Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

Dear HK, No that's not quite correct - 'occupancy group alts complete' means that both R120 and the ligand are constrained so that their occupancies sum to unity. In contrast, 'occupancy group alts incomplete' means that the occupancies of R120 and the ligand will not be constrained to sum to u

Re: [ccp4bb] Occupancy refinement of overlapping electron density of a residue and ligand

y co-crystallization of protein with the ligand itself. > The density seems to be the expected ligand. > > Thanks for the advice. > > Best regards > HK > > > Quoting Robert Nicholls : > >> Dear HK, >> >> No that's not quite correct - &

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

As a Caucasian male I hesitate to post; I know that there are a lot of people who are sensitive to this subject, so feel that I'm treading on eggshells in responding... Nevertheless I feel obliged to respond, having a certain amount of insight into the topic in the context of these workshops.

Re: [ccp4bb] Macromolecular Crystallography workshop in South America 2020

Dear Susan, For one I'm already committed to 7 workshops this year so far, with more to be confirmed. And for sure I'm by no means an anomoly - no doubt others within the community would tell a similar tale. The commitment to workshops for the CCP4 core team and various software deveopers is a b

Re: [ccp4bb] Protein-DNA covalent bond refinement

Dear Cristina, In CCP4 you've got two options that use the modern approach (Acedrg): (1) CCP4i2 -> Ligands -> Make Covalent Link. (2) Coot -> Calculate -> Modules -> CCP4. This will make a "CCP4" menu appear that contains the option: Make Link via Acedrg. Hopefully it's pretty self-explanatory

Re: [ccp4bb] Refmac Ideal Geometry Library

Hi Dale, Yes Refmac uses the dictionaries found in lib/data/monomers Of course these targets may differ from those used by validation tools. If you identify anything that's clearly wrong then do let us know! Regards, Rob > On 25 Jul 2020, at 17:22, Dale Tronrud wrote: > > Hi, > > I'm seeki

Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

To paraphrase from our 2018 Acta Cryst D74(6) paper: “There has been debate as to whether refinement should be performed in real space or reciprocal space; both approaches have advantages and disadvantages. In real space, refinement can be performed locally, which has advantages for computation

Re: [ccp4bb] AW: Going back to Coot 0.8

Hello Dirk, Upon reviewing this thread I saw your comment: > On 11 Sep 2020, at 08:41, Dirk Kostrewa > wrote: > > I'm still convinced since the beginning of Coot, that an implementation of > hydrogen-bond potentials in the RSR would give a huge improvement and > probably renders the use of s

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, Coming back to map blurring... > On 24 Nov 2020, at 16:41, John R Helliwell > wrote: > > [...] Coot’s blurring and sharpening tool is tethered directly to one’s > measured diffraction data. > [...] But, I have just rechecked the Coot manual and see no r

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear all, I feel the need to respond following last week’s critique of the use of Coot’s map blurring tool for providing diagnostic insight and aiding ligand identification… > On 24 Nov 2020, at 16:02, Dale Tronrud > wrote: > > To me, this sounds like a very dan

Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

m, when it > comes to a 4 A resolution map I'm no better than an undergrad. > > Your first experience with a new technique should never be with your > current project's data. You should work to add that technique to your tool > box, and then move back to your data

Re: [ccp4bb] RMSD of side chains

rote: > On Friday, January 13, 2012 09:07:07 am Appu kumar wrote: >> Firstly thanks to Robert Nicholls for making me aware of the software >> necessary for side chain RMSD calculation. I have installed and now going >> through manual to use it for exploiting the structural d

Re: [ccp4bb] Refmac and sigma value

Hi Uma, Altering sigma affects the strength of geometry restraints throughout the model - bonds, angles, etc. Choosing a very low sigma will cause geometry to be more tightly restrained towards "ideal" values, which is why you observe improvements in Coot validation. Note that strengthening th

[ccp4bb]

Or you can use ViewHKL if you want a graphical interface. Rob > On 7 Mar 2019, at 12:58, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > mtzdump hklin my.mtz > > That reads the header and the first 10 lines > > or if you want all as ASCII > mtzdump hklin my.mtz >

Re: [ccp4bb] Ramachandran outliers

Dear Tereza, It is highly recommended that you do not attempt to directly optimise the Ramachandran plot during refinement. Doing so would not guarantee you a better model, and would mean that you could no longer use the Ramachandran plot for validation purposes. I suggest that you inspect eac

Re: [ccp4bb] how to insert a ligand into a possible binding pocket of one protein strucure model?

If you're talking about fitting into density, I suggest having a look at this tutorial: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/tutorials/ligand_tutorial/index.html Regards, Rob > O

Re: [ccp4bb] PROSMART spectrum bar

Hi Chen, > could anybody suggest me an easy way to generate the spectrum bar for the > color-coded residue-wise scores? Generating a spectrum bar in Pymol seems > nontrivial to me… There are some HTML/javascript files that will allow you to reproduce the horizontal and vertical legends seen in

Re: [ccp4bb] problen in installing ProSMART

I'd recommend downloading the CCP4 suite, which contains pre-compiled ProSMART binaries: http://www.ccp4.ac.uk/download/index.php#os=mac Just download the Package Manager, which will automatically download and install CCP4 for you. The problem is that the -static-libgcc flag is specific to the g

Re: [ccp4bb] NCS rotamers

Hi Tony, If you're happy to go outside of Coot, you can use ProSMART to do this for you. You can view the results in a table, or coloured by residue using PyMOL or CCP4mg. It will also account for any backbone flexibility between the NCS-related copies, and tell you which side chains may be fli

Re: [ccp4bb] Changing HETATM to ATOM record

Hi, Something like this may do the trick: sed 's/HETATM/ATOM /' current.pdb > new.pdb Cheers Rob On 20 Aug 2012, at 16:14, Theresa Hsu wrote: > Dear all > > Is there any tool in CCP4 that can change all HETATM records in PDB file to > ATOM? I need the metals to be defined as ATOM for calcu

Re: [ccp4bb] Jelly body refinement?

Hi Nathan, Jelly body refinement is basically a way of stabilising refinement, helping to achieve a more robust estimate of the curvature of the likelihood function, thus leading to a more robust search direction. This is similar to other regularisers used in refinement, e.g. geometry restraint

Re: [ccp4bb] Jelly body refinement?

Hi Roger, You are correct, that *conceptually* the contribution to the target function is sum(w (|d|-|dcurrent|)^2)… however this is not actually applied to the target function. The target function remains unchanged. Only the 2nd derivative is affected by the jelly-body restraints. Also, note

Re: [ccp4bb] Jelly body refinement?

is altered, and the "springs between atoms" are not actually applied. This helps to stabilise refinement (purely because it is a regulariser and thus helps robustness to noise) without overly impeding speed of convergence. Still, many cycles may be required… Cheers Rob On 23 Aug 2012, a

Re: [ccp4bb] Jelly body refinement?

Hi Gunnar, A couple of comments, to clarify a few of the similarities and dissimilarities between DEN and analogous technologies: According to your very nice paper from 2010, DEN refinement with gamma=0 gives a higher weight to external information, whilst gamma=1 ignores external information

Re: [ccp4bb] Jelly body refinement?

Hi Gunnar, I generally agree with your comments. However, I'd like to clarify a couple of points: > For gamma=1 the DEN potential can follow anywhere, the entire conformational > space is accessible and dij(t+1) depends only on Dij(t) and dij(t). ... > But, again, the starting (or reference)

Re: [ccp4bb] Jelly body refinement?

the first > starting point (same atomic coordinates and same position of DEN minimum) > at some time t'. Then the new position of the DEN minimum at time t'+1 would > be > exactly at the same position that you get from the first path at time t+1. > This > shows t

Re: [ccp4bb] Calculating water accessible volume in active site

Hi Yarrow, You can use the likes of areaimol to calculate the surface accessible area, with or without accounting for crystal symmetry: http://www.ccp4.ac.uk/html/areaimol.html There are other alternatives, but I hope that helps, Rob On 8 Sep 2012, at 00:37, Yarrow Madrona wrote: > I have a

Re: [ccp4bb] Ligand geometry obs. vs. ideal

In case it helps… After you've done unrestrained refinement, you can use prosmart to generate external self-restraints to the current conformation (using the -self_restrain keyword). This is flexible - you can specify residue ranges, and it works for protein, ligand, DNA/RNA, waters, etc. These

Re: [ccp4bb] low-resolution refinement

Hi Andreas, In your case, it sounds like a reasonable strategy would be to use external restraints for a few rounds of refinement (as you have done), but then release them and instead use jelly-body restraints. This two-stage process will help to initially hold your model in a sensible conforma

Re: [ccp4bb] Planar restraints in Refmac

In the meantime, you can compact the line by replacing "external" with "exte" and "residue" with "resi". Not a general solution, but may help in the short term. Regards, Rob On 29 Nov 2012, at 11:10, Garib N Murshudov wrote: > Yes, it can be done. I may be able to do it soon. I have to find a

Re: [ccp4bb] O-linked glycans

Hi Matthew, I would recommend against creating a composite component (amino acid + sugar), in favour of modelling the covalent linkage explicitly. In general, the recommended approach is to use an AceDRG link dictionary. See here for practical options, recommendations and discussion: https://jo

Re: [ccp4bb] Refinement of occupancies in Refmac5 ccp4 cloud

Hi Urban, At present to do this in CCP4 Cloud you have to provide the Refmac5 keywords in the Additional Keywords box in the Advanced tab at the bottom. The syntax is explained here: http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy Regards, Rob On 20 Feb 2025, at 15:07,