FW: How can I find H-bond between ligand and protein residues within selected angstrom?
On 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly@bs.s.u-tokyo.ac.jp> wrote:
Dear Chimera creator,
I use Chimera to analyse protein-ligand interaction. Especially, I would like to find H-bond between these. I clicked HBonds and tried to search H-bond within selected distance. However,I could not. I guess the reason is that I was not able to understand "Relax constraints" in H-Bond parameter window. I ,of course, checked chimera's help. What is relax constraints? What does 0.4 angstroms indicate? Is this the Max distance between ligand and protein residue? I would like to find H-bond between them within selected angstrom. What should I do to know that? Please teach me how to do. Thank you for being patient with my English.
Best regards,
Yuriko Takagi Tokyo university student
Dear Yuriko Takagi, The values in the FindHBond are not the distance and angle cutoffs, they are extra “tolerance” values added to these cutoffs. The cutoffs are not shown in the FindHBond dialog because there are many different distance and angle cutoffs depending on the types of the atoms. For example, the distance and angle cutoff(s) would be different for N-H to O=C than for O-H to O=C. This is mentioned in bottom section of the the FindHBond help page, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> ...and the many different cutoff values are listed in tables 5-8 of the paper cited in that page: Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. <http://www.ncbi.nlm.nih.gov/pubmed/9007693> Then if you use a “relax” distance value of 0.4 angstrom, 0.4 will be added to all of those different distance cutoff values. With FindHBond you cannot just use a single same distance for everything, but you can show distance labels on the results and/or write output information (including distances) to the Reply Log or to a file. Then if you want to, you can ignore the results with longer than a certain distance. I hope this helps, 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 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly@bs.s.u-tokyo.ac.jp> wrote:
Dear Chimera creator,
I use Chimera to analyse protein-ligand interaction. Especially, I would like to find H-bond between these. I clicked HBonds and tried to search H-bond within selected distance. However,I could not. I guess the reason is that I was not able to understand "Relax constraints" in H-Bond parameter window. I ,of course, checked chimera's help. What is relax constraints? What does 0.4 angstroms indicate? Is this the Max distance between ligand and protein residue? I would like to find H-bond between them within selected angstrom. What should I do to know that? Please teach me how to do. Thank you for being patient with my English.
Best regards,
Yuriko Takagi Tokyo university student
Dear Meng, Thank you for your reply and kind description. I will try the way to find protein-ligand interaction. If I have some questions after this,I will ask your team. Best regards, Yuriko Takagi Tokyo university student ----- Original Message -----
From: Elaine Meng <meng@cgl.ucsf.edu> To: kagaribi-firefly@bs.s.u-tokyo.ac.jp Cc: Chimera_mailing_list <chimera-users@cgl.ucsf.edu> Date: 2015-09-25 01:40:16 Subject: Re: [Chimera-users] FW: How can I find H-bond between ligand and protein residues within selected angstrom?
Dear Yuriko Takagi, The values in the FindHBond are not the distance and angle cutoffs, they are extra “tolerance” values added to these cutoffs. The cutoffs are not shown in the FindHBond dialog because there are many different distance and angle cutoffs depending on the types of the atoms. For example, the distance and angle cutoff(s) would be different for N-H to O=C than for O-H to O=C.
This is mentioned in bottom section of the the FindHBond help page, <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
...and the many different cutoff values are listed in tables 5-8 of the paper cited in that page:
Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22. <http://www.ncbi.nlm.nih.gov/pubmed/9007693>
Then if you use a “relax” distance value of 0.4 angstrom, 0.4 will be added to all of those different distance cutoff values.
With FindHBond you cannot just use a single same distance for everything, but you can show distance labels on the results and/or write output information (including distances) to the Reply Log or to a file. Then if you want to, you can ignore the results with longer than a certain distance.
I hope this helps, 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 9/19/15 1:29 AM, "高木友理子" <kagaribi-firefly@bs.s.u-tokyo.ac.jp> wrote:
Dear Chimera creator,
I use Chimera to analyse protein-ligand interaction. Especially, I would like to find H-bond between these. I clicked HBonds and tried to search H-bond within selected distance. However,I could not. I guess the reason is that I was not able to understand "Relax constraints" in H-Bond parameter window. I ,of course, checked chimera's help. What is relax constraints? What does 0.4 angstroms indicate? Is this the Max distance between ligand and protein residue? I would like to find H-bond between them within selected angstrom. What should I do to know that? Please teach me how to do. Thank you for being patient with my English.
Best regards,
Yuriko Takagi Tokyo university student
participants (3)
-
Elaine Meng -
Williams, Joanne -
高木友理子