Re: [ccp4bb] merging parts of models in COOT - SOLVED
Dear all, thanks for replies! Indeed, text editing or other combinations of manipulations will do the trick of course, but I wanted to do it in one command, as I need to make many substitutions in a very big model as I go along. Suggested (replace-fragment) (or also (copy-residue-range)) do the desired job. Thanks! Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge On 19/10/2011 14:41, Ed Pozharski wrote: On Wed, 2011-10-19 at 12:20 +0100, Leonid Sazanov wrote: Hi, If I have two somewhat different overlayed models, is it possible in COOT to replace part of one model by another? Similarly to O command: merge_atoms? That's a useful feature in O, but could not find it so far in COOT. Thanks! IIUC what you want to do, shouldn't this be a trivial operation in a text editor?
Re: [ccp4bb] merging parts of models in COOT
On Wed, 2011-10-19 at 12:20 +0100, Leonid Sazanov wrote: > Hi, > If I have two somewhat different overlayed models, is it possible in > COOT to replace part of one model by another? > Similarly to O command: merge_atoms residue_end> ? > That's a useful feature in O, but could not find it so far in COOT. > Thanks! > IIUC what you want to do, shouldn't this be a trivial operation in a text editor? -- "Hurry up before we all come back to our senses!" Julian, King of Lemurs
Re: [ccp4bb] merging parts of models in COOT
You can also try Extensions->Modelling->Replace fragment (usage self-explanatory) > -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies. -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Tim Gruene > Sent: 19 October 2011 13:17 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] merging parts of models in COOT > > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear Leonid, > > To merge part of molecule B into molecule A you do in in steps: > - - remove the part from A that you want to replace > - - remove from B everything you do not want to merge with A > - - merge B into A (Calculate->Merge...) > - - change the newly created chain ID (Calculate->Change Chain ID...) > > Tim > > On 10/19/2011 01:20 PM, Leonid Sazanov wrote: > > Hi, > > If I have two somewhat different overlayed models, is it possible in > > COOT to replace part of one model by another? > > Similarly to O command: merge_atoms > residue_end> ? > > That's a useful feature in O, but could not find it so far in COOT. > > Thanks! > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFOnr/BUxlJ7aRr7hoRAqLeAKCXEnJKrm0wMMCHtYpvo22ZWJq2ZwCg9BFd > zFjXn9JhwhZzIXUSOYcI50I= > =Ge9y > -END PGP SIGNATURE-
Re: [ccp4bb] merging parts of models in COOT
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Leonid, To merge part of molecule B into molecule A you do in in steps: - - remove the part from A that you want to replace - - remove from B everything you do not want to merge with A - - merge B into A (Calculate->Merge...) - - change the newly created chain ID (Calculate->Change Chain ID...) Tim On 10/19/2011 01:20 PM, Leonid Sazanov wrote: > Hi, > If I have two somewhat different overlayed models, is it possible in > COOT to replace part of one model by another? > Similarly to O command: merge_atoms residue_end> ? > That's a useful feature in O, but could not find it so far in COOT. > Thanks! > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOnr/BUxlJ7aRr7hoRAqLeAKCXEnJKrm0wMMCHtYpvo22ZWJq2ZwCg9BFd zFjXn9JhwhZzIXUSOYcI50I= =Ge9y -END PGP SIGNATURE-
[ccp4bb] merging parts of models in COOT
Hi, If I have two somewhat different overlayed models, is it possible in COOT to replace part of one model by another? Similarly to O command: merge_atoms residue_end> ? That's a useful feature in O, but could not find it so far in COOT. Thanks! -- Dr. Leonid A. Sazanov Research group leader Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge
