[ccp4bb] On the rotamer of Arg
Dear All, I have a set of data, in which there are very nice electron density for several Arg residues. However MolProbity analysis demonstrated that the percentage of the Arg rotamer in my data is 0%. Although there is the possibility that the Arg rotamer in my data is 0%, I still wonder is any possibility that to correct the Arg rotamer in my data so that it would belong to the scope of commonly observed Arg rotamer. I am looking forward to getting a reply from you on it. Dialing
[ccp4bb] Ramachandran outlier
Dear All, Real space refinement in COOT is one important strategy to reduce Ramachandran outlier, right? Dialing
[ccp4bb] rebuild by coot
Dear All, If I rebuild a 4-residue peptide, and the first 1 is leu. When I rebuild the first one, the sidechain of leu occupies the electron density of the first 3 residues. Can you tell me the method to turn the side chain of Leu from position of the first 3 residues to its sidechain position in the electron density may? In addition, for coot real space refinement, can you tell me how many residues or the length of the fragment one time can process? Dialing
[ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal
Dear All, Suppose I delete a residue ( residue 100 for example) for outlier refinement, then I add the same residue at the C-terminal of residue 99 (by Add terminal residue function of the Coot). By coot, how can I connect the C-terminal of residue 100 to the N-terminal of residue 101? I am looking forward to getting your reply. DIaling
[ccp4bb] Ramachandran outlier
Dear All， If an initial PDB has only 86% residues in the Ramachandran favored region, it would mean there is a significant error (for example significant length of protein fragment in the total protein assigned to the wrong electron density map position) , right? Dialing
[ccp4bb] correction of Ramachandran outlier by Coot
Dear All, Will you please introduce me the ways to correct Ramachandran outlier by Coot? Dialing
[ccp4bb] a question related to WinCoot 0.8.1
Dear All, When I use WinCoot 0.8.1 to open a PDB file, it comes, Fix Nomenclature Errors. Correct them? Asp [spec: 1 A 128 ]PHE[spec: 1 A 134]PHE [spec: 1 A 371] But when I check the 3 residues, I cannot find any error. Will you let me know the issue? Dialing
[ccp4bb] Question on Refmac5
Dear All, When I run Refmac, it would produce a refined PDB file and mtz file. My question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, I find the refined PDB file and mtz file were created in the target directory at perhaps 6:30 pm. I think from 6:30 pm the created PDB file and mtz file in the target directory would be automatically updated to 8: 00 pm when the refinement finished, am I right? Dialing
Re: [ccp4bb] Question on Refmac5
I am talking the creating date. For my situation, once the PDB file and mtz file were created at around 6:00 pm, with the progression of the refinement and completed at 8:00 pm, the date shown in the directory folder is always 6:00 pm. After 8:00 pm when the refinement finished, I check the property of the PDB file and MTZ file, I find the modify time (should be by Refmac5) is only several seconds after the created time and the visited time, and the created time and the visited time are same. Clearly I cannot get the expected PDB file and the MTZ file after 2 hours refinement. Is any bug in my CCP4? Or there is something I do not understand? Dialing On Tuesday, 6 January 2015, 10:10, CHAVAS Leonard ccp4hnaa...@gmail.com wrote: Dear Dialing are you talking about the 'creating date' or the 'modified date'? Leo On Jan 6, 2015, at 2:55 AM, Dialing Pretty 03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk wrote: Dear All, When I run Refmac, it would produce a refined PDB file and mtz file. My question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, I find the refined PDB file and mtz file were created in the target directory at perhaps 6:30 pm. I think from 6:30 pm the created PDB file and mtz file in the target directory would be automatically updated to 8: 00 pm when the refinement finished, am I right? Dialing
[ccp4bb] a question on refmac5
Dear All, Will you please tell me what should I input for the LIB in for refmac5? How can I get the LIB in? Dialing
[ccp4bb] qualification to serve as the co-author for the protein 3D structure stored in RCSB
Dear All, Will you please show your opinion on the standards or qualifications to serve as the co-author for a protein 3D structure stored in RCSB? Cheers, Dialing
[ccp4bb] Fw: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work
I just have it successfully done: Import reflection file in mmCIF format and create MTZ file In 1w2i-sf.cif - Forwarded Message - From: Jayashankar s.jayashan...@gmail.com To: Dialing Pretty hdc123hdc...@yahoo.com Cc: CCP4BB@jiscmail.ac.uk Sent: Wednesday, 29 February 2012 7:05 PM Subject: Re: [ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work I face exactly the same problem. any advice in this regard would be greatful. S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Wed, Feb 29, 2012 at 2:58 AM, Dialing Pretty hdc123hdc...@yahoo.com wrote: Dear All, I want to use CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ to change a RCSB mmCIF file into MTZ file. It shows there are a lot of data name (related to _pdbx_.or something else) not present in dictionary, and shows CCP4I termination status 0 child process excited anormally. I am looking forward to getting a reply from you on how to solve the problem. Cheers, Dialing
[ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work
Dear All, I want to use CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ to change a RCSB mmCIF file into MTZ file. It shows there are a lot of data name (related to _pdbx_.or something else) not present in dictionary, and shows CCP4I termination status 0 child process excited anormally. I am looking forward to getting a reply from you on how to solve the problem. Cheers, Dialing
[ccp4bb] Server or software for B factor analysis
Dear All, Will you please tell me a server of software which can draw a curve for the B factor of the atoms in a protein PDB file from the first residue to the residue?Or a server or software by which we can easily order the B factors of the atoms in the PDB file according to the B factor in decrease or in increase? Or to get the residues with the highest B factor and the lowest B factor? Cheers, Dialing
[ccp4bb] a question for PDB_extract for RCSB depositation
Dear All, For the PDB_extract, one item to be filled is Deposit Structure Factor Used for Final Refinement. If this way the structure factor which could be downloaded from RCSB after depositation will be not the final structure factor corresponding to the final deposited PDB file, as for what we deposited is Structure Factor Used for Final Refinement, rather than the Structure Factor after Final Refinement. I am looking forward to getting a reply from you on whether I am right or not. Cheers, Dialing
[ccp4bb] on Rwork and Rfree
Dear All, After we refine the structure of the protein to satisfactory with satisfactory Rwork and Rfree, we pick water by phenix refine, and I find Rfree always increases slightly after the water picking refinment. Do you have nay idea to solve this problem or any comment? Cheers, Dialing
[ccp4bb] On sodium malonate
Dear All, For the 3.4 M sodium malonate of Hampton Research, will you please tell me how the pH was regulated to 6.0, 7.0 and 8.0 separately? Cheers, Dialing
[ccp4bb] on the electronic density of several maps
Dear All, For the electronic density of LEU and Pro in the electronic density map, which is much stronger? For the electronic density of LEU and Lys in the electronic density map, which is much stronger? The reason I ask the above questions is I need to distinguish them in the electronic density map. I am looking forward to getting your reply. Fenghui
[ccp4bb] Can the CCP4 software mix PHE and Arg
Dear All, Can the CCP4 software get mixed with the PHE and ARG? I use the Coot to build a peptide. 2 fragments of peptides are suitable for one specific part of electronic density map, and there is only one residue can distinguish which fragment of peptide is the real peptide fragment for that part of electronic density map, i.e., in one fragment of peptide it contains ARG, and in the other fragment of peptide it contains PHE. As for after Coot rebuild I still need the refinemnt, I am afraid whether the CCP4 can distinguish the PHE and ARG if I cannot distinguish it so nicely in the Coot when I rebuild the peptide. I am looking forward to getting your reply. Dialing
[ccp4bb] a question on Average Occupancy-weighted avg temperature factor (Deviation)
Dear All, For the RCSB depositation report, it gives the Average Occupancy-weighted avg temperature factor (Deviation). Will you please tell me what range the Average Occupancy-weighted avg temperature factor (Deviation) should be and what is the significance of that value? I am looking forward to getting your reply. Cheers, Dialing
[ccp4bb] a question related to SF-tool
Dear All, I am trying to convert a PDB and the corresponding mtz file to the mmcif file, and I got the following message: Converting structure factor to mmCIF format Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file . Will you please tell me how to solve the problem Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done? Cheers, Dialing
