[COOT] phosphorylate residues

2009-01-08 Thread SUBSCRIBE COOT Bo 
Hi, 

I install coot in linux (Fedora 8). It runs OK until when I try to
phosphorylate residues. 

Here is the messag:

(monomer-molecule-from-3-let-code "SEP" "")
passing libcheck these data lines: ("N" "MON SEP" "")
which: no libcheck in
(/home/Yang/Download/coot/coot-Linux-i386-fedora-6-gtk1/bin:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin:/usr/X11R6/bin:/home/Yang/bin)
command "libcheck" not found
INFO:: libcheck status: #t
(get-monomer "SEP")

At the end, the residue is not phosphorylated. 

Thank uou for your suggestion

Bo

Re: [COOT] Dropping Gtk1 version [was Re: overlapping buttons in molprobity check script]

2009-01-08 Thread Pete Meyer 
> Is there anyone who needs the GTK1 version?  (And if so, why?)

Last I checked, gtk1 is still the default in the build-it script.  Am I
using an outdated way of compiling coot?

Pete

[COOT] Dropping Gtk1 version [was Re: overlapping buttons in molprobity check script]

2009-01-08 Thread Paul Emsley 

Donnie Berkholz wrote:

On 16:00 Thu 08 Jan , Pete Meyer wrote:

Paul,

Using your coot-Linux-x86_64-centos-5-gtk2 binary fixes it, so I guess
it was a gtk1 issue.


Is there any particular reason to hang onto the gtk1 port? Seems like 
all it does is generate bug reports.



Indeed.

Is there anyone who needs the GTK1 version?  (And if so, why?)

Thanks,

Paul.

Re: [COOT] overlapping buttons in molprobity check script

2009-01-08 Thread Donnie Berkholz 
On 16:00 Thu 08 Jan , Pete Meyer wrote:
> Paul,
> 
> Using your coot-Linux-x86_64-centos-5-gtk2 binary fixes it, so I guess
> it was a gtk1 issue.

Is there any particular reason to hang onto the gtk1 part? Seems like 
all it does is generate bug reports.

-- 
Thanks,
Donnie

Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com


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Re: [COOT] overlapping buttons in molprobity check script

2009-01-08 Thread Pete Meyer 
Paul,

Using your coot-Linux-x86_64-centos-5-gtk2 binary fixes it, so I guess
it was a gtk1 issue.

Thanks,

Pete

Paul Emsley wrote:
> Pete Meyer wrote:
>> Using molprobity 3.15 with coot 0.5.2 (gtk1 on ubuntu 7.10 amd64), the
>> dialog box that results from running the molprobity-produced script has
>> overlapping buttons (so problems in one residue are masked by problems
>> in another).
>> Does anyone have any ideas if this is a molprobity (generated script)
>> issue, coot issue, or gtk1/gtk2 issue?
> 
> It is a gtk1 issue, I think.  How about using the gtk2 version?
> 
> Paul.
>

Re: [COOT] overlapping buttons in molprobity check script

2009-01-08 Thread Paul Emsley 

Pete Meyer wrote:

Using molprobity 3.15 with coot 0.5.2 (gtk1 on ubuntu 7.10 amd64), the
dialog box that results from running the molprobity-produced script has
overlapping buttons (so problems in one residue are masked by problems
in another).
Does anyone have any ideas if this is a molprobity (generated script)
issue, coot issue, or gtk1/gtk2 issue?


It is a gtk1 issue, I think.  How about using the gtk2 version?

Paul.

[COOT] overlapping buttons in molprobity check script

2009-01-08 Thread Pete Meyer 
Using molprobity 3.15 with coot 0.5.2 (gtk1 on ubuntu 7.10 amd64), the
dialog box that results from running the molprobity-produced script has
overlapping buttons (so problems in one residue are masked by problems
in another).
Does anyone have any ideas if this is a molprobity (generated script)
issue, coot issue, or gtk1/gtk2 issue?

Thank,

Pete