Re: [ccp4bb] Problems with HEC in CCP4

This is interesting. If the parameters for heme C reflect the molecule before linking to cysteines in the protein, and the modifications will be made as specified by link information in the dictionary, then actually heme C (HEC) should be the same as HEM (heme b, protoheme). HEC is superfluous,

Re: [ccp4bb] Problems with HEC in CCP4

As far as my understanding goes, LINK records will not be replaced by LINKR records by default. If the Link is in the monomer library one has to delete th right atoms and the atoms to be linked have to be within a reasonable distance. Than refmac will automatically recognize that for the two

Re: [ccp4bb] Problems with HEC in CCP4

Afaik Refmac will apply the right restraints, iff there is only one type of LINK between those atoms. Particularly with carbohydrates, it's better to be explicit. Cheers, Robbie Sent from my Windows 10 phone From: Edward A. Berry

Re: [ccp4bb] Problems with HEC in CCP4

Indeed LINKR replaces the length of the LINK (superfluous) with the identifier of the LINK type (useful info). Unfortunately, it is non-standard. mmCIF allows a better description of the type of LINK type, but as it has a fixed vocabulary it does not allow actual identifiers that would connect

Re: [ccp4bb] Problems with HEC in CCP4

Does this mean- if the pdb file has standard PDB link records involving HEC, like LINK SG CYS A 32 CAB HEM A 93 1555 1555 1.82 LINK SG CYS A 35 CAC HEM A 93 1555 1555 1.81 then refmac will look up the necessary modifications in

Re: [ccp4bb] Problems with HEC in CCP4

Hi, On Tue, May 15, 2018 at 02:21:59PM +, Robbie Joosten wrote: > A link describes a chemical bond between two residues. With each > LINK modifications of the residues are described (e.g. leaving atoms > and, in this case, changes of local chemistry such as bond orders). I guess that is not

Re: [ccp4bb] Problems with HEC in CCP4

Technically, if I recall that correct from my memory, if the link is in the monomer library and the correct atoms are deleted, Refmac will use the link from the library and create a LINKR record. I am not sure right now if they are handled properly in the deposition process. Cheers Christian On

Re: [ccp4bb] Problems with HEC in CCP4

Hi Eugene, A link describes a chemical bond between two residues. With each LINK modifications of the residues are described (e.g. leaving atoms and, in this case, changes of local chemistry such as bond orders). Each LINK type has a unique identifier that points to the descriptions in the

Re: [ccp4bb] Problems with HEC in CCP4

Hello Eugene, Andrey Lebedev has written a nice tutorial using JLigand for ligands: ftp://ftp.ccp4.ac.uk/JLigand/index.html You want, in particular, the "A new link..." section. You should work your way through it - you will find it enlightening. Regards, Paul. On 15/05/2018 13:53,

Re: [ccp4bb] Problems with HEC in CCP4

Hi Robbie, I thought LINK just adds another bond restrain to the refinement procedure and does not affect already existing restrains in library cif file. Am I wrong? Also, what do you mean by "modify the chemistry"? Just to test your suggestion, I have added LINKs for heme c vynil groups in 4qo5

Re: [ccp4bb] CCP4BB Digest - 13 May 2018 to 14 May 2018 (#2018-119)

Would you help me to place the following information? Thank you. Dear CCP4ers, Looking for collaborators to annotate articles relevant to your research If you have published any article indexed by PUBMED, we invite you to join the RELISH (relevant literature search) consortium, whereby

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

Hi Wim, I would use pdbset and the I213 symops to generate 23 copies of the ASU contents, and append them to the existing I213 PDB file. The resulting P1 PDB file has the same cell constants as the I213 one. But that's probably not what you want? Kay On Tue, 15 May 2018 10:51:15 +0200, Wim

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

Well - if you use reindex to change the reflections from I213 to P1 the log file gives the rotation matrix need to convert I213 coordinates using the same convention. There are various clever inputs to reindex which allow you to do this Then you can use pdbset xyzin I213.pdb xyzout P1.pdb

Re: [ccp4bb] Problems with HEC in CCP4

Addendum: 4qo5 actually lacks the right LINK records altogether. It will only work if you add these by hand. Perhaps you should ask the depositors or the PDB to add the appropriate LINK records. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On

[ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

Hello, does anybody have a script which transforms the pdb file of a structure in I-centred I213 into a pdb file based on the corresponding primitive P1 unit cell ? A rotation matrix would also do  which uses the matrix of the transformation from one coordinate

[ccp4bb] Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK

Dear colleagues, Please see below an advert for the position of Protein Crystallography Facility Manager at the MRC Laboratory of Molecular Biology. Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB)