Re: [COOT] Merge

Please ignore this... found in under Edit From: Mailing list for users of COOT Crystallographic Software On Behalf Of Joel Tyndall Sent: Tuesday, 15 March 2022 2:39 PM To: COOT@JISCMAIL.AC.UK Subject: Merge Hi folks, I cant find Merge... Its not under the Calculate menu as it states in the pd

[COOT] Merge

Hi folks, I cant find Merge... Its not under the Calculate menu as it states in the pdf online... “5.28 Merge Molecules This dialog can be found under “Calculate” in the main menubar.” I can work around... but would be handy to know where its gone Using Coot 0.9.4 via phenix (1.20) J Joel T

Re: [COOT] Merge molecules scripting function

The last function I posted didn’t work optimally - when merge_molecules is called, imol_daughter is undisplayed, but imol_ref is not updated straight away (which is a little confusing as it looks like you’ve deleted a mol rather than merged) - adding a toggle_display step fixes that, as below:

Re: [COOT] Merge molecules scripting function

I knew that I was missing something obvious. Thanks Paul. Although as it turns out, in Python the arguments are switched around (the first one is a list and the second one is imol_ref). Thanks! Then, for the record, the function that I wanted to write goes something like this: def merge_fragm

Re: [COOT] Merge molecules scripting function

On 03/04/14 04:45, Oliver Clarke wrote: Hi all, Is the functionality of ‘Calculate-->Merge Molecules’ available from the scripting interface? Yes. I couldn’t find it in the manual. There is a function named merge_molecules, but I don’t know what arguments it takes and it does not do what I

[COOT] Merge molecules scripting function

Hi all, Is the functionality of ‘Calculate-->Merge Molecules’ available from the scripting interface? I couldn’t find it in the manual. There is a function named merge_molecules, but I don’t know what arguments it takes and it does not do what I would expect - I’d like it to take two mol_ids

Re: [COOT] merge chains?

Thanks Carsten, that worked. Mirek > -Original Message- > From: Schubert, Carsten [PRDUS] [mailto:cschu...@its.jnj.com] > Sent: Wednesday, July 14, 2010 1:16 PM > To: mi...@bri.nrc.ca; COOT@JISCMAIL.AC.UK > Subject: RE: [COOT] merge chains? > > Mirek

Re: [COOT] merge chains?

rystallographic Software > [mailto:c...@jiscmail.ac.uk] On Behalf Of Mirek Cygler > Sent: Wednesday, July 14, 2010 1:03 PM > To: COOT@JISCMAIL.AC.UK > Subject: [COOT] merge chains? > > Hi, > I would like to combine two chains into one inside Coot. The > residue > numb

[COOT] merge chains?

Hi, I would like to combine two chains into one inside Coot. The residue numbers do not overlap. I cannot find the command to do it. Renaming the second chain does not work, Coot tells me that I alredy have a chain of that name. Thanks for your help,    

Re: [COOT] merge water chains

> From: Christian Roth > >> Hi all, >> >> I am not sure but If I remember correctly Bernhard mentioned on the >> last CCP4 >> study weekend in Nottingham that Coot is able to merge the >> different water >> chains, generated through repeated refinement runs, in one. If this >> function >> exist,

Re: [COOT] merge water chains

ail: bernhard.lohk...@ki.se - Original Message - From: Christian Roth Date: Tuesday, May 5, 2009 7:05 pm Subject: [COOT] merge water chains To: COOT@JISCMAIL.AC.UK > Hi all, > > I am not sure but If I remember correctly Bernhard mentioned on the > last CCP4 > study wee

[COOT] merge water chains

Hi all, I am not sure but If I remember correctly Bernhard mentioned on the last CCP4 study weekend in Nottingham that Coot is able to merge the different water chains, generated through repeated refinement runs, in one. If this function exist, how can I use it? Thanks in advance for your help

Re: [COOT] merge symmetry related atoms in coot

This is tricky I find .. You can use the NCS ghost to fit the bits of A you like over B, then work out what bits of B you want to shift into A. There are tools to rename that bit of B to A and if necessary renumber it as well.. Then output the renamed file and you will probably have to edit i

Re: [COOT] merge symmetry related atoms in coot

Hi, This is a good question, and I've been trying to do this myself. My solution is somewhat crude: take two input PDB files, one containing the majority that you want to keep, and one which acts as a mask to delete the atoms which overlap from the two structures. How do you define the overla

[COOT] merge symmetry related atoms in coot

Hello I have a partial model with 4 chains, but some part of A chain is in B chain, can I merge the symmetry related atoms to make a right A chain? thanks Qing Chen