Re: [COOT] Color chains or turn on environmental distances between molecules
I believe "bonds colour by chain" option in display manager does color chains differently. On Wed, Dec 25, 2019, 12:06 PM Ahmad Khalifa wrote: > I want to either color chains of the same structure differently, or turn > on environmental distances between molecules (which I can color > differently). > > If neither can be done, I think it's a feature worth adding in future Coot > releases. > > Regards. > > -- > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
Re: [COOT] Building a helix into an unknown density
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Place-Helix On Tue, Jan 29, 2019 at 3:09 PM Ahmad Khalifa wrote: > Hello, > > I'm a new user of Coot. I have a density that has the shape of a helix. I > sort of have an idea of what sequence should go in there, but I haven't > resolved the structure near it from both the C- and N-terminai sides. > > How can I start placing amino acids in the density without having a > terminus to "add terminal residue" to? > > Thank you. > > -- > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1 > To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
[COOT] sphere refine
Is there currently a way to auto-run the sphere refine on full sequence (similarly to stepped refine option, preferably with an option to enforce Ramachandran)? If not, are there plans to add such feature? Is there some fundamental objection to such feature? Thanks --- Coot verendus est To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT=1
Re: [COOT] pdb file problem with duplicate amino acid
Thanks - sorry I should have searched the archives first. As a suggestion, could you alter the warning text to include the fix decription (i.e. "include this in your .coot.py)? This way users would know what to do right away. On Tue, Jan 31, 2017 at 2:51 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 31/01/17 17:54, Edwin Pozharski wrote: > > Whatever the rationale was, there is a structure in the PDB that has > alternate conformer of a residue listed with different residue type - A is > arginine and B is glutamine. Coot fails to load the model complaining in > the command window > > WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb" >> There was an error reading /home/epo/coot/foo.pdb. >> ERROR 42 READ: Duplicate sequence number and insertion code. >> LINE #1571 >> ATOM 1666 N BGLN B 93 24.448 28.340 -33.325 0.50 >> 9.34 N >> >> No Spacegroup found for this PDB file >> There was a coordinates read error >> > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1503= > COOT===25056 > > Paul. >
[COOT] pdb file problem with duplicate amino acid
Whatever the rationale was, there is a structure in the PDB that has alternate conformer of a residue listed with different residue type - A is arginine and B is glutamine. Coot fails to load the model complaining in the command window WARNING:: Error reading small-molecule cif "/home/epo/coot/foo.pdb" > There was an error reading /home/epo/coot/foo.pdb. > ERROR 42 READ: Duplicate sequence number and insertion code. > LINE #1571 > ATOM 1666 N BGLN B 93 24.448 28.340 -33.325 0.50 > 9.34 N > > No Spacegroup found for this PDB file > There was a coordinates read error > One way to deal with it is to take the second conformer and manually add a sequence modifier (make it 93A), and that pdb file loads just fine. This is observed with Coot-0.8.8-pre, rev.6506. This is only a minor nuisance, of course, so I completely understand if no fix is made to load such strange models. Cheers, Ed. --- Coot verendus est
Re: [COOT] Coot "open file" dialogue connection to CCP4
Resetting $HOME won't work for me personally since I do have some custom
stuff in ~/.coot.py. I could symlink it to the coot home folder, of
course. Hopefully, no other problems pop up and coot does not rely on some
configuration file stored in the actual home folder.
Making .CCP4 folder unreadable is a better hack for sure - this way one
can't open CCP4 accidentally and overwrite the database.
Creating a separate account to just run coot (ideally configured to allow
su without a password) is another possibility.
None of this is ideal, of course. Adding option to coot preferences to
disable CCP4 folders is.
Probably the non-ugly one-way hack is to put return statement at the top of
add_ccp4i_projects_to_optionmenu in c-interface-gui.cc and compile from
source.
Cheers,
Ed.
---
Coot verendus est
On Thu, Nov 10, 2016 at 2:58 PM, Ethan A Merritt <merr...@u.washington.edu>
wrote:
> On Thursday, 10 November, 2016 14:01:01 Edwin Pozharski wrote:
> > This is an ugly hack, but here goes
>
> [...]
>
>
> Wouldn't it be cleaner to wrap coot in a script that either
> - resets $HOME to a directory that doesn't hold the .CCP4 folder
> - uses sgid + group permissions to prohibit read access to that directory
> - runs in a bind mount environment that does not contain .CCP4 or
> provides a minimal alternative file
>
>
> If you are using a bash shell, this can be as easy as invoking
> coot as:
>
> [1] HOME=/somewhere/else coot
>
>
> Ethan
>
> >
> > 1. Prior to opening coot, rename you .CCP4 folder. (bash: mv .CCP4
> > .CCP4_hidden)
> > 2. Open coot. Do what you need to do.
> > 3. Close coot.
> > 4. Restore .CCP4 folder (bash: mv .CCP4_hidden .CCP4)
> >
> > You can make a shortcut by putting this into your .bashrc
> >
> > coot_no_ccp4_folders ()
> > {
> > mv ~/.CCP4 ~/.CCP4_hidden
> > coot
> > mv ~/.CCP4_hidden ~/.CCP4
> > }
> >
> > Use with caution - if you mess up, you may lose all your CCP4
> configuration.
> >
> > This is not very convenient, since you cannot use ccp4 in the meantime -
> I
> > checked and the list of CCP4 folders does come up if you restore the CCP4
> > database folder while coot is still running. If you do use CCP4 in the
> > meantime, it will create an empty database, which is obviously not what
> you
> > want.
> >
> > If you are into hacking the coot source (with proper apologies to Paul),
> > then find src/graphics-info.cc file in your coot source, go to
> > ccp4_defs_file_name method and mess with it in an obvious way - it
> returns
> > the path to your CCP4 database folder, so just change it to something
> > non-existent. Compile custom coot binaries as usual and see what
> happens.
> > It might break spectacularly in case this method is used in a way other
> > than getting the CCP4 project folders listed in the file opening dialog.
> > Or it may behave exactly as you wish. Live dangerously :)
> >
> > My complaint about this feature is that it lists folder names, not
> project
> > names (I realize this might require customization of the dialog, so not
> > necessarily easy to fix). My habit is to create CCP4 projects as need
> and
> > name corresponding folders ccp4 inside another folder that holds the
> data.
> > As a result, I end up with a bunch of "ccp4" items in the list of
> folders,
> > which is unusable (I think it shows the full path if you hover over the
> > name, but that's not too helpful if you are looking for a particular
> > project. Of course, I should simply name folders in a more
> comprehensible
> > way.
> >
> > HTH,
> >
> > Ed.
> >
> > On Thu, Nov 10, 2016 at 12:30 PM, Gerhard Fischer <gf...@cam.ac.uk>
> wrote:
> >
> > > Dear all,
> > >
> > > I am having an issue with the "open file" dialogue in Coot:
> > >
> > > Apparently, there is some kind of connection between Coot and CCP4,
> which
> > > causes all the ccp4-project-directories to appear on the lefthand side
> > > under "places".
> > >
> > > Is there a way to avoid this - I have plenty of different
> CCP4-projects,
> > > many of them old, and I would like to use the space to manually link to
> > > relevant directories.
> > >
> > >
> > > I cannot manually remove these directories using the remove button
> (greyed
> > > out), and new directories can only be added manually to the very
> bottom of
> > > the list (and not moved up) - which is quite a way to scroll down, and
> not
> > > for qui
[COOT] fresh coot misbehaves? (well, not really)
I had an opportunity to build coot executable on a fresh ubuntu box. It compiles fine after you install few dependencies but I noticed the following: 1) it seems that coot won't work without CCP4. It won't load mtz files - complained that the map file wasn't proper format. 2) Even after I installed CCP4, it wants me to have ccp4 configuration script sourced or it won't refine even amino acids in real space. I was under impression that in the past standard amino acids were accessible even if ccp4 monomer libraries cannot be reached. Maybe it changed. None of this is a big deal, just surprising. Obviously, having coot installed without ccp4 is a bit unusual, although having a standalone coot (say, for teaching purposes on a flash drive) is not completely unimaginable. Cheers, Ed. --- Coot verendus est
Re: [COOT] Coot "open file" dialogue connection to CCP4
This is an ugly hack, but here goes:
1. Prior to opening coot, rename you .CCP4 folder. (bash: mv .CCP4
.CCP4_hidden)
2. Open coot. Do what you need to do.
3. Close coot.
4. Restore .CCP4 folder (bash: mv .CCP4_hidden .CCP4)
You can make a shortcut by putting this into your .bashrc
coot_no_ccp4_folders ()
{
mv ~/.CCP4 ~/.CCP4_hidden
coot
mv ~/.CCP4_hidden ~/.CCP4
}
Use with caution - if you mess up, you may lose all your CCP4 configuration.
This is not very convenient, since you cannot use ccp4 in the meantime - I
checked and the list of CCP4 folders does come up if you restore the CCP4
database folder while coot is still running. If you do use CCP4 in the
meantime, it will create an empty database, which is obviously not what you
want.
If you are into hacking the coot source (with proper apologies to Paul),
then find src/graphics-info.cc file in your coot source, go to
ccp4_defs_file_name method and mess with it in an obvious way - it returns
the path to your CCP4 database folder, so just change it to something
non-existent. Compile custom coot binaries as usual and see what happens.
It might break spectacularly in case this method is used in a way other
than getting the CCP4 project folders listed in the file opening dialog.
Or it may behave exactly as you wish. Live dangerously :)
My complaint about this feature is that it lists folder names, not project
names (I realize this might require customization of the dialog, so not
necessarily easy to fix). My habit is to create CCP4 projects as need and
name corresponding folders ccp4 inside another folder that holds the data.
As a result, I end up with a bunch of "ccp4" items in the list of folders,
which is unusable (I think it shows the full path if you hover over the
name, but that's not too helpful if you are looking for a particular
project. Of course, I should simply name folders in a more comprehensible
way.
HTH,
Ed.
On Thu, Nov 10, 2016 at 12:30 PM, Gerhard Fischer wrote:
> Dear all,
>
> I am having an issue with the "open file" dialogue in Coot:
>
> Apparently, there is some kind of connection between Coot and CCP4, which
> causes all the ccp4-project-directories to appear on the lefthand side
> under "places".
>
> Is there a way to avoid this - I have plenty of different CCP4-projects,
> many of them old, and I would like to use the space to manually link to
> relevant directories.
>
>
> I cannot manually remove these directories using the remove button (greyed
> out), and new directories can only be added manually to the very bottom of
> the list (and not moved up) - which is quite a way to scroll down, and not
> for quickly switching folders.
>
> I am on Kubuntu 16.04 LTS, but had this issue on openSUSE 13.2 as well. I
> have recently tried with Coot 0.8.7-pre (standalone) and 0.8.3 (installed
> through CCP4).
> I can see the folders even when I start standalone coot and do not source
> CCP4.
>
> Any ideas?
>
>
> Best wishes,
>
> Gerhard
>
> --
> Gerhard Fischer, PhD
> Postdoctoral Research Associate
>
> University of Cambridge
> Department of Biochemistry
> 80 Tennis Court Road
> CB2 1GA Cambridge
> United Kingdom
>
> ---
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>
> If you have received this message in error, please contact
> the sender by reply e-mail message and destroy all copies of the
> original message (including attachments).
>
Re: [COOT] Add OXT broken?
Funny, but your email consistently crashes my Evolution Email client. Not a coot problem, I presume :) Cheers, Ed. When I try to add an OXT to my model, coot crashes. Specifically, when I try to change the chain from the list in the popup window (below), it hangs then completely crashes. I'm on an intel mac running 10.6.8, with Coot 0.7-pre-1 (revision 3628). Bug? Thanks, Jon -- Edwin Pozharski, PhD University of Maryland, Baltimore
