### Re: [PyMOL] How to get TTT matrix in PyMOL 1.7.6?

```Thanks Jared,
I have tried the transformations.py script, and here is what I've got:
- I get a quaternions from external source (a 3d manipulator) in a
classical form: [x,y,z,w]
- I use function: quaternion_matrix(quaternion) from transformations.py
script:

m = quaternion_matrix([x, y, z, w])# m is an array of an arrays (4x4)
M = [m[0,0], m[0,1], m[0,2], m[0,3], m[1,0], m[1,1], m[1,2], m[1,3],
m[2,0], m[2,1], m[2,2], m[2,3], m[3,0], m[3,1], m[3,2], m[3,3]]   # so i
need to convert it to a vector 16x1
cmd.transform_selection(all, M, homogenous=1)  # its time to apply the
vector into a transform_selection function; homogenous=0 also doesn't work
print M # print works fine ;)

But the function transform_selection does not work and I don't really know
why, rotation doesn't occur.
Maybe it's because the selection is wrong? On the scene I have a CGO (an
arrow) and even when I change the selection string from all to arrow it
doesn't rotate either.
What exactly is the selection, could this be a CGO?

I have also noticed, that function cmd.rotate(...) works for my CGO arrow
when I set property object=arrow and I put some arbitrary hardcoded
parameters (axis and angle).
Maybe the better way would be use this function?
But I'm not really sure which function from transformations.py script
should I use to convert quaternions to axis and angle params required by
cmd.rotate() function...
any ideas?

Cheers,
Pawel T.

2015-08-13 18:34 GMT+02:00 Sampson, Jared jared.samp...@nyumc.org:

Hi Paweł -

Honestly, if you prefer to use matrices, I'd say just go ahead and use
get_object_matrix; I doubt it's going away any time soon.  You may want to
use this in combination with transform_selection
http://www.pymolwiki.org/index.php/Transform_selection.

Also maybe check out Christoph Gohlke's transformations.py script
http://www.pymolwiki.org/index.php/Transformations.  It offers several
tools for manipulating quaternions, matrices, and angle/axis operations.  I
think there's also a newer version on his website, which is linked from the
wiki page.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/

On Aug 6, 2015, at 4:04 AM, Paweł Tomaszewski croov...@gmail.com wrote:

Hello,
I've created a CGO in pymol script (a cone) and I need to make some
transformations on it. I've found that it is easier for me to modify a TTT
matrix rather than using translate/rotate functions.

Documentation says [http://www.pymolwiki.org/index.php/Get_object_matrix]
get_object_matrix is unsupported operation. So how to get/set TTT?

The problem is, that I get (from external source) position in quaternions
and now I need to make my CGO position equal to those quaternion. How can I
make it work?

Thanks
Paweł Tomaszewski

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

This email message, including any attachments, is for the sole use of the
intended recipient(s) and may contain information that is proprietary,
confidential, and exempt from disclosure under applicable law. Any
unauthorized review, use, disclosure, or distribution is prohibited. If you
have received this email in error please notify the sender by return email
and delete the original message. Please note, the recipient should check
this email and any attachments for the presence of viruses. The
organization accepts no liability for any damage caused by any virus
transmitted by this email.
=

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
```

### Re: [PyMOL] Pymol crash when raytracing empty graphics

```Thanks for the quick fix! I would love to get a hotfix if possible.

The PDBe API is a nice solution. I think that detecting CA traces will fix
90% of the cases. There are still a few edge cases besides CA which don't
have a cartoon mode (e.g. 1hzs, which has a polydeoxyribonucleotide polymer
type but lacks phosphate atoms needed for cartoon), but these are rare
enough to be handled individually.

-Spencer

On Mon, Aug 17, 2015 at 7:54 PM, Thomas Holder
thomas.hol...@schrodinger.com wrote:

Hi Spencer,

Thank you for the bug report. We could reproduce and fix the crash, if you
want I can send you a hotfix build. I will also push the fix to the open
source SVN repository soon.

I second John's suggestions to query the ca_p_only property from the
PDBe API. Also, the next PyMOL version will read that property from the
mmCIF file and automatically set the cartoon_trace_atoms and
ribbon_trace_atoms settings.

Cheers,
Thomas

On 17 Aug 2015, at 10:58, John Berrisford j...@ebi.ac.uk wrote:

Dear Spencer
It is possible to work this out using the PDBe API.
for our interactive API see:
http://www.ebi.ac.uk/pdbe/api/doc/
The molecules url will give you this information:
http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/1a1q
entity 1 has ca_p_only: true,
which means cartoon will not work for this chain - so we use ribbon
instead with the command
pymol.cmd.set(ribbon_trace_atoms, 1)
This test allows us to make images such as those shown on the entry page
for 1a1q at PDBe
http://www.ebi.ac.uk/pdbe/entry/pdb/1a1q
The images are made with pymol (currently 1.6, but also works in 1.7)
Regards
John
PDBe
On Monday 17 August 2015 15:40:14 Spencer Bliven wrote:
We have a pipeline that uses pymol to create images using the headless
command line interface. I've discovered that PyMOL 1.7.4 and 1.7.6 (at
least) crash if you try to ray-trace an empty viewport.

Example:

pymol -q -c -d 'fetch 1a1q,async=0;as cartoon;ray'

This particular example only has CA atoms, so the cartoon mode doesn't
show
anything. In interactive mode I would `set cartoon_trace_atoms,1` but
when
batch processing there isn't a good way of detecting whether anything
is
showing or not.

The error is:

*** glibc detected ***
/home/user/software/packages/pymol-v1.7.4.4/pymol.exe: double free or
corruption (out): 0x7f11f8744f40 ***

I've reproduced the error on Redhat 6 and Ubuntu 14.04, with PyMOL
1.7.4.1
through 1.7.6.3.

Attached is a stack trace.

Any suggestions on ensuring that there are some polygons in frame would
also be appreciated. Say, if there was a way to detect that cartoon
would
fail so that I can switch to a lines or nonbonded representation (I
wish
that was the default fallback for cartoon).

Thanks,
Spencer

--
John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492529

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
```