Re: [ccp4bb] SHELXL/ BAVERAGE

[Fátima Fonseca]

Dear George,

I really appreciate your kind offer but I have just solved 
the problem.


To all that may have the same issue in the future, I 
should say that in my case the problem was related to the 
use of SHELXPRO. I was not using it properly to transform 
the chains read by SHELXL (numbered) to chains A, B . 
read by the programs of the CCP4 suite.


I was using the G option but I didn't know how to rename 
the chains. To do that just use the $ symbol and then 
you'll be asked the chain ID (type A, B, C ), which 
residues you want to include in that chain and the number 
of the first residue in the new chain. Do this for all the 
chains you have in your model.


I hope this can help other newbies like me :D

Cheers,
Fátima

Em Mon, 2 May 2011 16:34:50 +0200
 George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de 
escreveu:


Dear Fatima,

Maybe one of the CCP4 experts has been able to answer 
your question. In 
case this has not happened, I have attached a little 
(linux) program
that should do what you want. To find out how to run it, 
enter the program 
name without any parameters:


./b-mean

I have also attached the Fortran source, you will see 
that it is a very 
simple-minded program.


Best wishes, George 


Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582


On Wed, 27 Apr 2011, Fatima Fonseca wrote:


Dear all:

I am dealing with a SHELXL/ BAVERAGE issue.

I have refined a few structures in SHELXL but I think I 
am not converting properly the coordinates into the .pdb 
format. I am trying to use Baverage but I get an error 

The program run with command: baverage XYZIN 
C:/datasets/34_MolP.pdb XYZOUT 
C:/datasets/34_MolP_baverage1.pdb RMSTAB 
C:/datasets/34_MolP_bavrmstab1.txt 
has failed with error message

 BAVERAGE:   XYZOPEN: Error opening logical name XYZIN

Thank you very much. Any comments will be appreciated.

Fátima




---
Maria Fátima da Fonseca
PhD student
CESAM  Dep. Biologia
Campus Universitário de Santiago, Universidade de Aveiro
3810-Aveiro, Portugal
Fax: 234 372 587
E-mail: ffons...@ua.pt
http://biomicrolab.web.ua.pt

Re: [ccp4bb] Ligand weak density in SHELXL

[Fátima Fonseca]

Dear Tim,

Thanks for your advice.

I am refining my structure anisotropically.
 
If, as you suggested, I did something wrong converting 
files to use in SHELXL I would expect that the whole 
structure to have problems or am I wrong?


And how can I assign a free variable to the whole ligand? 
I've just started using SHELXL.


Best,
Fátima



Em Mon, 7 Jun 2010 20:54:07 +0200
 Tim Gruene t...@shelx.uni-ac.gwdg.de escreveu:

Dear Fatima,

just a couple of things you may consider:
- you can let shelxl refine the occupancy by assigning a 
free variable to the

 whole ligand
- did you refine the structure anisotropically? At this 
resolution you certainly

 should.
- maybe you made a mistake converting the files from 
refmac to shelxl, e.g. you
 might have used amplitudes where shelxl expects 
intensities or vice versa.


Good luck, Tim

On Mon, Jun 07, 2010 at 05:46:01PM +0100, Fatima Fonseca 
wrote:

Dear all,

I solved the structure of an enzyme at resolution of 
1.1A with a bound substrate using Refmac5 and Coot for 
refinement/building. I have a very nice density for my 
ligand and a very good structure, as judged by Molprobity 
analysis.


Now I'm using SHELXL to finish refinement but most of 
the density for my ligand disappears when I put it in, 
and it gets very high B factors. I though it could be 
some problem with the occupancy so I did a set of runs 
with different occupancies ranging from 0.2 to 1 and I 
got the best R factors when using 0.4/0.5 for the 
occupancy.


However, I still have most of the ligand outside 
electron density… In Coot I get no ligand with “Find 
ligand” even when I reduce the cluster sigma level to 
0.8.


What am I missing here?

Just another question, how to reduce the acceptable fit 
fraction in Coot “Find ligand”?


Thanks for any advice,
Fátima


--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A



---
Maria Fátima da Fonseca
PhD student
CESAM  Dep. Biologia
Campus Universitário de Santiago, Universidade de Aveiro
3810-Aveiro, Portugal
Fax: 234 372 587
E-mail: ffons...@ua.pt