Re: [ccp4bb] issue with running ccp4i2

Doc File "src/lxml/parser.pxi", line 711, in lxml.etree._handleParseResult File "src/lxml/parser.pxi", line 640, in lxml.etree._raiseParseError File "", line 1 lxml.etree.XMLSyntaxError: Document is empty, line 1, column 1 From: Bo

[ccp4bb] issue with running ccp4i2

Hi Group I currently updated my ccp4 to the latest version. I have also made python3.7 the default version. The log when I run ccp4i2 & from the command line is appended below. I suspect it is the python version but please guide me for the same. Python 3.7.12 (default, Jan 6 2022, 21:30:12) [

[ccp4bb] Multiplicity is more than 20

Hi All: I have collected a dataset for a crystal of a 30 residues long helical peptide that makes a trimer in the solution. I also solved the structure to get a trimer. My issues start when I start preparing for a deposition. Details about the data: space group: I 21 3 Resolution: 1.6 Current

[ccp4bb] Helix class identifier in Helix Record of PDB

Hi All Happy New Year to All. I have a PDB file that has left-handed 310 helices. However, the helix class in PDB documentation (https://www.wwpdb.org/documentation/file-format-content/format33/sect5.html) does not have any number assigned to the left-handed 310-helix. The auto annotation soft

Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

, Winfried Sent: 16 November 2021 19:24 To: Prasun Kumar Subject: Re: [ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues Dear PR, 0.1Angstrom is not a general disaster - you should talk to a chemist. Best, Winfried Hinrichs

[ccp4bb] Refmac is changing the bond lengths, torsion angle of modified residues

Hi Group I am refining one of the structures that has modified amino acid and it is not defined in the CCP4 dictionary. I got the restrains using ELBOW and used it for refinement. However, when I refine the structure using REFMAC, the bond length deviates significantly from the ideal/ given val

[ccp4bb] Specifying achiral residue as D-amino acid

Hi All: I am trying to solve a structure that has got D-amino acids. The sequence has also got few achiral residues but is mentioned as a part of L-peptide in the monomer library. For example GLY or AIB. Since my sequence has all D-amino acids, I was thinking of some method by which these achir

Re: [ccp4bb] Saving multi-state obj in Pymol

I think the chain identifier for both the states is same. If it is, change it and hopefully it should work . Cheers, Prasun From: CCP4 bulletin board on behalf of Sam Tang Sent: 30 January 2021 13:24 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Saving multi-sta

[ccp4bb] Crystal dissolved while checking under microscope

Hi Group: I have a peptide that got crystallized within 20-25 minutes after putting down the tray. The condition has 1.8M Ammonium Salt, 0.01 Cobalt (ii) Chloride hexahydrate and MES (0.1M) pH 6.5. I dissolved my peptide in 25 mM Sodium Accetate (pH=5). PI of my peptide is 10.2 When I checked

Re: [ccp4bb] Racemic crystallography and structure solving problem

replacement is a problem for me. However, I am on it. Regards Prasun From: Tim Gruene Sent: 05 March 2019 10:02:53 To: Prasun Kumar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Racemic crystallography and structure solving problem Dear Prasun, in case you

Re: [ccp4bb] Racemic crystallography and structure solving problem

Thank You Pierre! I will have a look and let you know. Regards Prasun From: LEGRAND Pierre Sent: 04 March 2019 16:33:56 To: Prasun Kumar; CCP4BB@JISCMAIL.AC.UK Subject: RE:[ccp4bb] Racemic crystallography and structure solving problem Hi Prasum, In such

[ccp4bb] Racemic crystallography and structure solving problem

Hi All: I have performed racemic crystallography and got crystals that diffracted. The automatic processing softwares, XIA2 DIALS, (available in Diamond, UK) gives the space group as P1 and cell dimension 42.78 52.16 54.49 114.11 92.16 92.31. Challanges start from here: 1) How much