Re: [ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

2015-05-05 Thread Finke Aaron (PSI) 
I’ll add to this that you should also set the relevant path in launchd.conf as 
well to access other external programs (SHELXC/D/E) when opening ccp4i via the 
Finder/Spotlight.

setenv PATH /where/ever/shelx

Cheers,
Aaron

--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch<mailto:aaron.fi...@psi.ch>

On May 5, 2015, at 11:00, Finke Aaron (PSI) 
mailto:aaron.fi...@psi.ch>> wrote:

Dear Mark,

Indeed there is a way. You have to set the environment variable so that all Mac 
apps can access it. This is most easily done via launchd.

In the Terminal, type ‘sudo vi /etc/launchd.conf’

and add the following text (the file will likely be blank):

setenv SHARP_home /where/ever/SHARP/

Save, and reboot. Now when you access ccp4i in a Finder window or Spotlight, 
autoSHARP should be accessible. More info can be found here: 
http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x/3756686#3756686

I hope this works for you. (It worked for me.)

Cheers,
Aaron


--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch<mailto:aaron.fi...@psi.ch>

On May 5, 2015, at 1:17, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:

Dear All,

when starting CCP4i via the icon, AutoSharp remains greyed out, suggesting it 
is not installed. However, when I start CCP4i in an XQuartz window (i.e. “ccp4i 
&”), AutoSharp can be run.
I guess this may be because in first way my “.profile” file is not read, any 
ideas how to fix this?

Greetings,

Mark J van Raaij
mjvanra...@cnb.csic.es<mailto:mjvanra...@cnb.csic.es>
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

2015-05-05 Thread Finke Aaron (PSI) 
Dear Mark,

Indeed there is a way. You have to set the environment variable so that all Mac 
apps can access it. This is most easily done via launchd.

In the Terminal, type ‘sudo vi /etc/launchd.conf’

and add the following text (the file will likely be blank):

setenv SHARP_home /where/ever/SHARP/

Save, and reboot. Now when you access ccp4i in a Finder window or Spotlight, 
autoSHARP should be accessible. More info can be found here: 
http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x/3756686#3756686

I hope this works for you. (It worked for me.)

Cheers,
Aaron


--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch

On May 5, 2015, at 1:17, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:

Dear All,

when starting CCP4i via the icon, AutoSharp remains greyed out, suggesting it 
is not installed. However, when I start CCP4i in an XQuartz window (i.e. “ccp4i 
&”), AutoSharp can be run.
I guess this may be because in first way my “.profile” file is not read, any 
ideas how to fix this?

Greetings,

Mark J van Raaij
mjvanra...@cnb.csic.es
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

2015-04-01 Thread Finke Aaron (PSI) 
--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch

On Apr 1, 2015, at 13:03, Keller, Jacob  wrote:

> Can anyone index this? It's got mostly split spots and a strange diffuse 
> scattering background
> 
> JPK
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
> 
> 
>

Re: [ccp4bb] Absorption correction in small molecule crystals

2015-03-04 Thread Finke Aaron (PSI) 
Dear all,

Thanks for the insights. 

Cheers,
Aaron

--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch

On Mar 3, 2015, at 18:43, George Sheldrick  wrote:

> Dear Finke,
> 
> SADABS and similar programs work best when given scans about several axes 
> relative to the crystal. Scanning about a single axis can do more harm than 
> good especially if the symmetry is low. SADABS can also do a face-indexed 
> numerical absorption correction too, but this assumes that the crystal is 
> uniformly bathed in the beam, which is unlikely to be the case with highly 
> focussed beams.  Why don't you use the PSI PRIGO goniometer to scan about 
> several axes?!
> 
> Best wishes, George
> 
> 
> On 03.03.2015 17:35, Finke Aaron (PSI) wrote:
>> Dear comrades,
>> 
>> This is slightly off-topic but there are enough experts here to warrant 
>> asking. Here at SLS I occasionally get asked to collect small molecule data 
>> on the synchrotron. By convention, post-refinement corrections for X-ray 
>> absorption by the crystal are required for publication in Acta C and E. XDS, 
>> to my knowledge, does not do this, it just corrects for other absorption 
>> sources like air. Currently, the most popular absorption correction method 
>> for small molecules is the psi-scan correction implemented in programs like 
>> SADABS, but I am wondering if SADABS is appropriate for data collected on a 
>> single axis, as most synchrotron data is. Also, since we use photon-counting 
>> detectors (Pilatus), the other correction options for CCD detectors probably 
>> aren’t appropriate either. I rarely if ever see an improvement in R-factors 
>> nor other improvements in disagreeable reflections after using SADABS from 
>> data collected here. What does everyone think? Is psi-scan appropriate, or 
>> should I resort other methods?
>> 
>> Any insights would be much appreciated.
>> 
>> Best regards,
>> Aaron
>> --
>> Dr. Aaron Finke
>> Postdoctoral Fellow
>> Swiss Light Source
>> WSLA/217
>> CH-5232 Villigen-PSI
>> phone: +41 56 310 5652
>> e-mail: aaron.fi...@psi.ch
>> 
> 
> 
> -- 
> Prof. George M. Sheldrick FRS
> Dept. Structural Chemistry,
> University of Goettingen,
> Tammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or -33068
> Fax. +49-551-39-22582
> 
>

[ccp4bb] Absorption correction in small molecule crystals

2015-03-03 Thread Finke Aaron (PSI) 
Dear comrades,

This is slightly off-topic but there are enough experts here to warrant asking. 
Here at SLS I occasionally get asked to collect small molecule data on the 
synchrotron. By convention, post-refinement corrections for X-ray absorption by 
the crystal are required for publication in Acta C and E. XDS, to my knowledge, 
does not do this, it just corrects for other absorption sources like air. 
Currently, the most popular absorption correction method for small molecules is 
the psi-scan correction implemented in programs like SADABS, but I am wondering 
if SADABS is appropriate for data collected on a single axis, as most 
synchrotron data is. Also, since we use photon-counting detectors (Pilatus), 
the other correction options for CCD detectors probably aren’t appropriate 
either. I rarely if ever see an improvement in R-factors nor other improvements 
in disagreeable reflections after using SADABS from data collected here. What 
does everyone think? Is psi-scan appropriate, or should I resort other methods?

Any insights would be much appreciated.

Best regards,
Aaron
--
Dr. Aaron Finke
Postdoctoral Fellow
Swiss Light Source
WSLA/217
CH-5232 Villigen-PSI
phone: +41 56 310 5652
e-mail: aaron.fi...@psi.ch