Hello, In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so. Cheers, Oli
Hi Oliver, I haven’t tried these things in a situation similar to yours, but some initial ideas are: (1) use two “vop morph” commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame (2) use “perframe” (possibly with “alias”) to specify running “scolor" zone command(s) at each frame I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I’m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hello,
In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so.
Cheers, Oli
Thanks for the helpful suggestions Elaine! I will look into them and see where it gets me - I have a feeling I have tried the perframe/scolor idea in the past without success but I may be misremembering. One other thing - I'd like a one command way to convert a full atom model to a Calpha model, keeping the helix/sheet records at the start intact. This would be very helpful when running morphs of a large protein (where often I do not need to display sidechains, just ribbon), because it makes the calculations much faster (e.g. rather than 120,000 atoms I have ~17000 using CAs only). Currently what I do is I delete all the non-CA atoms in chimera, save the pdb, remove all the TER flags chimera has added between each CA atom using grep, and then replace the HELIX/SHEET records with those from the original file (because they get corrupted for some reason in the process. This works fine but it would be nice to have a one liner in chimera to handle the same at some point (although I realize it is a pretty niche functionality and maybe not worth it). (alternatively a "coarse grained" morph where parameters for each residue only take into account the CA would accomplish the same thing I guess.) Cheers, Oli On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Oliver, I haven’t tried these things in a situation similar to yours, but some initial ideas are:
(1) use two “vop morph” commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame
(2) use “perframe” (possibly with “alias”) to specify running “scolor" zone command(s) at each frame
I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I’m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke@gmail.com> wrote:
Hello,
In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so.
Cheers, Oli
Hi Oliver, If you delete everything except CA (command “delete ~@CA”) you lose the ribbons. This is because Chimera needs a fake bond between consecutive CA atoms to make the ribbon. If Chimera reads a CA only PDB file it makes those fake bonds. But I don’t know another way to make those bonds. I’ve wanted this capability, requested it 4 years ago http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875> but think it will have to wait for ChimeraX. You could make a Python script that added a Chimera command that did all the steps you are doing now. Tom
On Jan 30, 2016, at 1:44 PM, Oliver Clarke <olibclarke@gmail.com> wrote:
Thanks for the helpful suggestions Elaine! I will look into them and see where it gets me - I have a feeling I have tried the perframe/scolor idea in the past without success but I may be misremembering.
One other thing - I'd like a one command way to convert a full atom model to a Calpha model, keeping the helix/sheet records at the start intact. This would be very helpful when running morphs of a large protein (where often I do not need to display sidechains, just ribbon), because it makes the calculations much faster (e.g. rather than 120,000 atoms I have ~17000 using CAs only). Currently what I do is I delete all the non-CA atoms in chimera, save the pdb, remove all the TER flags chimera has added between each CA atom using grep, and then replace the HELIX/SHEET records with those from the original file (because they get corrupted for some reason in the process. This works fine but it would be nice to have a one liner in chimera to handle the same at some point (although I realize it is a pretty niche functionality and maybe not worth it). (alternatively a "coarse grained" morph where parameters for each residue only take into account the CA would accomplish the same thing I guess.)
Cheers, Oli
On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Oliver, I haven’t tried these things in a situation similar to yours, but some initial ideas are:
(1) use two “vop morph” commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame
(2) use “perframe” (possibly with “alias”) to specify running “scolor" zone command(s) at each frame
I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I’m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Hello,
In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so.
Cheers, Oli
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Oliver, Of course you can keep the entire backbone (command “delete ~@CA,C,N,O”) and then you keep your ribbon, but it is 4 times more atoms than CA only. Tom
On Feb 1, 2016, at 11:57 AM, Tom Goddard wrote:
Hi Oliver,
If you delete everything except CA (command “delete ~@CA”) you lose the ribbons. This is because Chimera needs a fake bond between consecutive CA atoms to make the ribbon. If Chimera reads a CA only PDB file it makes those fake bonds. But I don’t know another way to make those bonds. I’ve wanted this capability, requested it 4 years ago
http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875>
but think it will have to wait for ChimeraX. You could make a Python script that added a Chimera command that did all the steps you are doing now.
Tom
On Jan 30, 2016, at 1:44 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Thanks for the helpful suggestions Elaine! I will look into them and see where it gets me - I have a feeling I have tried the perframe/scolor idea in the past without success but I may be misremembering.
One other thing - I'd like a one command way to convert a full atom model to a Calpha model, keeping the helix/sheet records at the start intact. This would be very helpful when running morphs of a large protein (where often I do not need to display sidechains, just ribbon), because it makes the calculations much faster (e.g. rather than 120,000 atoms I have ~17000 using CAs only). Currently what I do is I delete all the non-CA atoms in chimera, save the pdb, remove all the TER flags chimera has added between each CA atom using grep, and then replace the HELIX/SHEET records with those from the original file (because they get corrupted for some reason in the process. This works fine but it would be nice to have a one liner in chimera to handle the same at some point (although I realize it is a pretty niche functionality and maybe not worth it). (alternatively a "coarse grained" morph where parameters for each residue only take into account the CA would accomplish the same thing I guess.)
Cheers, Oli
On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Oliver, I haven’t tried these things in a situation similar to yours, but some initial ideas are:
(1) use two “vop morph” commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame
(2) use “perframe” (possibly with “alias”) to specify running “scolor" zone command(s) at each frame
I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I’m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Hello,
In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so.
Cheers, Oli
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Hi Oliver, And you can resort to a fairly simple Python script to re-establish bonds between the CAs after deleting all the other atoms: from chimera import openModels, Molecule for m in openModels.list(modelTypes=[Molecule]): prev_res = None for r in m.residues: if prev_res == None: prev_res = r continue if prev_res.id.chainId == r.chainId: r.molecule.addBond(prev_res.atoms[0], r.atoms[0]) prev_res = r —Eric
On Feb 1, 2016, at 12:01 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Oliver,
Of course you can keep the entire backbone (command “delete ~@CA,C,N,O”) and then you keep your ribbon, but it is 4 times more atoms than CA only.
Tom
On Feb 1, 2016, at 11:57 AM, Tom Goddard wrote:
Hi Oliver,
If you delete everything except CA (command “delete ~@CA”) you lose the ribbons. This is because Chimera needs a fake bond between consecutive CA atoms to make the ribbon. If Chimera reads a CA only PDB file it makes those fake bonds. But I don’t know another way to make those bonds. I’ve wanted this capability, requested it 4 years ago
http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/9875>
but think it will have to wait for ChimeraX. You could make a Python script that added a Chimera command that did all the steps you are doing now.
Tom
On Jan 30, 2016, at 1:44 PM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Thanks for the helpful suggestions Elaine! I will look into them and see where it gets me - I have a feeling I have tried the perframe/scolor idea in the past without success but I may be misremembering.
One other thing - I'd like a one command way to convert a full atom model to a Calpha model, keeping the helix/sheet records at the start intact. This would be very helpful when running morphs of a large protein (where often I do not need to display sidechains, just ribbon), because it makes the calculations much faster (e.g. rather than 120,000 atoms I have ~17000 using CAs only). Currently what I do is I delete all the non-CA atoms in chimera, save the pdb, remove all the TER flags chimera has added between each CA atom using grep, and then replace the HELIX/SHEET records with those from the original file (because they get corrupted for some reason in the process. This works fine but it would be nice to have a one liner in chimera to handle the same at some point (although I realize it is a pretty niche functionality and maybe not worth it). (alternatively a "coarse grained" morph where parameters for each residue only take into account the CA would accomplish the same thing I guess.)
Cheers, Oli
On Sat, Jan 30, 2016 at 9:23 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: Hi Oliver, I haven’t tried these things in a situation similar to yours, but some initial ideas are:
(1) use two “vop morph” commands separated by only a semicolon so that (if it is possible to run two map-morphs concurrently), they will start at the same frame
(2) use “perframe” (possibly with “alias”) to specify running “scolor" zone command(s) at each frame
I would try those things one at a time, for example, perframe scolor with a single vop morph. Even in that case, I’m not sure it will work. We may be able to come up with better answer or at least a more definite answer of whether it is possible next week. In the meanwhile, these are just some things to look into. 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 Jan 30, 2016, at 10:16 AM, Oliver Clarke <olibclarke@gmail.com <mailto:olibclarke@gmail.com>> wrote:
Hello,
In a situation where I have maps for two conformations, and I've extracted out domain specific maps in both cases, is it possible to run morph maps on both groups of maps simultaneously? Or is there any way to apply color zone to the trajectory generated by morph maps? I would like to generate a morph map movie where the map is colored by domain throughout the morph, and can't figure out how to do so.
Cheers, Oli
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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participants (4)
-
Elaine Meng -
Eric Pettersen -
Oliver Clarke -
Tom Goddard