how to copy partial charges from a .mol2 file to another
Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas -- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang@bioacademy.gr tevang3@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
Hi Thomas, If the residue and atom names are identical, it might work to open the structure with the charges, export the charge attribute to a file, close that structure and open the other one, assign the charge attribute from the file. I don't know if that qualifies as "straightforward," however! How to export the attribute: start Render by Attribute (under Tools... Depiction), in that dialog choose "File... Save Attributes", specify the charge attribute of atoms, save file where you will be able to find it later. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> How to read in the file to assign the attribute: start Define Attribute (under Tools... Structure Analysis), browse to the file and open it. Remember to close the first structure and open the other one first. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html> There is an "mcopy" command that copies attributes from one molecule to another, but I believe it only includes stuff like color and display style, not charge. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.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 Feb 29, 2012, at 11:57 AM, Thomas Evangelidis wrote:
Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas
Thank you Elaine for the swift reply! It was straight forward, although the atom names were not identical and had to change them manually. ~Thomas On 29 February 2012 22:11, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Thomas, If the residue and atom names are identical, it might work to open the structure with the charges, export the charge attribute to a file, close that structure and open the other one, assign the charge attribute from the file. I don't know if that qualifies as "straightforward," however!
How to export the attribute: start Render by Attribute (under Tools... Depiction), in that dialog choose "File... Save Attributes", specify the charge attribute of atoms, save file where you will be able to find it later. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
How to read in the file to assign the attribute: start Define Attribute (under Tools... Structure Analysis), browse to the file and open it. Remember to close the first structure and open the other one first. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
There is an "mcopy" command that copies attributes from one molecule to another, but I believe it only includes stuff like color and display style, not charge. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.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 Feb 29, 2012, at 11:57 AM, Thomas Evangelidis wrote:
Dear Chimera community, Is there any straight forward way to copy the partial charges from one .mol2 file to another? Thanks in advance. Thomas
-- ====================================================================== Thomas Evangelidis PhD student Biomedical Research Foundation, Academy of Athens 4 Soranou Ephessiou , 115 27 Athens, Greece email: tevang@bioacademy.gr tevang3@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
You're welcome! You may want to doublecheck that the charges were assigned correctly by saving to another mol2 file, or by showing charge values as labels on the structure with the menu "Actions... Label... other" (label with attribute charge) or commands: Command: labelopt info charge Command: label Best, Elaine On Feb 29, 2012, at 1:48 PM, Thomas Evangelidis wrote:
Thank you Elaine for the swift reply! It was straight forward, although the atom names were not identical and had to change them manually.
~Thomas
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Thomas Evangelidis