how to make/delete hydrogen bond and delete chains
Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris
Hi Paris, You can do all of these things quite simply, it is just a matter of learning how to interact with Chimera. See the “Getting Started” tutorials for learning basic interactions with Chimera: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> and/or <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.html> Also, this tutorial includes using FindHBond: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> (1) You do not have to make the two parts for hbond as two separate models: you can specify any 2 sets of atoms even if they are in the same model. If you are using the “hbond” (findhbond) command, this is done by selecting some of the atoms and using the “selRestrict” option, for example commands: select nucleic acid hbond selRestrict protein reveal true ~select The FindHBond dialog also has options to do this. Click the Help button on the dialog or use command “help hbonds” to see the help because there are lots of other options you could also use at the same time. There are several different ways to select, as explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html> (2) As explained in the hbonds command help, you can remove hbonds, for example with command ~hbond (3) You must be specifying the chain incorrectly. For example this deletes chain B: delete :.B (or if you find it difficult to use commands, you can select the chain with the Select menu and delete it with the menu Actions… Atoms/bonds… delete). Command-line specification is explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 17, 2018, at 5:43 PM, Paris Tzou <paristzou@gmail.com> wrote:
Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris
This is great, thank you so much! Paris Elaine Meng <meng@cgl.ucsf.edu> 於 2018年11月19日 週一 上午2:24寫道：
Hi Paris, You can do all of these things quite simply, it is just a matter of learning how to interact with Chimera. See the “Getting Started” tutorials for learning basic interactions with Chimera: <http://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> and/or <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/menutut.html> < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/getting_started.h...
Also, this tutorial includes using FindHBond: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
(1) You do not have to make the two parts for hbond as two separate models: you can specify any 2 sets of atoms even if they are in the same model. If you are using the “hbond” (findhbond) command, this is done by selecting some of the atoms and using the “selRestrict” option, for example commands:
select nucleic acid hbond selRestrict protein reveal true ~select
The FindHBond dialog also has options to do this. Click the Help button on the dialog or use command “help hbonds” to see the help because there are lots of other options you could also use at the same time. There are several different ways to select, as explained here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
(2) As explained in the hbonds command help, you can remove hbonds, for example with command
~hbond
(3) You must be specifying the chain incorrectly. For example this deletes chain B:
delete :.B
(or if you find it difficult to use commands, you can select the chain with the Select menu and delete it with the menu Actions… Atoms/bonds… delete). Command-line specification is explained here: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 17, 2018, at 5:43 PM, Paris Tzou <paristzou@gmail.com> wrote:
Hi, I have a protein-dna complex structure with protomer as A as protein and B as DNA. It is impossible in hbond function to "generate" hbonds between two chains (A and B). One have to parse protein and DNA into two files and load into Chimera as two models. Another question is that, once generated, hbonds cannot be "erased" in the chimera view. And "delete chain ID" cannot really delete one chain from protein-DNA complex. What I am doing is 5MCT, p53-DNA complex. Thanks a lot for your help. Paris
Dear Chimera, Is there a command or a way to use the function "Values at Atom Positions" within a script. Thanks Hernando
Dear Hernando, Yes, the command version of “Values at Atom Positions” is “measure Mapvalues”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues> Then you could use “rangecolor” to color atoms etc. by the attribute values, or specify/select the atoms by attribute value in other commands, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 5:57 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera, Is there a command or a way to use the function "Values at Atom Positions" within a script. Thanks Hernando
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file> OR measure mapValues map-model atom-spec <outfilename> Thanks again Hernando. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 1:28 PM To: Hernando J Sosa Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Values at Atom Oositions Dear Hernando, Yes, the command version of “Values at Atom Positions” is “measure Mapvalues”: <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeasure.html%23mapValues&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf37f61452f9e4e0509d008d64e4ccf53%7C04c70eb48f2648079934e02e89266ad0%7C1%7C1%7C636782489133107236&sdata=gtHkSuM3CdjKaXCE%2FBX5LU0htZy6DNOkLyBcmYTnzYE%3D&reserved=0> Then you could use “rangecolor” to color atoms etc. by the attribute values, or specify/select the atoms by attribute value in other commands, etc. <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Frangecolor.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf37f61452f9e4e0509d008d64e4ccf53%7C04c70eb48f2648079934e02e89266ad0%7C1%7C1%7C636782489133107236&sdata=TmCWWQIyfYfA36mfb%2F0ypycehhnsu4gmNPmvyp767Lo%3D&reserved=0> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fatom_spec.html%23descriptors&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf37f61452f9e4e0509d008d64e4ccf53%7C04c70eb48f2648079934e02e89266ad0%7C1%7C1%7C636782489133107236&sdata=PcUX27BWvnWVDK1caA9SrqoUteoSxd%2FZkbehJXyMe5M%3D&reserved=0> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fdefineattrib%2Fdefineattrib.html%23attribdef&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf37f61452f9e4e0509d008d64e4ccf53%7C04c70eb48f2648079934e02e89266ad0%7C1%7C1%7C636782489133107236&sdata=IPptgLhqptCNJmE0mpruwGxD6dE2bcvBmLh0YfHAdTM%3D&reserved=0> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 19, 2018, at 5:57 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Chimera, Is there a command or a way to use the function "Values at Atom Positions" within a script. Thanks Hernando
Hi Hernando, Unfortunately there is no command to save attributes directly to file. One idea is use the “report all” option of “measure mapValues” to send the values to the Reply Log and then save the Reply Log as described at the bottom of this page: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> The “list atoms” command does a similar thing, lists values of an existing attribute in the Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/listen.html#listatoms> Best, Elaine
On Nov 19, 2018, at 10:49 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file>
OR measure mapValues map-model atom-spec <outfilename>
Thanks again
Hernando.
Thanks Elaine and I guess then I could use something like the code below (found it in an old thread) to save the Reply Log within the script: from chimera.tkgui import saveReplyLog saveReplyLog("savefilename") H. Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:07 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions Hi Hernando, Unfortunately there is no command to save attributes directly to file. One idea is use the “report all” option of “measure mapValues” to send the values to the Reply Log and then save the Reply Log as described at the bottom of this page: <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FProgrammersGuide%2FbasicPrimer.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C9d512ab7df674c3e90b108d64e5233f4%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636782512294370427&sdata=aTW4EFNl5V%2FRTVvED4H5Ynqe8LSPgTIiBLGZFfgUlG8%3D&reserved=0> The “list atoms” command does a similar thing, lists values of an existing attribute in the Reply Log. <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Flisten.html%23listatoms&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C9d512ab7df674c3e90b108d64e5233f4%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636782512294370427&sdata=fpDY7yXP%2BTRcbAKFJj6OSnko4GE2gx7Sec0YLulp4vU%3D&reserved=0> Best, Elaine
On Nov 19, 2018, at 10:49 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file>
OR measure mapValues map-model atom-spec <outfilename>
Thanks again
Hernando.
Yes, that’s basically the same as in the link sent in my previous reply. Elaine
On Nov 19, 2018, at 11:34 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine and I guess then I could use something like the code below (found it in an old thread) to save the Reply Log within the script:
from chimera.tkgui import saveReplyLog saveReplyLog("savefilename")
H.
Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:07 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions
Hi Hernando, Unfortunately there is no command to save attributes directly to file.
One idea is use the “report all” option of “measure mapValues” to send the values to the Reply Log and then save the Reply Log as described at the bottom of this page: <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FProgrammersGuide%2FbasicPrimer.html&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C9d512ab7df674c3e90b108d64e5233f4%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636782512294370427&sdata=aTW4EFNl5V%2FRTVvED4H5Ynqe8LSPgTIiBLGZFfgUlG8%3D&reserved=0>
The “list atoms” command does a similar thing, lists values of an existing attribute in the Reply Log. <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Flisten.html%23listatoms&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7C9d512ab7df674c3e90b108d64e5233f4%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C636782512294370427&sdata=fpDY7yXP%2BTRcbAKFJj6OSnko4GE2gx7Sec0YLulp4vU%3D&reserved=0>
Best, Elaine
On Nov 19, 2018, at 10:49 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file>
OR measure mapValues map-model atom-spec <outfilename>
Thanks again
Hernando.
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Dear Elaine from chimera.tkgui import saveReplyLog saveReplyLog("savefilename") Does not seem work, the resulting file is empty. I think the reason is that when idle is open the output of a command like from chimera import runCommand as rc rc("measure mapValues #0 #3 name vdatatom report all") is directed to the python shell instead to the Reply log. So I am still unclear on how I can save the output to a file within a python script? Thanks Hernando Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:39 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions Yes, that’s basically the same as in the link sent in my previous reply. Elaine
On Nov 19, 2018, at 11:34 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine and I guess then I could use something like the code below (found it in an old thread) to save the Reply Log within the script:
from chimera.tkgui import saveReplyLog saveReplyLog("savefilename")
H.
Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hernando.sosa@einstein.yu.edu
-----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 2:07 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions
Hi Hernando, Unfortunately there is no command to save attributes directly to file.
One idea is use the “report all” option of “measure mapValues” to send the values to the Reply Log and then save the Reply Log as described at the bottom of this page: <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r bvi.ucsf.edu%2Fchimera%2Fdocs%2FProgrammersGuide%2FbasicPrimer.html&am p;data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf92bc6244f7f4604ab1 a08d64e56b43c%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C63678253162 6670241&sdata=l5CAni%2BZTL6ldDMek%2BlNioVzu7bE%2BlDjh0TH3UFJ%2FNs% 3D&reserved=0>
The “list atoms” command does a similar thing, lists values of an existing attribute in the Reply Log. <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r bvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Flisten.html%23lis tatoms&data=02%7C01%7Chernando.sosa%40einstein.yu.edu%7Cf92bc6244f 7f4604ab1a08d64e56b43c%7C04c70eb48f2648079934e02e89266ad0%7C1%7C0%7C63 6782531626680250&sdata=JBs4UUR8Z%2Br9fG3kHY8Q7NVelC9fWY%2FrQ%2Buk8 Dm4JBk%3D&reserved=0>
Best, Elaine
On Nov 19, 2018, at 10:49 AM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Thanks Elaine, and it would be possible to save the resulting attributes to a file within the script without using the GUI? Something like: measure mapValues map-model atom-spec <my_att_name> saveattributes2file <my_att_name> <my_file>
OR measure mapValues map-model atom-spec <outfilename>
Thanks again
Hernando.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fplato. cgl.ucsf.edu%2Fmailman%2Flistinfo%2Fchimera-users&data=02%7C01%7Ch ernando.sosa%40einstein.yu.edu%7Cf92bc6244f7f4604ab1a08d64e56b43c%7C04 c70eb48f2648079934e02e89266ad0%7C1%7C1%7C636782531626680250&sdata= yZN7Oon%2BsGRd2Msfs8a5y6rD0Fsu0gFeHDOscNoYt9c%3D&reserved=0
Hi Hernando, The answer is to close IDLE — you don’t need it to enter your script. Instead put your script in a python file (something.py) and then open this file with the open command or menu: File… Open. Best, Elaine
On Nov 19, 2018, at 12:50 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Elaine
from chimera.tkgui import saveReplyLog saveReplyLog("savefilename")
Does not seem work, the resulting file is empty. I think the reason is that when idle is open the output of a command like from chimera import runCommand as rc rc("measure mapValues #0 #3 name vdatatom report all")
is directed to the python shell instead to the Reply log.
So I am still unclear on how I can save the output to a file within a python script?
Thanks
Hernando
Ok, now it works. Thanks Elaine! H. -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Monday, November 19, 2018 4:15 PM To: Hernando J Sosa Cc: chimera-users Subject: Re: [Chimera-users] Values at Atom Oositions Hi Hernando, The answer is to close IDLE — you don’t need it to enter your script. Instead put your script in a python file (something.py) and then open this file with the open command or menu: File… Open. Best, Elaine
On Nov 19, 2018, at 12:50 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Dear Elaine
from chimera.tkgui import saveReplyLog saveReplyLog("savefilename")
Does not seem work, the resulting file is empty. I think the reason is that when idle is open the output of a command like from chimera import runCommand as rc rc("measure mapValues #0 #3 name vdatatom report all")
is directed to the python shell instead to the Reply log.
So I am still unclear on how I can save the output to a file within a python script?
Thanks
Hernando
participants (3)
-
Elaine Meng -
Hernando J Sosa -
Paris Tzou