[ccp4bb]

Hi Prashant, You need to go really slow when concentrating, not more than 2000 rpm for proteins that precipitate easily. Your protein could be sticking to the sides of your centricon or precipitating. Follow the manual in getting your protein out of the filter (I believe you invert the filter i

Re: [ccp4bb] Removing PEG3350

Hi Reza, I had to do this before. This protocol works for any PEG and any chemical to be removed from a solution: buffer exchange into the new buffer you want your protein to be in. There are ways to do that by 15 mL Amicon concentrators from millipore for large volumes, or if your protein is

Re: [ccp4bb] desiring untouched ligand

tion. Let me know if you want help to do this. > > Regards, > Rob > > > On 14 Aug 2014, at 16:11, Remie Fawaz-Touma wrote: > >> Thank you Dr. Murshudov for the information. But please I still need help. >> >> In restrained refinement, I could not find whe

Re: [ccp4bb] desiring untouched ligand

> > > Regards > Garib > > > On 13 Aug 2014, at 15:44, Remie Fawaz-Touma wrote: > >> Hi everyone, >> >> Does anyone know of a way to refine with CCP4 - Refmac5 (restrained >> refinement is what I do) fixing a part of the the ligand? >>

[ccp4bb] desiring untouched ligand

Hi everyone, Does anyone know of a way to refine with CCP4 - Refmac5 (restrained refinement is what I do) fixing a part of the the ligand? Thank you very much for your input, Remie

[ccp4bb] chain identifiers

; Read about the PyMOL slash notation here: > http://www.pymolwiki.org/index.php/Selection_Macros > > Cheers, > Marlene > > On 08.08.2014 16:20, Remie Fawaz-Touma wrote: >> Thanks for all the valuable comments. >> >> In fact, chain “A” shows up first in my p

[ccp4bb] Chains view

Thank you so much Thomas and Marlene, yea I missed the email from Thomas the first time. Your suggestion solved my problem. I appreciate your help very much, Remie On Aug 8, 2014, at 7:35 PM, Marlene Holder wrote: > Dear Remie, > > the first A is the segment identifier and the second A is th

Re: [ccp4bb] Chains view

t; actually >> reordered the chains inside the file? Maybe chain C is still listed first, >> and >> maybe this is what pymol takes as order. >> >> Regards, >> Tim >> >> On Thu, Aug 07, 2014 at 11:19:42AM -0400, Remie Fawaz-Touma wrote: >>> Hi

Re: [ccp4bb] Chains view

> did you check (with a text editor) the PDB file saved from coot if it actually > reordered the chains inside the file? Maybe chain C is still listed first, and > maybe this is what pymol takes as order. > > Regards, > Tim > > On Thu, Aug 07, 2014 at 11:19:42AM -0400,

[ccp4bb] Chains view

Hi everyone, Does anyone know how to rearrange chains when looking at a structure in PyMol (maybe it has to be done in coot, don’t know). I have the ligand first now in PyMol and would like to see the sequence of the protein first, then ligand. It is worth mentioning that I did reorder the ch

[ccp4bb] Refinement

Hi all, I need to refine a structure keeping the ligands or some of the ligands intact (in same positions as before refinement). Please give me specific instructions if you are familiar with this procedure. I am using Refmac 5 in CCP4. Thanks so much for your help. Remie

[ccp4bb] Refmac5

Hello everyone, When I refine in CCP4 a structure with Glc units attached every few of them as a ligand and there are several of them in the same file, I start off with a PDB that shows the LINK records between the GLC units as LINKR because I add the links by > Extensions > Modelling > Make Li

Re: [ccp4bb] R Factor

odel - several things that are not part > of your model and that need to be adjusted by the refinement program > during refinement. > > That's why I think what you observe is pretty normal - I wouldn't worry. > > Best, > Tim > > On 05/20/2014 06:55 PM, Remie Fa

[ccp4bb] R Factor

Hi all, I am trying to refine a structure in CCP4 and the final R factor is about 1% lower than the initial but for the first “task/cycle” within the same refinement job in CCP4, R factor starts off higher than the input data R factor. I have a structure with multiple sugars attached, I did the

Re: [ccp4bb] Create Links in PDB

nected bonds. The LINK I see in pdb as text is for Arg and other residues but not for the sugars Please advise on what I should do to see the sugars connected after refinement, Thank you so much, Remie On Apr 4, 2014, at 10:45 PM, Remie Fawaz-Touma wrote: > Hi all, > > I need help

[ccp4bb] Create Links in PDB

Hi all, I need help creating links between units of sugar (ligands) in the PDB file before refining so that CCP4 recognizes the sugars are attached. I tried the one suggestion I got before Extension > Make a Link, but I get discontinued bonds instead of full bonds. Thanks so much for all you

[ccp4bb] Add an atom in Coot

Thanks to all who answered. In fact my question is as below: how do you place the pointer if there is no bond there? (just density) I am trying to connect 2 sugars creating 2 bonds to one oxygen that I have to add (oxygen does not exist now). and I got the answer from mjvanra...@cnb.csic.es: "

[ccp4bb] Add an atom in Coot

Can anyone give directions on how to add an atom in coot?? Thank you very much, Remie

[ccp4bb] CCP4 lib file

>>> Hi, >>> >>> I am trying to refine (Refmac5 on CCP4) a protein structure containing >>> ligands that are exclusively glucose units but refinement fails because I >>> don't have a lib file for the sugars. Can I get help on making lib files >>> please? >>> >>> Thank you, >>> >>> Remie