[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

Re: [ccp4bb] desiring untouched ligand

conformation. 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 where to enter the residues I want to restrict from

Re: [ccp4bb] desiring untouched ligand

Regards Garib On 13 Aug 2014, at 15:44, Remie Fawaz-Touma remiefa...@gmail.com 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? Thank you very much for your input, Remie Dr

[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

, 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 pdb, then comes “B” then “C”. Also the atom/hetatm number are in order starting from the first atom all the way to the end. And resSeq number is in order

[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 gruenwaldmarl...@googlemail.com wrote: Dear Remie, the first A is the segment

Re: [ccp4bb] Chains view

:17 PM, Remie Fawaz-Touma remiefa...@gmail.com wrote: Hi Dr. Gruene, Thanks for your input. I have actually checked pdb and the chains are listed in the order A, B then C; except for the LinkR between the ligand units and between some amino acids where there are gaps (those link records

[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

Re: [ccp4bb] Chains view

: Dear Remie, 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, Remie Fawaz-Touma

[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 Link

Re: [ccp4bb] R Factor

factors and solvent model - 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 Fawaz-Touma wrote: Hi all

[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

[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

[ccp4bb] Add an atom in Coot

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

[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] 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