Water/residue alternative conformations
Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.
Roeland, Have you checked that that water altloc should be B and not A? i.e. if your water replaces side chain altloc A, then water altloc should be B and not A. This works in my lab. -----Original Message----- From: Roeland Boer [mailto:[email protected]] Sent: Fri 5/29/2009 3:58 AM To: [email protected] Subject: [phenixbb] Water/residue alternative conformations Dear all, I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)? The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13. I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } } Thanks, Roeland Boer.
Dear Mark, Thanks for the suggestion. I changed the altlocs of the residue and the water so that they are consistent (the water molecule replaces alt conf B of res 13, which is the lower occupancy alt conf, and makes a H-bond with alt conf A of res13) but the water is still pushed away. The updated lines used for the occupancy refinement: constrained_group { selection = chain A and resseq 13 and altloc B selection = (chain A and resseq 13 and altloc A) or (resname HOH and resseq 1519 and altloc A) } Any help would be greatly appreciated, because I see this happening a lot throughout the structure. Thanks, Roeland. Mayer, Mark (NIH/NICHD) [E] escribió:
Roeland,
Have you checked that that water altloc should be B and not A? i.e. if your water replaces side chain altloc A, then water altloc should be B and not A. This works in my lab.
-----Original Message----- From: Roeland Boer [mailto:[email protected]] Sent: Fri 5/29/2009 3:58 AM To: [email protected] Subject: [phenixbb] Water/residue alternative conformations
Dear all,
I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)?
The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13.
I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } }
Thanks, Roeland Boer.
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Hi Roeland, could you please send the fragment of PDB file that contains residues and waters in question, or just send the whole PDB? What you are trying to do is definitely possible in phenix.refine so I presume there must be something obvious (oversight somewhere) that makes it not working as expected. Pavel. On 5/29/09 12:58 AM, Roeland Boer wrote:
Dear all,
I'm refining a 1.45 Ang structure in which I have several residues that have alternate conformations. These alternate conformations in some cases coincide with additional density that suggests the presence of a water molecule, appropriately positioned to make hydrogen bonds with near atoms. I have modeled partially occupied waters in these additional densities and linked their occupancies with the alternate conformation that is not clashing with the water in question. My problem is that these partially occupied waters are pushed away by the 'overlapping' alternate conformation of the amino acids. I guess there's an antibump restraint somewhere? How can I tell phenix that these alternate waters are not sterically clashing with the amino acid (since the sum occupancies of the water plus alternate conformation is 1)?
The attached image shows one of those disordered residues after refinement. Water 1519 is pushed away from one alt conf (A) of Gln13, whereas the density suggests it should be making a hydrogen bond to OE1 of the altconf B of Gln13.
I describe the occupancies of the situation in the attached image as below. refinement { refine { occupancies { constrained_group { selection = chain A and resseq 13 and altloc A selection = (chain A and resseq 13 and altloc B) or (resname HOH and resseq 1519 and altloc A) } } } }
Thanks, Roeland Boer.
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Dear Pavel, Thanks for the reply. I got it working, you were probably right that it was an oversight. I have a follow-up question concerning triple conformations: if I have sidechain confs A, B and C and a water molecule sitting in the position of C, can I phenix that it should have the 1-C occupancy (or 1 minus A+B)? I've tried this: constrained_group { selection = (chain A and resseq 595 and altloc A) or (resname HOH and resseq 1033) selection = (chain A and resseq 595 and altloc B) or (resname HOH and resseq 1033) selection = (chain A and resseq 595 and altloc C) } but it gave me an error (obviously) Thanks, Roeland. Pavel Afonine escribió:
Hi Roeland,
could you please send the fragment of PDB file that contains residues and waters in question, or just send the whole PDB? What you are trying to do is definitely possible in phenix.refine so I presume there must be something obvious (oversight somewhere) that makes it not working as expected.
Pavel.
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Hi Roeland, if you have a triple conformation A, B and C, then their occupancies should be qA+qB+qC=1. Now if you get a water that is coupled with altloc C, then qHOH+qC=1. Currently you cannot do it in phenix.refine, sorry. In fact, you can make it running, but currently I think it will do something different from what one would expect. Say you have this artificial molecule in PDB file, that mimics your case: ATOM 1 O AHOH H 1 8.767 5.853 7.671 0.30 10.00 O ATOM 2 O BHOH H 1 7.767 7.853 7.671 0.50 12.00 O ATOM 3 O CHOH H 1 7.767 5.853 5.671 0.20 19.00 O ATOM 4 K H 2 7.000 5.000 7.671 0.80 25.00 K then what you want to do is defined by the following selections: refinement { refine { occupancies { constrained_group { selection = resseq 1 and altloc A selection = resseq 1 and altloc B selection = resseq 1 and altloc C } constrained_group { selection = resseq 1 and altloc C selection = resseq 2 } } } } Unfortunately, for the moment the automatic procedure outsmarts itself and automatically removes "altloc C" selection from the first group since it is present in the second group, and therefore the algorithm "thinks" it is a duplicate unwanted selection. I will fix it once I get a chance (it is not an easy-fix). However, with some manual work you can approximate what you want to do. Refine that triple conformation as it refines by default in phenix.refine and keep occupancy of water (the one that is coupled with C, qHOH) fixed to some value. Then re-set qHOH = 1-qC and repeat refinement again (do not refine qHOH, keep it fixed). Since by default phenix.refine will refine partial occupancies, make sure you use "remove_selection=resname HOH and resseq 1033" to not refine qHOH but keep it at preset value. Please let me know if you have any questions. Pavel. On 6/8/09 2:32 AM, Roeland Boer wrote:
Dear Pavel,
Thanks for the reply. I got it working, you were probably right that it was an oversight.
I have a follow-up question concerning triple conformations: if I have sidechain confs A, B and C and a water molecule sitting in the position of C, can I phenix that it should have the 1-C occupancy (or 1 minus A+B)? I've tried this:
constrained_group { selection = (chain A and resseq 595 and altloc A) or (resname HOH and resseq 1033) selection = (chain A and resseq 595 and altloc B) or (resname HOH and resseq 1033) selection = (chain A and resseq 595 and altloc C) }
but it gave me an error (obviously)
Thanks, Roeland.
participants (3)
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Mayer, Mark (NIH/NICHD) [E]
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Pavel Afonine
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Roeland Boer