Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?

2014-09-28 Thread Wang, Bing 
Thank you guys for the replies!  I tried the PISCO method from Marlene Holder. 
It is pretty cool, and clear method which could used directly in PYMOL. Thank 
Thomas Holder for the help of PISCO installation!

I also tried the method from Matthew Franklin. From this method, I learned the 
theory behind the measurement of two planes. It is awesome!

Thank Oliver about the method Geomcalc in CCP4 suit. I will try to get this 
useful software to calculate the angel 
 later.

Anyway, thank all the replies here and you guys have a good weekend!

Bing 

From: Oliver Smart [osm...@globalphasing.com]
Sent: Friday, September 26, 2014 8:36 AM
To: Wang, Bing
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] how to measure the angle between two aromatic ring plane 
in PYMOL?

On Thu, 25 Sep 2014, Wang, Bing wrote:

 Hi everyone,

 I want to tell an angel between two aromatic planes which comes from two 
 different molecules and cross each other.

 First, I tried the easier ways. I presume these two aromatic rings are in the 
 perfect planes, that is why I tried
 plane_wizard.py and draw_plane_cgo.py which work very well. However after I 
 got two plates by plane_wizard or draw_plane, I
 don't know how to measure the angle between these two plates. I also don't 
 know whether I could get the angle I wanted from
 these two ways. I tried vector_angly.py which cann't loaded into pymol 
 properly. If it could, how can i do to get the angel from
 these two plates I drew. Solutions? Since I am in the beginner state, please 
 show me details which i could follow step by step.

 Second, If these two aromatic rings are not in the perfect planes, how can i 
 find the best fit planes? And then find the angle
 between the best fit planes? I tried svdplos.py and makeCGOplates.py which 
 are downloaded on line. unfortunately both of these
 can't be loaded into pymol properly. Solutions?

 Thanks!

 Bing Wang



Wang,

I am sure the other replies will sort your problem in PyMOL itself. But I
thought it might be useful for you to consider checking any calculation of
the angle works properly by using the well-established CCP4 tool GEOMCALC:

http://www.ccp4.ac.uk/html/geomcalc.html

I (and others) use the tool to calculate butterfly bend angles in flavin
rings (this involves finding the angle between two mean-plane rings). If
you want any help on running it then contact me off list and I would be
happy to help.

Good luck,

Oliver

PS. I really like the phrase tell an angel. Paul Emsley's coot refers to
geometry only optimization as send in the bond angels.

| Dr Oliver Smart |
| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] is small dialysis tubes reusable??

2014-09-28 Thread Andreas Förster 
If cost is an issue, I recommend preparing your own MINI Dialysis 
Devices at 99.74% savings.


Cut a hole in the lid of an Eppendorf tube, put your sample in the tube, 
then close the lid over a small piece of dialysis tubing, trapping it as 
a cover.  Float inverted in dialysis buffer and Bob's your uncles for 
pennies.



Andreas



On 26/09/2014 4:51, Manjula Ramu wrote:

Hi all,

I use Slide-A-Lyzer MINI Dialysis Devices from Thermo for dialysis of
small protein volumes. Are they reusable? if so how can we store them??

Thanks and Regards,
Manjula R
Research Scholar
Department of Biophysics
National Institute of Mental Health and Neurosciences
Bengaluru-29, Karnataka
INDIA
E-mail: manjula@gmail.com mailto:manjula@gmail.com
Mobile no:+91-9538553356
http://www.nimhans.kar.nic.in/
https://www.nimhans.kar.nic.in/


--
  Andreas Förster
 Crystallization and X-ray Facility Manager
   Centre for Structural Biology
  Imperial College London

Re: [ccp4bb] is small dialysis tubes reusable??

2014-09-28 Thread Edward A. Berry 

For even smaller volumes, make a dialysis button from an eppendorf tube:
With a razor blade, cut the tube off leaving only the rim
that the cap snaps into.
Put your sample in the depression in the middle of the cap (inside).
cover with membrane and snap the rim down over it.
(I have done this but never actually used it for dialysis or crystallization)

For volumes .5 ml or larger, just get the pencil diameter tubing,
(soak and maybe boil it), cut off the right length and use
reusableclips to hold the ends.

eab

On 09/28/2014 01:30 PM, Andreas Förster wrote:

If cost is an issue, I recommend preparing your own MINI Dialysis
Devices at 99.74% savings.

Cut a hole in the lid of an Eppendorf tube, put your sample in the tube,
then close the lid over a small piece of dialysis tubing, trapping it as
a cover.  Float inverted in dialysis buffer and Bob's your uncles for
pennies.


Andreas



On 26/09/2014 4:51, Manjula Ramu wrote:

Hi all,

I use Slide-A-Lyzer MINI Dialysis Devices from Thermo for dialysis of
small protein volumes. Are they reusable? if so how can we store them??

Thanks and Regards,
Manjula R
Research Scholar
Department of Biophysics
National Institute of Mental Health and Neurosciences
Bengaluru-29, Karnataka
INDIA
E-mail: manjula@gmail.com mailto:manjula@gmail.com
Mobile no:+91-9538553356
http://www.nimhans.kar.nic.in/
https://www.nimhans.kar.nic.in/


--
   Andreas Förster
  Crystallization and X-ray Facility Manager
Centre for Structural Biology
   Imperial College London