Query regarding Ksdssp assignment
Dear Users and Developers, I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera? Looking forward for the advices. Thank you. with best regards, Arun Prasad
On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
Dear Users and Developers,
I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera?
Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature- request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi Arun, A related possibility is to use the FindHBond tool (or command) in Chimera. Then you would get a "visual" of which strands are tied together with H-bonds into sheets. This H-bond detection tool is completely separate from ksdssp and uses different criteria. The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file. However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html> Criteria: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria> 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 Jul 14, 2011, at 3:30 PM, Eric Pettersen wrote:
On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
Dear Users and Developers,
I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera?
Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature-request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it.
--Eric
Dear Eric and Elaine, Thank you for adding the new implementation of ksdssp into the recent daily build. The new -v switch works fine and I am able to read the details of the secondary structural assignments from the reply log. For each residue, the reply log gives details about the helix and strand (ladder) assignment but not about the sheet information (i.e. to know which group of strands make up a sheet). I would like to know whether its possible to add a sheet label along with the strand assignment letter 'E' for each strand residues so that it will aid the identification of all the strands that belong to a sheet? Or to make things simple is it possible to add a sheet summary along with the helix and ladder summary in the reply log? That would be very helpful in annotating seconday structural assignments. I thank Elaine, for your alternative suggestions using FindHBond tool. Thank you. with kind regards, Arun Prasad Eric Pettersen wrote:
On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
Dear Users and Developers,
I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera?
Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature-request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi Arun, A related possibility is to use the FindHBond tool (or command) in Chimera. Then you would get a "visual" of which strands are tied together with H-bonds into sheets. This H-bond detection tool is completely separate from ksdssp and uses different criteria. The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file. However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
Criteria: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html#criteria>
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
Hi Arun, What Chimera returns is pretty much a straight transcription of what its predecessor, Midas, used to return. I agree it would be nice if it returned a succinct representation of the sheets but unfortunately it does not. I will add that to my to-do list but no guarantees as to when I'll be able to get to it. In the interim you can at least use the "Ladder Summary" to deduce the sheets, e.g. in entry 1WWW, chain V, the summary is: Ladder Summary 17.V -> 22.V antiparallel 53.V -> 58.V 27.V -> 29.V antiparallel 35.V -> 37.V 41.V -> 43.V antiparallel 48.V -> 50.V 76.V -> 92.V antiparallel 97.V -> 114.V Since none of the residue ranges overlap, you have four 2-strand sheets. Whereas for chain X: Ladder Summary 287.X -> 290.X antiparallel 303.X -> 306.X 299.X -> 305.X antiparallel 342.X -> 348.X 312.X -> 317.X antiparallel 359.X -> 364.X 328.X -> 332.X antiparallel 344.X -> 348.X 357.X -> 365.X antiparallel 368.X -> 376.X numbers 1, 2, and 4 overlap, and 3 and 5 overlap. Therefore you have a 4-strand sheet and a 3-strand sheet. --Eric On Jul 24, 2011, at 4:56 AM, Arun Prasad Pandurangan wrote:
Dear Eric and Elaine,
Thank you for adding the new implementation of ksdssp into the recent daily build. The new -v switch works fine and I am able to read the details of the secondary structural assignments from the reply log. For each residue, the reply log gives details about the helix and strand (ladder) assignment but not about the sheet information (i.e. to know which group of strands make up a sheet). I would like to know whether its possible to add a sheet label along with the strand assignment letter 'E' for each strand residues so that it will aid the identification of all the strands that belong to a sheet? Or to make things simple is it possible to add a sheet summary along with the helix and ladder summary in the reply log? That would be very helpful in annotating seconday structural assignments.
I thank Elaine, for your alternative suggestions using FindHBond tool.
Thank you.
with kind regards, Arun Prasad
Eric Pettersen wrote:
On Jul 14, 2011, at 8:52 AM, Arun Prasad Pandurangan wrote:
Dear Users and Developers,
I would like to know whether its possible to retrieve the full secondary structural assignment using Ksdssp within Chimera. For instance, I would like to know all the strands that belong to a beta sheet. If I am right, running Ksdssp from Chimera only gives details of the strand (using isStrand) and helix (using isHelix) assignment and not about sheet information. Using the full output of an another program DSSP, I am able deduce which strands belongs to which sheets. I would like to know whether similar kind of detailed output is available from Ksdssp as well. If so how to retrieve those information within Chimera?
Hi Arun, The short answer is no. The C++ function that does the computation does have the ability to output the same kind of summary information that the KSDSSP program itself outputs, but due to some shortcomings in Chimera's Python/C++ API interface when the function was written there is currently no way to communicate that information up to the Python layer for display. However, between when the function was written and now we have improved that API interface and with some work it would now be possible to pass the information up and show it. That doesn't really help you a lot right now, but I will open a feature-request ticket in Chimera's Trac database with you on the recipient list so that you will be notified when we've had time to implement it. It may take awhile before we get to it.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi Arun, A related possibility is to use the FindHBond tool (or command) in Chimera. Then you would get a "visual" of which strands are tied together with H-bonds into sheets. This H-bond detection tool is completely separate from ksdssp and uses different criteria. The resulting H-bond info (donor and acceptor atoms, distances) can be written to a file. However, it would take a fair amount of postprocessing effort to combine this with the strand assignments to identify the sheets.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>
Criteria: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond...
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
participants (3)
-
Arun Prasad Pandurangan -
Elaine Meng -
Eric Pettersen