Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B Is there a way to get the list? Best and thank you in advance Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta@nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029
Dear Max, The best way is to use the Find Clashes/Contacts tool (in menu under Tools... Structure Analysis) or its command version "findclash". Either way you can define two sets of atoms, chain A and chain B in your case, and a cutoff distance, and then get a list of the distances saved to a file or to the Reply Log. The cutoff you specify is not center-to-center distance, but "overlap" = the overlap between the surfaces of the VDW spheres, where 0 is exactly touching, positive is intersecting, negative is the separation of the VDW surfaces. Nevertheless the list of pairwise atom-atom results will include both the overlap values and the center-to-center distances, and if you really prefer the strict center-to-center distance cutoff, you can (manually) filter the results by that criterion. For example, commands including option to write results to the Reply Log: open 1zik preset apply int 2 findclash :.a&protein test :.b&protein overlap -0.5 hbond 0.0 log true The command has several options including "saveFile" as an alternative to "log", selecting the atoms, and drawing lines. The center-to-center distances are the last column in the results. To get larger distances you would use a larger negative overlap cutoff. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> The graphical interface (Find Clashes/Contacts tool) can do the same things. It is fairly self-explanatory, but to define two sets of atoms you'd first select one set, then "Designate", then select the second set and "Designate... as second set": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> I hope this helps, 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 25, 2014, at 5:13 AM, <m.maletta@nki.nl> <m.maletta@nki.nl> wrote:
Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B
Is there a way to get the list? Best and thank you in advance Max
Dear Elaine, Thank you a lot for your help. It really worked perfectly. I changed the radius of all the atoms with vdwdefine so that only the distance from the center matter. Best Max __________________________________ Massimiliano Maletta post-doc in NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam group of Peter Peters www.nki.nl/research/peters/ | www.necen.nl m.maletta@nki.nl Tel : +31 20 512 2022 Fax : +31 20 512 2029 ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Friday, 25 April 2014 10:52 PM To: Massimiliano Maletta Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Print selected Dear Max, The best way is to use the Find Clashes/Contacts tool (in menu under Tools... Structure Analysis) or its command version "findclash". Either way you can define two sets of atoms, chain A and chain B in your case, and a cutoff distance, and then get a list of the distances saved to a file or to the Reply Log. The cutoff you specify is not center-to-center distance, but "overlap" = the overlap between the surfaces of the VDW spheres, where 0 is exactly touching, positive is intersecting, negative is the separation of the VDW surfaces. Nevertheless the list of pairwise atom-atom results will include both the overlap values and the center-to-center distances, and if you really prefer the strict center-to-center distance cutoff, you can (manually) filter the results by that criterion. For example, commands including option to write results to the Reply Log: open 1zik preset apply int 2 findclash :.a&protein test :.b&protein overlap -0.5 hbond 0.0 log true The command has several options including "saveFile" as an alternative to "log", selecting the atoms, and drawing lines. The center-to-center distances are the last column in the results. To get larger distances you would use a larger negative overlap cutoff. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> The graphical interface (Find Clashes/Contacts tool) can do the same things. It is fairly self-explanatory, but to define two sets of atoms you'd first select one set, then "Designate", then select the second set and "Designate... as second set": <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html> I hope this helps, 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 25, 2014, at 5:13 AM, <m.maletta@nki.nl> <m.maletta@nki.nl> wrote:
Dear all, I would like to select all the atoms of the chain B that are less than 3.5A far away from chain A. And I would also like to print out all the distances that Chimera finds. I manage to do the first part with this command, but I do not manage to have a list of all the distances found. select #0:.A za<3.5 & #0:.B
Is there a way to get the list? Best and thank you in advance Max
participants (2)
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Elaine Meng -
m.maletta＠nki.nl