Re: [ccp4bb] Removing PEG3350

with large hard to express proteins. Best of luck, Remie On Aug 19, 2014, at 10:45 AM, Alexander Aleshin aales...@sanfordburnham.org wrote: Remie, Actually, concentrating of a protein solution is not the best approach to removing low MW impurities, gel filtration chromatography is more

[ccp4bb]

if further concentration on this sample is worthwhile. If not, start with a fresh sample. Good luck, Remie On Aug 19, 2014, at 1:42 PM, Prashant Deshmukh prashantbiophys...@gmail.com wrote: Hi, i am concentrating my protein using centricon filter, but it is precipitated soon. Please help me

Re: [ccp4bb] desiring untouched ligand

help, Remie On Aug 14, 2014, at 11:53 AM, Robert Nicholls nicho...@mrc-lmb.cam.ac.uk wrote: Hi Remie, You could always generate self-restraints using one chain or a specific part of a chain using prosmart. These will ensure that the model does not move too far from its current

Re: [ccp4bb] desiring untouched ligand

file (before refinement). Is it normal to get a higher R factor when doing rigid body refinement? if not, any suggestion regarding what could be wrong? Is there a way to restrict one chain or part of a chain from moving much while doing restrained refinement? Thank you for any input, Remie

[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

it? I have another molecule with 4 asymmetric units, and every chain has multiple SegIDs. And of course the segments show each chain is split in PyMol. Thanks very much for any help, Remie On Aug 8, 2014, at 7:32 PM, Marlene Holder gruenwaldmarl...@googlemail.com wrote: Dear Remie, the first

[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

that chain A does not appear first? How can I fix this? Thank you very much for any idea, Remie On Aug 8, 2014, at 8:50 AM, Avinash Punekar avinash.s.pune...@gmail.com wrote: Dear Remie, PyMol considers both chain identifier (chainID, column 22 in a PDB file) as well as the Residue sequence

[ccp4bb] Chains view

the chains in coot: Extensions Modelling Reorder chains, and chain A is my protein, B is the ligand and C are the waters. So why don’t I see the same order in PyMol and how do I fix that? Thanks for any help, Remie

Re: [ccp4bb] Chains view

to the ligands and put them right after the ligand atoms list (even though I didn’t think it matters), but I still have the same problem: PyMol shows chain B first in the sequence display. Any suggestion? Thank you, Remie On Aug 7, 2014, at 2:30 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote

[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

they all show detached, but if I do a real space refinement for those sugars of the same ligand in the output file, they come close together and attached? Any suggestions? Thank you very much in advance. Remie

Re: [ccp4bb] R Factor

dotted lines instead of bonds, but when I do a real space refinement, the Glc come closer together and show full bonds then. Am I on the right track here? Thanks again, Remie On May 21, 2014, at 7:28 AM, Jon Agirre jon.agi...@york.ac.uk wrote: Hi, be very careful with the link records

[ccp4bb] R Factor

the first refinement after building the sugars with a lib file that worked well and the R factor did go down significantly but every time I try to refine again to lower it more, the above happens. Any suggestions? Thank you. Remie

[ccp4bb] Create Links in PDB

your help in advance. Remie

[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

: in that case I would just add it by hand in the pdb file using a text editor, guessing the values for the coordinates by interpolating between the two atoms it should be in between of. Then do a regularize zone and/or real space refinement to make sure geometry is ok.” Remie

Re: [ccp4bb] CCP4 lib file

Thanks Eleanor, I ended up using a glucose ligand lib file from a different protein that my friend used and refinement Refmac5 worked out. However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses connected. Can I get help please? Thank you, Remie On Mar 5, 2014, at 10

[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