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Re: [ccp4bb] A quick question - monomer lib cif

Dear Stephen, First you change cife file to pdb file of your structure using CCDC mercury program. It's freely available in the CCDC site. Then use CCP4 Sketcher program to create the monomer library file with the pdb file of your structure. Wishes, Sampath N 2011/1/5 Dr. STEPHEN SIN-YIN, CH

[ccp4bb] Data processing problem with mosflm

Dear All, I have the problem in processing the data with imosflm. The data was collected with 2.5A resolution about 300 images. Auto index found the space group P222 with unit cell a= 40.2; b= 79.2; c= 194.7 and α=b=γ = 90.0. For this cell, the penalty is 7. I feel this penalty is good enough to

[ccp4bb] Question about R/Rfree value difference

Dear all, I have a question about the R free value. I refined a structure with 2A resolution. After model building and restraint refinement using Refmac program, the average B factor was around 50 for all atoms. The R/Rfree were around 22/34. Then used the TLS refinement choosing entire molecule.

[ccp4bb] Sampath Natarajan has sent you a 8thwonder invitation

Hi, I have just joined the 8thwonder network. I wish to invite you to 8thwonder as well. See you at 8thwonder Sampath Natarajan To accept the invitation copy the link given below and paste it in the address bar of your browser http://invite.8thwonder.ws/?saaAr6

[ccp4bb] Question about the covalent Link between PLP & Lysine

Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is clearly indicates lysine residue is covalently bound with PLP cofactor. But I don’t know how to link the cofactor and lysine residue for further refinement. Any suggestions on how to create the link betwe

Re: [ccp4bb] Self rotation function calculation

, Nov 20, 2008 at 11:18 PM, Sampath Natarajan <[EMAIL PROTECTED]>wrote: > Dear All, > > I have a problem in analyze the self rotation function. My crystal is > belongs to C2 space group. According to Mathews calculation, this crystal > shows 7 or 8 molecules in the asymmetric

[ccp4bb] Map conversion

Dear all, Is any other program for map conversion other than MAPMAN? If so please tell me. Thanaks! Regards, Sampath

[ccp4bb] Thanks

Dear all, Thank you so much for the good responses. I will try to get good model again with your suggessions. If I have problem again I will let you know. Thank you very much again for your suggessions who are all responded me. With Regards, Sampath

[ccp4bb] Refinement problem

Dear all, Now I'm solving a structure with 1.6A resolution. The data seems good with R-sym (12.4) and all other parameters. Actually the data was collected with SAD phasing. When we checked the data we couldn't find the Se atom in the structure. Since the data resolution is good, we tried to do

[ccp4bb] B-factor problem

Dear All, I am refining a structure with 2.5A resolution by refmac5. I could find the solution by MR using molrep. After fitting the model, I refined the structure again with 0.3 weighting term, but the output PDB file shows many splits in the residues. So I used 'auto' as a weighting te

[ccp4bb] problem in creation of symmetrycal molecules- thank you

Dear all, Thank you very much for all who are all responded to my query that problem in creation of symmetrycal molecules. I received all mails which contains valuable information. Finally I had created the symmetrical molecules using PISA server. Thanks for all and thank you very much. With Re

[ccp4bb] Problem is creation of Symmetry molecule PDB

Dear all, I solved a structure with four molecules in the assymetric unit which form a dodecameric oligomeric structure in the biological process. I need to create the symmetrical molecules to find out the cavity size of the entire molecule. I tried in coot, but I was not able to save the PDB file

[ccp4bb] DNA gel digestion to confirm the chemical cross-linking

Dear all, First I apologize for posting off topic question here. I am working in the field of DNA-chemical cross-linking. So I need to confirm the chemical cross-linking by DNA digestion gel. Since I don't have any prior experience in this, I need some help regarding running the polyacrylamide

Re: [ccp4bb] Problem in CNS refinement

Dear all, I thank each and everyone who extended his/her hands to help me regarding problem in CNS refinement. Everyone gave valuable suggestions regarding the same. I could find the problem in converting to hkl file from mtz from your suggestions. I rectified it and now it works well. Thank y

[ccp4bb] Problem in refining the complex structure with REFMAC

Dear All, I have a problem while refining (using refmac5) the structure with ligand in 2.5A resolution data. After restraint refmac refinement, I tried to fit the ligand molecule into the difference map. For this purpose, I created the substrate lib file using a pdb file from PRODRG

[ccp4bb] Problem in refinement with ligand

Dear all, I am new to the CCP4 program for structure determination. Now I am trying to solve a complex structure with 2.5A resolution. I refined the structure with Refmac5 and built the model also using coot. Now I'm trying to insert the ligand molecule into the active site of electron den