Re: [COOT] pre-proline peptide restraints

[Paul Emsley]

Oh Wolfram, you top-poster, you..!

On 02/12/2016 17:25, wtempel wrote:


I am again struggling with a similar problem and have only (re?-)discovered 
Paul's May 23
reply today. Thus, I pushed that " Trans>" button and, yes, I now can 
still
recognize the proline after real-space refinement. But the COOT planar 
restraints for the
cis-peptide appear to be much weaker than for trans-peptides.


The planar peptide restraints are independent of cis/trans configuration.


It almost feels like the
"Cis<->Trans" lifts the trans restraints without imposing cis restraints.


Yes. That right. The trans peptide restraints only work with the configuration was 
previously trans.  There is no cis equivalent.


From the point of view of the peptide: If you were trans and were considering cis, then 
coot will encourage you to be trans.  If you are cis and are considering trans, then coot 
will let you go ahead without additional intervention.



I have
experimented with the "add planar peptide restraints" menu, but did not notice 
any effect.


I can believe that. That's toggling an additional plane restraints, not a 
torsion restraint.


Am I going about this problem in the "right" COOT way?


It sounds that you are thinking the right thoughts. I'm not sure about the details for the 
particular problem though... perhaps a cis-model for a cis pre-Pro that won't stay cis?


Paul.



On Mon, May 23, 2016 at 3:28 PM, Paul Emsley > wrote:

On 17/05/2016 15:52, wtempel wrote:


is it only my perception that COOT handles real-space refinement of
Xxx-Pro peptide bonds,(specifically cis peptides?) less gracefully than
in the past?


It handles it differently, well spotted.

If you had a decent or good map and a model that was trans (and it should 
be cis) [1]
then Coot will now have additional restraints to keep it trans that will 
thwart you. Now
you need to explicitly use the Cis <-> Trans tool to fix the problem (and 
then refine).

Why? Because (it seemed to me) that unintentional trans->cis conversion was 
far more
problematic than easy intentional trans->cis was useful.

[1] If you ever did it, my validation tutorial had such a case and "solved" 
the problem
beautifully.

Paul.

Re: [COOT] pre-proline peptide restraints

[wtempel]

Hello,
I am again struggling with a similar problem and have only (re?-)discovered
Paul's May 23 reply today. Thus, I pushed that " Trans>" button
and, yes, I now can still recognize the proline after real-space
refinement. But the COOT planar restraints for the cis-peptide appear to be
much weaker than for trans-peptides. It almost feels like the "Cis<->Trans"
lifts the trans restraints without imposing cis restraints. I have
experimented with the "add planar peptide restraints" menu, but did not
notice any effect.
Am I going about this problem in the "right" COOT way?
Best regards.
Wolfram


On Mon, May 23, 2016 at 3:28 PM, Paul Emsley 
wrote:

> On 17/05/2016 15:52, wtempel wrote:
>
>>
>> is it only my perception that COOT handles real-space refinement of
>> Xxx-Pro peptide bonds,(specifically cis peptides?) less gracefully than
>> in the past?
>>
>
> It handles it differently, well spotted.
>
> If you had a decent or good map and a model that was trans (and it should
> be cis) [1] then Coot will now have additional restraints to keep it trans
> that will thwart you. Now you need to explicitly use the Cis <-> Trans tool
> to fix the problem (and then refine).
>
> Why? Because (it seemed to me) that unintentional trans->cis conversion
> was far more problematic than easy intentional trans->cis was useful.
>
> [1] If you ever did it, my validation tutorial had such a case and
> "solved" the problem beautifully.
>
> Paul.
>
>

Re: [COOT] stuck with black fonts

[Paul Emsley]

Quite Right Folmer,

I am pretty sure that this was fixed in 0.8.2:

Release Notes has this item:

  o BUG-FIX: Resetting of Own font colour on opening the preferences
 dialog fixed.

Paul.


On 02/12/2016 10:45, Folmer Fredslund wrote:

Dear Andrea,

I would suggest, if at all possible, to use a more recent version of coot, or 
at least test it.
0.8.1 is almost 2 years old, and the new ones are available for debian as tar 
files here:
 http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/

Even if you are not an administrator on the system, it is easy to use coot 
locally on your
own system.

Best regards,
Folmer

On 2016-12-02 11:24, Andrea PICA wrote:

Hi everybody,

I am using coot (version 0.8.1) on a linux debian system. Atom labels are shown 
in black
and on a black background this is not ideal. Unfortunately changing the color in
Edit>Preferences>Others>Fonts doesn't seem to work (color is always black even 
if I select
a different one). How can I solve this issue?

Thanks,

Andrea

Re: [COOT] Coot crashing after "Add OXT terminal" revision 6498

[Paul Emsley]

On 30/11/2016 10:25, Folmer Fredslund wrote:


As was mentioned, there were some problems with COOT and mutations
after a recent CCP4 update.

I've seen crashes after "Add OXT to Residue..." (from Calculate->Other
Modelling Tools) in revision 6498 provided by CCP4-7.0 (update 24),
but I don't see the same problem with revision 6506 (the latest
nightly build made for Ubuntu 14.04, running on Ubuntu 14.04)

So, I hope the 6506 changes can be delivered in the next CCP4 update.


I hope so too. I do, from time to time, correspond with the CCP4 team, but the problem that 
you mention above was never apparent in my builds and (thanks to Oliver Clarke) the fix for 
which was already in place in the pre-release binaries weeks before it was mentioned on CCP4BB.


Paul.

Re: [COOT] stuck with black fonts

[Folmer Fredslund]

Dear Andrea,

I would suggest, if at all possible, to use a more recent version of 
coot, or at least test it.
0.8.1 is almost 2 years old, and the new ones are available for debian 
as tar files here:

 http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/

Even if you are not an administrator on the system, it is easy to use 
coot locally on your own system.


That being said, without knowing anything else about your system, it 
could also be some sort of graphics card/driver issue, but that is not 
easy to tell from the information provided.



Best regards,
Folmer

On 2016-12-02 11:24, Andrea PICA wrote:

Hi everybody,

I am using coot (version 0.8.1) on a linux debian system. Atom labels 
are shown in black and on a black background this is not ideal. 
Unfortunately changing the color in Edit>Preferences>Others>Fonts 
doesn't seem to work (color is always black even if I select a 
different one). How can I solve this issue?


Thanks,

Andrea

[COOT] stuck with black fonts

[Andrea PICA]

Hi everybody,

I am using coot (version 0.8.1) on a linux debian system. Atom labels 
are shown in black and on a black background this is not ideal. 
Unfortunately changing the color in Edit>Preferences>Others>Fonts 
doesn't seem to work (color is always black even if I select a different 
one). How can I solve this issue?


Thanks,

Andrea