when will NoResidueRotamersError be raised?
I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original. I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY. If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error. XBL
Hi XBL, Do you really need to use python? You can just use the Chimera command "swapaa" to mutate between any of the standard amino acid types. It does the hard work of calling the right code for you, the same code as the Rotamers tool. Here is more information on that command and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> Most users prefer to use the command and/or graphical interfaces, when possible. These are more thoroughly documented than the code. (If you are doing a lot with the python code, it might be a question for chimera-dev@cgl.ucsf.edu instead of chimera-users@cgl.ucsf.edu) 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 Feb 12, 2014, at 5:45 AM, Xiao-Bo Li wrote:
I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original.
I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY.
If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error.
XBL _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL On 02/12/14 13:07, Elaine Meng wrote:
Hi XBL, Do you really need to use python? You can just use the Chimera command "swapaa" to mutate between any of the standard amino acid types. It does the hard work of calling the right code for you, the same code as the Rotamers tool. Here is more information on that command and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
Most users prefer to use the command and/or graphical interfaces, when possible. These are more thoroughly documented than the code. (If you are doing a lot with the python code, it might be a question for chimera-dev@cgl.ucsf.edu instead of chimera-users@cgl.ucsf.edu) 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 Feb 12, 2014, at 5:45 AM, Xiao-Bo Li wrote:
I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original.
I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY.
If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error.
XBL _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL
Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with: #0:15.A Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html> You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html> Elaine P.S. better to send Chimera questions to chimera-users@cgl.ucsf.edu than to only me - thanks!
On 02/12/14 13:07, Elaine Meng wrote:
Hi XBL, Do you really need to use python? You can just use the Chimera command "swapaa" to mutate between any of the standard amino acid types. It does the hard work of calling the right code for you, the same code as the Rotamers tool. Here is more information on that command and its options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
Most users prefer to use the command and/or graphical interfaces, when possible. These are more thoroughly documented than the code. (If you are doing a lot with the python code, it might be a question for chimera-dev@cgl.ucsf.edu instead of chimera-users@cgl.ucsf.edu) 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 Feb 12, 2014, at 5:45 AM, Xiao-Bo Li wrote:
I would like to mutate one residue to another. So far, the only way I found is to use the rotamers of the other residues on the original.
I'm using chimera's python script. I would like to know if the NoResidueRotamersError will only be raised for residues that don't have rotamers like GLY.
If not, then how can I replace the amino acid residue that I want to mutate? I am using the "getRotamers" function, which returns this error.
XBL _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi XBL, Maybe the confusing part is the word "model." In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model: <http://hmg.oxfordjournals.org/content/23/4/949.long> I was guessing that your two structures are "models" from the Chimera point of view. If not, and I still didn't answer your question, feel free to write back. I hope this helps, Elaine On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL
Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with:
#0:15.A
Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
Elaine
Wow, I don't know what my problem is today! That link should have been to the Model Panel documentation: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html> The only other thing I can think of that you might have meant is that your proteins were two different chains in the same model. In that case, you would include the chain ID in the specification, as in my earlier example. Elaine On Feb 12, 2014, at 4:51 PM, Elaine Meng wrote:
Hi XBL, Maybe the confusing part is the word "model." In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model: <http://hmg.oxfordjournals.org/content/23/4/949.long>
I was guessing that your two structures are "models" from the Chimera point of view. If not, and I still didn't answer your question, feel free to write back. I hope this helps, Elaine
On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL
Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with:
#0:15.A
Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
Elaine
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
When I open a model, using "chimera.openModels.open(pdbID, type='PDB'), I dont get one model, I actually get a list. So I thought the #0 referred to this list. So my question was about how to references one model in this list of models, vs different models opened using this python call for different PDB IDs. XBL On 14-02-12 07:56 PM, Elaine Meng wrote:
Wow, I don't know what my problem is today! That link should have been to the Model Panel documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
The only other thing I can think of that you might have meant is that your proteins were two different chains in the same model. In that case, you would include the chain ID in the specification, as in my earlier example.
Elaine
On Feb 12, 2014, at 4:51 PM, Elaine Meng wrote:
Hi XBL, Maybe the confusing part is the word "model." In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model: <http://hmg.oxfordjournals.org/content/23/4/949.long>
I was guessing that your two structures are "models" from the Chimera point of view. If not, and I still didn't answer your question, feel free to write back. I hope this helps, Elaine
On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with:
#0:15.A
Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
Elaine
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
My advice is to not worry about the python: just look in the Model Panel to see the #N of the structure you want, and then use it in the command as explained in my first reply. Elaine On Feb 12, 2014, at 6:14 PM, Xiao-Bo Li <x22li@cs.uwaterloo.ca> wrote:
When I open a model, using "chimera.openModels.open(pdbID, type='PDB'), I dont get one model, I actually get a list. So I thought the #0 referred to this list.
So my question was about how to references one model in this list of models, vs different models opened using this python call for different PDB IDs.
XBL
On 14-02-12 07:56 PM, Elaine Meng wrote:
Wow, I don't know what my problem is today! That link should have been to the Model Panel documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
The only other thing I can think of that you might have meant is that your proteins were two different chains in the same model. In that case, you would include the chain ID in the specification, as in my earlier example.
Elaine
On Feb 12, 2014, at 4:51 PM, Elaine Meng wrote:
Hi XBL, Maybe the confusing part is the word "model." In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model: <http://hmg.oxfordjournals.org/content/23/4/949.long>
I was guessing that your two structures are "models" from the Chimera point of view. If not, and I still didn't answer your question, feel free to write back. I hope this helps, Elaine
On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with:
#0:15.A
Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
Elaine
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
You can use the "oslIdent" method for a model. For example, to print the ids of the models opened and color the first one red, you can do: import chimera modelList = chimera.openModels.open(pdbID, type="PDB") for m in modelList: print m.oslIdent() cmd = "color red %s" % modelList[0].oslIdent() chimera.runCommand(cmd) Conrad On 2/12/2014 6:14 PM, Xiao-Bo Li wrote:
When I open a model, using "chimera.openModels.open(pdbID, type='PDB'), I dont get one model, I actually get a list. So I thought the #0 referred to this list.
So my question was about how to references one model in this list of models, vs different models opened using this python call for different PDB IDs.
XBL
On 14-02-12 07:56 PM, Elaine Meng wrote:
Wow, I don't know what my problem is today! That link should have been to the Model Panel documentation:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
The only other thing I can think of that you might have meant is that your proteins were two different chains in the same model. In that case, you would include the chain ID in the specification, as in my earlier example.
Elaine
On Feb 12, 2014, at 4:51 PM, Elaine Meng wrote:
Hi XBL, Maybe the confusing part is the word "model." In Chimera, we just use that word to mean a structure with atomic coordinates, which could be from experiments (crystallography, NMR, etc. such as entries in the Protein Data Bank) or calculations (protein structure prediction, etc.). Essentially each structure file you open becomes one model: <http://hmg.oxfordjournals.org/content/23/4/949.long>
I was guessing that your two structures are "models" from the Chimera point of view. If not, and I still didn't answer your question, feel free to write back. I hope this helps, Elaine
On Feb 12, 2014, at 3:50 PM, Elaine Meng wrote:
On Feb 12, 2014, at 10:45 AM, Xiao-Bo Li wrote:
Hi Elaine, If I have two different protein structure open (not models), how can I reference one of them using the commandline? I want to mutate one of them not the other. Best, XBL Hi XBL, The command-line specifications of different models are #0, #1, etc. You can see in the Model Panel (in Favorites menu) which number goes with which structure. Also, there may be different chains even in one structure. For example, residue 15 in chain A of model 0 is specified with:
#0:15.A
Please see the atom-specification documentation for more details and several examples. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
That page is also linked to "atom-spec" in the Usage line of the "swapaa" command description. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html>
You might also want to take a look at the "getting started - command line" tutorial. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html>
Elaine
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participants (3)
-
Conrad Huang -
Elaine Meng -
Xiao-Bo Li