[ccp4bb] molprobity

2013-11-11 Thread SD Y
Hi,
I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant upload my files (some times it gave error).
ThanksSDY 

Re: [ccp4bb] molprobity

2013-11-11 Thread SD Y

It works now. Thanks for fixing.
Sincerely,SDY
Date: Mon, 11 Nov 2013 16:13:52 +
From: tanne...@missouri.edu
Subject: [ccp4bb] molprobity
To: CCP4BB@JISCMAIL.AC.UK







I encountered the same problem last night.   The server won't upload the PDB 
file.  I didn't check this morning. 





On Nov 11, 2013, at 10:02 AM, SD Y wrote:



Hi,



I was wondering if molprobity server is down 
(http://molprobity.biochem.duke.edu/index.php) or its just my files or our 
network has problem because I cant
 upload my files (some times it gave error).



Thanks
SDY












John
 J. Tanner

Professor of Biochemistry  and Chemistry
University
 of Missouri-Columbia

125 Chemistry Building

Columbia, MO  65211

email: tanne...@missouri.edu

phone: 573-884-1280

fax: 573-882-2754

web: http://www.chem.missouri.edu/tannergroup/tanner.html







  

Re: [ccp4bb] low-resolution and zinc

2012-11-09 Thread SD Y


I am using  Refmac_5.7.0029 in CCP4ThanksSDY Date: Fri, 9 Nov 2012 20:35:48 
+0200
From: mbfro...@post.tau.ac.il
Subject: Re: [ccp4bb] low-resolution and zinc
To: CCP4BB@JISCMAIL.AC.UK

What program do you use for refinement?FF

Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608


On Nov 9, 2012, at 20:09 , SD Y ccp4...@hotmail.com wrote:Dear All,
Thanks for all the suggestions on low resolution, SG and Zn and I learned a  
lot. I am not done yet.
I am trying model co-ordinated ZN+2. I got lot of help from Prof. Roger 
Rowlett. Also an excellent protocol is available at 
http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement. 
Protocol seems to be very straight forward. I am not getting the result I 
wanted.
1. When ever I generate cif file,  its not writing any for ZN-SG links at all.
2. After refmac refinement it only draw in LINK for His-ZN. Please see the 
imageshttps://www.dropbox.com/s/7sl01pcdmxxcu2z/ZN-cpoordination-1.pnghttps://www.dropbox.com/s/cxlp2m2stbple02/ZN-cpoordination-2.png
3. I get this His-Zn link without using .cif file, so what stage do I use this 
.cif file?
4. Though cysteines were placed around 2.2 - 2.5 A from ZN, its not writing 
LINK in PDB. I only see LINKR   ZNZN H   1 SG  CYS A  
83ZN-CYS
I dont know what is missing, I also attached the log file which generated the 
ZN-His coordination.
Any help is highly appreciated.
ThanksSDY
Date: Thu, 8 Nov 2012 14:36:59 +0200
From: mbfro...@post.tau.ac.il
Subject: Re: [ccp4bb] low-resolution and zinc
To: CCP4BB@JISCMAIL.AC.UK

The experiment should be very problematic if I can't determine point group on 
the base of the symmetry merging statistics.Watch CHI2 :-)
Dr Felix Frolow   
Professor of Structural Biology and Biotechnology, Department of Molecular 
Microbiology and Biotechnology
Tel Aviv University 69978, Israel

Acta Crystallographica F, co-editor

e-mail: mbfro...@post.tau.ac.il
Tel:  ++972-3640-8723
Fax: ++972-3640-9407
Cellular: 0547 459 608
On Nov 8, 2012, at 14:29 , herman.schreu...@sanofi.com wrote:Then we agree. I 
got confused because you mentionedspace group and not point group in your 
phrase about PHASER and MOLREP and was afraid others might have gotten confused 
as well. Also, in case of twinning or almost crystallographic 
non-crystallographic symmetry, determining the point group on the basis of 
processing statistics alone can be inconclusive or even misleading. If I recall 
correctly, there has recently been a thread about this in the bulletin 
board.Herman



74_refmac5_1.log
  

[ccp4bb] low-resolution and zinc

2012-11-07 Thread SD Y




Dear all,

I have a related question to the one I have posted low resolution and SG, on 
which I am still working based on the suggestions I have got.

The model I have used, has Zn co-ordinated well in tetrahydral fashion by 3 cys 
and 1 His residues. They have  add Zn in to their experiment.
In my 3.4 A structure  (I am still working on right SG), initial maps  show 
very strong positive density (sigma=6.5) at the place of Zn ( 
https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I have not used 
Zn in my experiment. I could only suspect Tryptone and yeast extract which I 
used to make media.
I would like to know how likely  this positive density belongs to Zn? How to 
reason the presence of Zn when its not been used?Is there is any way to confirm 
if its Zn. If this is not Zn, what else could it be? Any thing I could try to 
rule out or in Zn or other ions.
I appreciate your help and suggestions.

Sincerely,
SDY

  

Re: [ccp4bb] protein cleavage

2012-11-04 Thread SD Y

Rana,
I understood that these proteases are very efficient in cleavage. One time, I 
had a construct MBP-3C-protein, I never able to cleave this particular 
construct while I could do well with other truncations.The MBP you are seeing 
might be co-purified with DHBx and unless gel band intensity suggest that its 
coming from fusion protein. I feel cleavage site may not be  accessible for the 
protease. Might be adding few more residues might help. 
Good luckSDY

Date: Sun, 4 Nov 2012 07:24:42 -0800
From: rna19792...@yahoo.com
Subject: [ccp4bb] protein cleavage
To: CCP4BB@JISCMAIL.AC.UK

Dear CCP4
 I am having a problem with cleaving my fusion protein and I would be 
grateful if you advice me regarding this situation,  I have an MBP-DHBx fusion 
protein and I am trying to cleave it using TEV protease, I have tried different 
ratios and different temperatures  with different incubation time but still it 
will not cleave, all I observe on the gel is the bands of the fusion protein 
which is 59kDa and the MBP which is 42kDa and the TEV protease which is 27kDa 
and no sign of the DHBx which is 17kDa,I have also checked the sequence if 
there was any problem but I could not find anything unusual the sequence was 
fine ,
 so if you have any suggestions regarding this situation I will be thankful 
Best Regards
Rana