Re: [COOT] deleting atoms from alternate conformations
I agree with wtempel Once a residue is split it means there is evidence for 2 conformations. If one atom in one conformation has occupancy reset to 0.00, that certainly does not imply that the other NZ A say should have occupancy 1.00 It wont the refinement in REFMAC anyway Eleanor Paul Emsley wrote: wtempel wrote: Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Like Linux (haha). Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? Would the answer be different if a C or an O had been deleted? I'd rather ask: is Coot doing the right thing in such a case? I suspect that Garib or Pavel may know. 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Yes. Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. I think that that is just doing the above for many atoms. Paul.
Re: [COOT] deleting atoms from alternate conformations
Paul Emsley wrote: wtempel wrote: Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Like Linux (haha). Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? Would the answer be different if a C or an O had been deleted? I'd rather ask: is Coot doing the right thing in such a case? I suspect that Garib or Pavel may know. My problem is that I agree with the original poster that the remaining NZ atom should continue with a confID of A, but I also agree with Paul that the deleted C atom should be changed to a single conformation. However, if the residue that the C atom is linked to is also split I would feel differently. In my favorite structure there is a stretch of five residues where the main chain has two conformation. If I deleted a C atom from the B conformer in the middle it would not be my intention to have only a single conformation for that atom. How about this suggestion? If the deleted atom is bonded to an atom with a single conformation then the other conformer becomes a single conformation. If the deleted atom makes bonds only with atoms that also have alternative conformations then the remaining atom retains its partial occupancy. This would keep the poster happy, keep Paul happy with his C atom when the neighbor has a single conformation, and will keep me happy when there is a stretch of main chain disorder. A problem with this scheme occurs with the lysine mentioned before. If the user decides to delete the entire B conformation one atom at a time the result will differ depending on the end of the side chain they start deleting atoms from. I don't know if this is a serious problem, or even a problem at all. Dale Tronrud 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Yes. Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. I think that that is just doing the above for many atoms. Paul.
[COOT] deleting atoms from alternate conformations
Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Time to learn how to use it myself then... Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. Thank you for your consideration. Happy Holidays to everyone! Wolfram Tempel
Re: [COOT] deleting atoms from alternate conformations
wtempel wrote: Hi all, judging from what I see being used by my colleagues, COOT is well on its way to world domination. Like Linux (haha). Anyway, suppose I have split a residue, say lysyl, to model alternate conformations of its side chain. Suppose further that I would like to remove NZ from conformer B. Upon doing so, the current COOT implementation will remove the atom. Good. It will also remove the confID from what was conformer A's NZ atom and re-set its occupancy to 1. On the latter part, intuition tells me that instead, conformer A's atoms should be unaffected, namely keep their confID and sub-unity occupancy. My questions: 1) What behavior is expected by other COOT users in comparable situations? Would the answer be different if a C or an O had been deleted? I'd rather ask: is Coot doing the right thing in such a case? I suspect that Garib or Pavel may know. 2) Should a few folks align themselves with my opinion, can COOT's behavior be modified without unintended side effects? Yes. Specifically, I like COOT's current behavior when Delete Residue is applied to alternative conformations: Delete the conformer completely and set the remaining conformer's atoms to Occ=1 and remove the confID. I think that that is just doing the above for many atoms. Paul.
