Hello users group, I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances
A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table.
I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking"
So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane".
Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program.
Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance?
Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"?
Thanks! Patti
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Hi Patti, If you click the Help button on the Distances dialog, the resulting page lists three different ways to add the distance measurement: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances
• The Create button creates a distance monitor between two atoms that have been selected (exactly two atoms must be selected). • Picking one atom and Shift-double-picking the second atom (that is, doubleclicking it with the button assigned to picking) elicits a button marked Show Distance. Clicking it creates the distance monitor and leaves the atoms in a selected state. Clicking elsewhere removes the button without creating a distance monitor but leaves the atoms in a selected state. • The command distance can also be used.
I'll try to clarify: Picking from the screen is one way to make a selection. Selection can also be done with menu or command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html
So, you could either select two atoms (using picking or menu or command) and then click the Create button, as in method 1 above, or use method 2 picking with doubleclicking the second atom as you pick it instead of using the Create button. Or method 3, distance command, for example:
distance :234.g@o :295.g@o
The bottom example in the "distances" manual page is for two atoms -- the only difference between turning a distance on and off is whether you use "distance" or "~distance" http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html
Finally, this tutorial includes examples of measuring distances. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html
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 Apr 29, 2012, at 4:49 PM, Patricia LiWang wrote:
Hello users group,
I don't want anything complicated-- I just want to get some rough distances between atoms. So I go to Tools Structure Analysis Distances
A window comes up with an empty table. (No instructions on how to pick atoms) A search of the Chimera documentation tells me I have to Control-leftclick to pick two atoms But no matter how often I click and click and click, it never gives me anything. I can't get even one atom to show up in the panel, let alone two. The side chains are sitting right there, getting clicked away, with nothing happening in the table.
I am reading so many similar documentation pages, and apparently there is a difference between "selecting" and "picking"
So I figure I'll just use the command line. But the instructions don't even bother to tell you how to use the command line to get the distance between two atoms. There is documentation on how to get distances between something and a "plane".
Why do they make this so hard? Surely this is the main "simple" thing people want to do with this program.
Would someone please tell me how to Pick or Select or Whatever two amino acids (any atom in them would be fine) and get a distance?
Or better yet, please tell me the exact command line command I can use to get the distance between Asparate 234 carboxyl oxygen and Aspartate 295 carboxyl oxygen, both from chain "G"?
Thanks! Patti
On Apr 30, 2012, at 9:54 AM, Elaine Meng wrote:
I'll try to clarify: Picking from the screen is one way to make a selection. Selection can also be done with menu or command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html
So, you could either select two atoms (using picking or menu or command) and then click the Create button, as in method 1 above, or use method 2 picking with doubleclicking the second atom as you pick it instead of using the Create button
Patricia, I think the thing you're missing is that control-click will select an atom but in order to select a second atom without de-selecting the first you need to shift-control-click the second atom.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
Hi everyone,
This brings up a feature that I've been missing in all visualizers that I've tried. It exists (or at least used to) in "O". When you click on and select an atom using a special mouse modifier, the software would "reach out" and display all distances to other atoms within a pre-specified radius. Sometimes it is hard to judge how far away other atoms are from a selected atom. The times I use measuring tools the most is when I'm trying to identify "nearby" atoms. While it is true that we have the "Zone" selection and similar tools, I think that it would be really nice to have a tool that "looks for" close contacts and displays their distances using pseudobonds given a simple click. The next click would either turn off the pseudobonds or display those associated with the next selected atom.
Can you see what I'm trying to describe? Is this already possible using a macro of some kind?
Thanks, Darrell
Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
From: Eric Pettersen <pett@cgl.ucsf.edumailto:pett@cgl.ucsf.edu> To: "chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu> Cc: Patricia LiWang <pliwang@ucmerced.edumailto:pliwang@ucmerced.edu> Subject: Re: [Chimera-users] Just want atom distances
On Apr 30, 2012, at 9:54 AM, Elaine Meng wrote:
I'll try to clarify: Picking from the screen is one way to make a selection. Selection can also be done with menu or command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html
So, you could either select two atoms (using picking or menu or command) and then click the Create button, as in method 1 above, or use method 2 picking with doubleclicking the second atom as you pick it instead of using the Create button
Patricia, I think the thing you're missing is that control-click will select an atom but in order to select a second atom without de-selecting the first you need to shift-control-click the second atom.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Hi Darrell, Good idea. I've implemented a version of this by adding an entry to the popup menu you get when you control-double-click an atom. The menu will have a "Show distances to nearby atoms" entry that shows all distances to non-bonded atoms within 4 angstroms (and hides distances you showed previously). If you bring up the menu a second time on the same atom the entry will be "Hide...(etc)". The feature will be in tonight's daily build. The actual menu text isn't set in stone so it might change slightly in the next few days but it'll still be obvious which entry it is.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 30, 2012, at 12:52 PM, Hurt, Darrell (NIH/NIAID) [E] wrote:
Hi everyone,
This brings up a feature that I've been missing in all visualizers that I've tried. It exists (or at least used to) in "O". When you click on and select an atom using a special mouse modifier, the software would "reach out" and display all distances to other atoms within a pre-specified radius. Sometimes it is hard to judge how far away other atoms are from a selected atom. The times I use measuring tools the most is when I'm trying to identify "nearby" atoms. While it is true that we have the "Zone" selection and similar tools, I think that it would be really nice to have a tool that "looks for" close contacts and displays their distances using pseudobonds given a simple click. The next click would either turn off the pseudobonds or display those associated with the next selected atom.
Can you see what I'm trying to describe? Is this already possible using a macro of some kind?
Thanks, Darrell
Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH
31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public)
Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
From: Eric Pettersen <pett@cgl.ucsf.edumailto:pett@cgl.ucsf.edu> To: "chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edumailto:chimera-users@cgl.ucsf.edu> Cc: Patricia LiWang <pliwang@ucmerced.edumailto:pliwang@ucmerced.edu> Subject: Re: [Chimera-users] Just want atom distances
On Apr 30, 2012, at 9:54 AM, Elaine Meng wrote:
I'll try to clarify: Picking from the screen is one way to make a selection. Selection can also be done with menu or command. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html
So, you could either select two atoms (using picking or menu or command) and then click the Create button, as in method 1 above, or use method 2 picking with doubleclicking the second atom as you pick it instead of using the Create button
Patricia, I think the thing you're missing is that control-click will select an atom but in order to select a second atom without de-selecting the first you need to shift-control-click the second atom.
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (4)
-
Elaine Meng -
Eric Pettersen -
Hurt, Darrell (NIH/NIAID) [E] -
Patricia LiWang