[ccp4bb] ligand fitting, refinement?

Hi, I found this old post in ccp4 and it's very useful. I used the same procedure Scott described to add a ligand into pdb file. What I did, is in coot, search for the ligand in the library and find the ligand and then merge. However, when I tried to refine in refmac, it has some problems, it comp

[ccp4bb] tutorial / pipeline for refmac refinement

Hi, Is there any tutorial that describe the refinement procedure with refmac? There are several options, restrained, rigid body, TLS...,I have a crystal has 2 copies in ASU, and currently I'm just using restrained refinement, but wonder if I should also try some other type of refinement too . Than

[ccp4bb] How to add a single water molecule

Hi, All, I tried to use phenix to add water molecules, and when I check those waters in coot, I can easily delete them if they are not in right spot. However, if I see some clear positive maps that seems like water, can I add manually at that position? How to do this in coot?Or any other way?

Re: [ccp4bb] How to add a single water molecule

Thank you all for the quick reply. Kim and Ingrid both pointed me to the same direction!! Thanks a bunch :-) On Thu, Dec 3, 2009 at 2:37 PM, Frederic VELLIEUX < frederic.velli...@orange.fr> wrote: > Hi Rui, > > I am at home so this is all from memory. In coot. > > Use the

[ccp4bb] When can I say the refinement is done?

Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap > 0.4 A.

[ccp4bb] generate conformer library for small molecule

Hi All, Can anyone suggest a good way to generate conformer library for small molecules?Thanks.

[ccp4bb] how to improve resolution

Hi, All, We are trying to crystallize a protein and found some initial hit in the following conditions, pH 4.8, 0.2 M AS or some other salts ( NaCl,LiCl, MgCl2 ), 32% PEG4000 or PEG3350 ). However the quality of the crystal is not so great,some of them look like needle cluster(very long in length

[ccp4bb] slow coot in mac 10.6

ct? I wonder how feasible it is to do modeling in laptop. Sorry for the dumb question, but I just want to get a sense how fast it should be, so that I can have things fixed. THanks. Rui

[ccp4bb] slow graphic in mac 10.6

shing. Does anyone know why? Thanks a bunch. Rui

[ccp4bb] structure alignment based on the ligand

Hi, All I have dozens of complex structures ( protein + ligand ) and want to align the structures based on the ligand. Does anyone know such kind of program? Or if can get the information around the ligand site, that would be even better. Thanks. R

Re: [ccp4bb] structure alignment based on the ligand

Thanks for the answer. Actually, it's the opposite. I have many structures that have different protein but with the same ligand(sugar). And I want to fixed the ligand and align the different proteins to see the active site. On Sun, Apr 12, 2009 at 7:36 PM, John Badger wrote: > If you mean that y

[ccp4bb] build fragment library from pdb based on a specific geometry

Dear all, I want to pull out the sugar binding proteins from the pdb, however, there are so many different names for the ligand ( GAL, GLC, RIP... ) and it's not easy to get a complete list. If I want to pull out some fragments based on a specific geometry ( for instance, the glucose has C1 C2 C3 C

[ccp4bb] microbatch vs hanging drop

Hi, I have a question about the method for crystallization. With traditional hanging drop(24 wells), one slide can also hold for multiple drops but it requires the buffer quite a lot, > 600uL? Microbatch can save buffers,only 100uL is required, and also can hold up to three samples in the sitting

Re: [ccp4bb] microbatch vs hanging drop

i'm trying to ask is that with this type of plates, the reservoir buffer volume is 100 uL, vs hanging drop with 600 uL, that will it be harder to get crystals? On Fri, Apr 24, 2009 at 1:54 PM, Patrick Shaw Stewart wrote: > Rui > > > > Microbatch – which I take to mean cry

[ccp4bb] homology modeling

re because the number of residues are different and there might be gaps and insertions in the alignment. Any suggestions of good programs? Thanks. Rui

[ccp4bb] can I try crystallization in high salt?

Dear All, I have a peri domain protein that is stable in high salt concentration(500 mM), if I dialysis to a lower salt buffer and then concentrate, it'll preticipate out. If I need to crystallize it, can I use the high salt buffer? Is there any optimization kits that could help to increase the sol

[ccp4bb] cryosolvent

Hi, All, What's the general rules for selecting cryosolvent?I got crystals in 30% PEG4000/PEG3350, 0.2M AS and 0.1M NaAC,how should I choose cryosolvent? Thanks. Rui

[ccp4bb] trouble running coot on MacOSX 10.5

read. Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90 Gdk-ERROR **: BadRequest (invalid request code or no such operation) serial 97 error_code 1 request_code 128 minor_code 1 Does anyone know how to fix this problem? Thanks. Rui

[ccp4bb] how to find missing density or fill gap

this moment, my solution has the same number of residues as the template and it's hard to see extra densities. Should I delete some residues before and after the loop first then try to bring up the missing densities?Any suggestions would be appreciated. Thanks. Rui

[ccp4bb] fragment searching

Does anyone know a good way to search for a fragment matches(~16 residue long helix or loop) from pdb?I have a fragment of pdb and want to pull out all the similar structures from the pdb, any easy way to do that? Thanks a lot. On Tue, Oct 30, 2012 at 9:34 AM, David Briggs wrote: > Hello Adrian

[ccp4bb] MR solution

refinement, it's ok and Rfree is 52%. Does that mean the solution might not be correct? What's the acceptable Rfree for the initial refinement? Thanks a lot. Rui

[ccp4bb] Postdoc position at University of Colorado School of Medicine

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[ccp4bb] Fwd: job opening: Scientist, X-ray Crystallography - San Diego, CA

*Scientist, X-ray Crystallography - San Diego, CA* Pharmaceuticals *Job Description * Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies is recruiting for a Scientist, X-ray Crystallography, located in La Jolla, CA! At the Janssen Pharmaceutical Compan

[ccp4bb] job opening: Scientist, X-ray Crystallography - San Diego, CA

*Scientist, X-ray Crystallography - San Diego, CA* Pharmaceuticals *Job Description * Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies is recruiting for a Scientist, X-ray Crystallography, located in La Jolla, CA! At the Janssen Pharmaceutical Compan

[ccp4bb] Scientist position available at Janssen Pharmaceutical in San Diego

Janssen Research & Development, L.L.C., a division of Johnson & Johnson's Family of Companies is recruiting for a Scientist, Structural Biology, located in San Diego, CA. At the Janssen Pharmaceutical Companies of Johnson & Johnson, we are working to create a world without disease. Transforming l