Re: [ccp4bb] Hello

Hey Dr Afshan, You can also check the tab menu: Measure>Go to Atoms. There you can enter the residue number. The particular residue will be selected, and centred. Thereafter go to the Measure tab, and click residue info. A dialogue box will pop open, and there you may edit the values. I hope this

Re: [ccp4bb] Hello

I don't know about solving this in Coot but would using a plain text editor on the PDB file be a way to work around the issue? There is also the spreadsheet-style PDB editor in i2?? Sent from ProtonMail mobile Original Message On 27 Jul 2021, 15:21, Afshan Begum wrote: > Hi

[ccp4bb] Hello

Hi Experts,  I have a problem to see the residue information on COOT if I click on residue info and place the curser their its just blink and disappear as I want to reduce some occupancy manually and it did not work but for water and the other stuff its work completely fine but not for the

[ccp4bb] Hello

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[ccp4bb] hello.

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Re: [ccp4bb] hello

5:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] hello Dear all, I have facing one problem during the refinement of my protein . Actually in my protein there are some modified amino acids are present like Cystein is modified into CME

Re: [ccp4bb] hello

Dear AfshanMake sure that group name for CME is peptide (or L-peptide). In the new version CME is peptide. I am not sure it was the case in older versions. I attach CME as a peptide. You can add this into your dictionary.Then CME can become part of a peptde. It would also be good to remove all the

Re: [ccp4bb] hello

I recall using CME some time ago (within last couple of years) without problems. Also, an alternative approach is to incorporate BME as a separate residue instead - the disulfide bond will be correctly identified by refmac. I would think ideologically this is more appropriate - using a different

[ccp4bb] hello

Dear all, I have facing one problem during the refinement of my protein . Actually in my protein  there are some modified amino acids are present  like Cystein is modified into CME which i can get easily from monomer libraray in coot . but after refinement in Pdb text file  indicated some gaps

Re: [ccp4bb] hello

Hello Afshan, Maybe the programm that you use for refinement need specific entry with restraint for your modified amino acids. More precisely, i think about the *.cif file for exemple. HTH. Nicolas Le 21/07/11 17:13, Afshan Begum a écrit : Dear all, I have facing one problem during the

[ccp4bb] hello

Dear all,  Could any one help me regarding my serious problem actually i have collected data at 3.0 and cut off 3.1 where the data statics showed the good  values for the further processing.  According to the methew coefficient there would be two molecule in the asymmetric unit but after

Re: [ccp4bb] hello

Hi, The R-factor you mention, is it an R-factor before any refinement of the model ? Like an R-factor at the very beginning of the entire modeling procedure, right after molecular replacement ? If this is so: you should always compare such initial R-factors to the R-factors for the atoms

Re: [ccp4bb] hello

In addition to Fred's suggestion, are you certain about your space group ? I assume you tried phaser with different space groups turned on ? Another thing to look at maybe the model you are using for MR has some extensions that lead to clashes in your crystal packing and therefore the second