defeats the purpose of using them in the first place. Until COOT is updated I found a pretty easy way around things as long as you have access to the internet. Just use the MOLPROBITY site (http://molprobity.biochem.duke.edu/). In addition to it being a fantastic tool for really cleaning up structures, you can quickly upload your refined file from Phenix with hydrogens, then hit the button to downgrade to PDB v23. It creates the appropriate file with renamed hydrogens that work great in COOT. You can then re-upload the COOT rebuilt model and it will "upgrade" naming to the latest PDB version. Download that file and there you go for Phenix refinement. Sounds like a bit but very fast and easy to implement until COOT is upgraded.
Joe
This is indeed what we have also been doing, and I can confirm that it appears to work just fine! Best, Luca
participants (5)
-
Jeff Headd -
Joseph Noel -
Jovine Luca -
Pavel Afonine -
Phil Evans