Combine atom-spec non-alphanumeric no-nunderscore character error
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working! Regards.
Hi Ahmad, The specification is wrong for two reasons: (1) need colon instead of comma, for example #1:.k:.e (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e" However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> So what you really wanted to do is to delete all the other atoms before you combine the two models, something like select #1:.k:.e #2:.k:.e delete ~sel combine #1,2 (also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working!
Regards.
Thanks, I will try that, but quickly, I often use commas with selection and it works fine, what's the difference between the commas and the colons? On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, The specification is wrong for two reasons: (1) need colon instead of comma, for example #1:.k:.e (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e"
However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
So what you really wanted to do is to delete all the other atoms before you combine the two models, something like
select #1:.k:.e #2:.k:.e delete ~sel combine #1,2
(also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working!
Regards.
Hi Ahmad, Commas separate items at the main symbol level # (model) : (residue) @ (atom). They cannot be used to separate items at the sub-levels with dots after those symbols #. (submodel) :. (chain ID) @. (atom alternate location). <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy> I agree it can be confusing. In our next-gen program ChimeraX we only use the dot for submodels, and chain has its own symbol. Best, Elaine
On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks, I will try that, but quickly, I often use commas with selection and it works fine, what's the difference between the commas and the colons?
On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, The specification is wrong for two reasons: (1) need colon instead of comma, for example #1:.k:.e (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e"
However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
So what you really wanted to do is to delete all the other atoms before you combine the two models, something like
select #1:.k:.e #2:.k:.e delete ~sel combine #1,2
(also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working!
Regards.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thanks Elaine, but after I combine using the syntax that you mentioned, I get the entire molecule and not the chains that I selected. I also tried selecting the that chains that I want to combine from different models, and used "combine sel", I got the same result. On Wed, Jan 30, 2019 at 6:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, Commas separate items at the main symbol level # (model) : (residue) @ (atom). They cannot be used to separate items at the sub-levels with dots after those symbols #. (submodel) :. (chain ID) @. (atom alternate location).
< http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierar...
I agree it can be confusing. In our next-gen program ChimeraX we only use the dot for submodels, and chain has its own symbol. Best, Elaine
On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks, I will try that, but quickly, I often use commas with selection and it works fine, what's the difference between the commas and the colons?
On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, The specification is wrong for two reasons: (1) need colon instead of comma, for example #1:.k:.e (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e"
However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
So what you really wanted to do is to delete all the other atoms before you combine the two models, something like
select #1:.k:.e #2:.k:.e delete ~sel combine #1,2
(also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working!
Regards.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ahmad, In my first reply (and in the manual page), I already told you that “combine” would give the whole models. In the second part of that reply, I gave commands to select and DELETE the unselected parts before you use “combine.” See previous reply below or at <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-January/015390.html> Best, Elaine
On Feb 1, 2019, at 7:27 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks Elaine, but after I combine using the syntax that you mentioned, I get the entire molecule and not the chains that I selected.
I also tried selecting the that chains that I want to combine from different models, and used "combine sel", I got the same result.
On Wed, Jan 30, 2019 at 6:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, Commas separate items at the main symbol level # (model) : (residue) @ (atom). They cannot be used to separate items at the sub-levels with dots after those symbols #. (submodel) :. (chain ID) @. (atom alternate location).
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#hierarchy>
I agree it can be confusing. In our next-gen program ChimeraX we only use the dot for submodels, and chain has its own symbol. Best, Elaine
On Jan 30, 2019, at 2:18 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks, I will try that, but quickly, I often use commas with selection and it works fine, what's the difference between the commas and the colons?
On Wed, Jan 30, 2019 at 4:03 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, The specification is wrong for two reasons: (1) need colon instead of comma, for example #1:.k:.e (2) you would need to either remove the space between the two models or put quotes around the whole thing like "#1:.k:.e #2:.k:.e"
However, more important is that “combine” will include all the atoms in the whole models even if you only specify some chains. It says this in the second paragraph: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
So what you really wanted to do is to delete all the other atoms before you combine the two models, something like
select #1:.k:.e #2:.k:.e delete ~sel combine #1,2
(also make sure you really have models #1 and #2, since the first model is #0 and you might need to use #0 and #1 instead… check in the Model Panel, opened from Favorites menu)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 30, 2019, at 11:23 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
I'm trying to combine a few chains from different models. I'm using: combine #1:.k,.e #2:.k,.e. I'm getting the above error, and I'm not sure why my selection isn't working!
Regards.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Ahmad Khalifa -
Elaine Meng