Re: [ccp4bb] add ligand with AceDRG

On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligand. With small letters it says: The chemical component you are trying to view (LIG) has been obsoleted. You have been redirected to the component

Re: [ccp4bb] add ligand with AceDRG

Thank you Paul. I did not think about it. Stefanie, could you please send the log file to me? Regards Garib > On 26 Apr 2024, at 14:17, Paul Emsley wrote: > > > On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: >> >> >> >> I have trouble adding a ligand with AceDRG in CCP4i2 into my

Re: [ccp4bb] add ligand with AceDRG

Refmac by itself should not care about duplicated residue names in the monomer library. It takes the last monomer. There should be something on the interface preventing this. Longer than three letters should be available from the next release of ccp4. New acedrg and Refmacat should be able to

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

s independent of twin laws show no twinning (more close to > untwinned than perfect twin). > Please suggest to me on how I proceed with refinement (twin OFF or ON). > > Thank you, > Venkat > > > > > > > > On Fri, Apr 5, 2024 at 1:00 AM Garib Murshud

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Did you use twin refinement (is it really twin if you used that). If twin refinement was used then twin related intensities might have different resolution, in case when your crystal are pseudomerohedral twinned. Regards Garib > On 4 Apr 2024, at 18:40, venkatareddy dadireddy wrote: > >

Re: [ccp4bb] Output from AUSPEX

Pseudotranslation (strong and weak intensities)? You could inspect Patterson map. Regards Garib > On 13 Sep 2023, at 15:58, Armando Albert wrote: > > Dear all, > Please look at the plots bellow. > What is the meaning of a bimodal distribution of Fs and sigmaF versus > resolution I observe

Re: [ccp4bb] in memoriam of Raimond Ravelli

It is shocking. I remember him as a thoughtful and pleasant person. It is a huge loss. Very, very sad news. > On 6 Jul 2023, at 09:58, Janesh wrote: > > Really shocking and sad news. He was an excellent scientist but an even > better human being and friend. -Janesh > > On Thu, Jul 6, 2023 at

Re: [ccp4bb] metal coordination at low resolution - restraints

ement? all difficult at low resolution.. > > On Tue, 8 Sep 2020 at 20:29, Garib Murshudov <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: > Hi Jan, > > > It is my experience also that if atoms are in more or less correct positions > then non-bonding interaction together ke

Re: [ccp4bb] metal coordination at low resolution - restraints

ures restraining the coordination geometry > is not necessary, they hold nice. > > Jan > >> >> Jan >> >> >> On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov > <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: >> What are these numbers? >>

Re: [ccp4bb] metal coordination at low resolution - restraints

residues. For general solution we need a bit different approach (e.g. coordination analysis). Regards Garib > > Jan > > > On Tue, Sep 8, 2020 at 12:22 PM Garib Murshudov <mailto:ga...@mrc-lmb.cam.ac.uk>> wrote: > What are these numbers? > > If I understand t

Re: [ccp4bb] metal coordination at low resolution - restraints

1.00 13.12 > Z 403 ZN B Z 601 O4 B 1.938 X,Y,Z 0.70 14.10 > Z 403 ZN B O 825 OC 2.322 X,Y,Z 0.20 10.61 > ~ > > >

Re: [ccp4bb] metal coordination at low resolution - restraints

Hi Robbie and Eleanor There are links for Zn-His and Zn-Cys. They meant to be used automatically, obviously something is not entirely right. Link names are: ZN-CYS It has a bond between Zn and S as well as an angle: ZN-CYS 1 ZN 2 SG 2 CB 109.0003.000 This also removes H

Re: [ccp4bb] Quote source inquiry

n quite stable, and the distance can vary by about 5%... > > Best regards, > Tim > > On Thu, 16 Jul 2020 23:21:54 +0100 > Garib Murshudov mailto:ga...@mrc-lmb.cam.ac.uk>> > wrote: > >> One correction: Model should after molecular replacement and

Re: [ccp4bb] Quote source inquiry

Garib > On 16 Jul 2020, at 22:34, Garib Murshudov wrote: > > Hi Tim, > > There is an option to do unit cell parameter refinement (for all six > parameters in general which can only happen in P1). It is undocumented. > > Celrefine/lattice refine all # if you give scale

Re: [ccp4bb] Quote source inquiry

Hi Tim, There is an option to do unit cell parameter refinement (for all six parameters in general which can only happen in P1). It is undocumented. Celrefine/lattice refine all # if you give scale instead of all then only one parameter is refined. Cellrefine select . # use only atomic B

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Dear Kevin, You can have access to all these resources (And ccpem, ccp4). They are free for non-commercial users. (You can also have access to any papers you want via https://sci-hub.tw/ , it is also free but …) If you want to see some of the maps then you can go to emdb

Re: [ccp4bb] O-linked glycans

There are NAG-SER, NAG-THR links in the monomer library. I do not know if you are looking for these links. If you need any other link you can use AceDRG to generate them. Regards Garib > On 23 Jul 2018, at 23:07, Goran Bajic wrote: > > Hi all, > > I may have an O-linked glycan in one of

Re: [ccp4bb] Interpretation of Cromer-Mann coefficients

As far as I know that is true (that is an approximation to the electron density of course. True density is a bit more complex. This approximation works for isolated atoms up to resolution 0.5 or so) if you have infinity resolution. I.e. perfect data. When you have limited resolution then

Re: [ccp4bb] Resolution mismatch aimless/refmac

data . I find that > quite useful in some cases, but if you do not wish to use the terms there are > ways of excluding them from subsequent calculations.. > > Eleanor > > > > On 18 March 2018 at 12:04, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: >

Re: [ccp4bb] Resolution mismatch aimless/refmac

Dear All, As far as I know it could happen when you are using i2. We are working to fix this problem. At the moment the best solution is to use advanced options in the refmac interface and define resolution limits explicitly. For example you can add in the advanced options: resolution 37 2.5

Re: [ccp4bb] Looking at an EM map..

Yes. that is how it should be done. if you have a map then you convert them to Fourier coefficients directly using Fourier transformation. Only for some particles density maps are positive everywhere. X-ray particles are one of them. For neutron and electron scattering maps could be negative as

Re: [ccp4bb] Unknown density

You could try to put CA (as you have CA in your crystallisation condition) and waters for coordinating atoms. If after refinement distances are around 2.3-2.4 (if I remember correctly) and B values of atoms (CA and waters) are consistent, i.e. similar to each other then CA is good

Re: [ccp4bb] Unknown density

It looks like 6 coordinated metal atom with coordinated (possibly) with waters. The simplest case could be NA. You could use anomalous difference map to see if there is any anomalous signal there. Regards Garib On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > Dear All,

Re: [ccp4bb] Automatic restraints in Refmac too loose?

Hi Maria, What is the refmac version? It should be on the top of the log file. Regards Garib On 29 Jan 2018, at 17:03, Maria Håkansson wrote: > Hi, > > I have a question regarding the automatic restraints in Refmac5 and > CCP4Interface 7.0.050. > > For a few

Re: [ccp4bb] TYC not linked to previoys amino-acid

gt; forms the peptide link GLY-TYC > > Eleanor > > On 16 October 2017 at 12:32, Garib Murshudov <ga...@mrc-lmb.cam.ac.uk> wrote: > These are default values. > > Decision about standard residue types are made using the info from the > dictionary. In the current ver

[ccp4bb] Post doctoral position

st/1354/en-GB and/or contact Garib Murshudov via email ga...@mrc-lmb.cam.ac.uk. With kind regards Garib Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

[ccp4bb] Conference on Methods and applications in the frontier between MX and CryoEM.

etails how to apply can be found on the conference website. Garib Murshudov and Isabel Uson Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/

[ccp4bb] IUCr computing school

Dear All, Just before IUCr main congress there is going to be a Crystallographic Computing School. It will take place on 15th-20th of August 2017 in Bangalore. It promises to be very exciting school with lectures from various experts in Crystallography and some tutorials and with a lot of

Re: [ccp4bb] desiring untouched ligand

Hi Remie, You can add harmonic restraints for parts you do not want to move too much. Instructions could be found here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html#Harmonic Regards Garib On 13 Aug 2014, at 15:44, Remie Fawaz-Touma remiefa...@gmail.com

Re: [ccp4bb] Twin refinement in Refmac

Dear Uli, It seems that you are dealing with psued-twinning when cell do not overlap after rotation with twin operator. In these case what is in one resolution on one of the orientation becomes another resolution in another orientation of crystals In short:. You have an operator R that

Re: [ccp4bb] Acetyl link problems.

Hi Ian dod you try without link and standard ACE atom naming. Refmac should be able to deal N-terminal activation and few other things. At least it was the intention when it was written. Bugs may have been (self)introduced to prevent this from happening. If it is so then I would like to know.

Re: [ccp4bb] no link_id

If there is a covalent link between CYS and UNK then it is better to create that using jligand from ccp4. There are nice tutorials designed by Andrey Lebedev. Tutorials are on this site: http://www.ysbl.york.ac.uk/mxstat/JLigand/ Regards Garib On 5 Feb 2014, at 15:59, Ronnie

Re: [ccp4bb] Weird MR result

Hello Niu, Do you have pseudo translation. It could echo of another molecule that might be in correct orientation. Regards Garib On 14 Nov 2013, at 22:47, Phil Jeffrey pjeff...@princeton.edu wrote: Hello Niu, 1. We need extra information. What program did you use ? What's the

Re: [ccp4bb] Local real-space refinement by phenix

Are you suggesting ccp4 is collapsing and people are coming back to the original source? Garib On 25 Aug 2010, at 22:17, Pavel Afonine wrote: On 8/25/10 2:11 PM, George M. Sheldrick wrote: I would like to propose that we rename this list to the Phenix (and CCP4) Bulletin Board. Sounds

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

Why you do not use coot? It does exactly what you want. regards Garib On 25 Aug 2010, at 22:33, Hailiang Zhang wrote: Hi, Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified? By the way, I have registered phenix bb. Just didn't

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

I think Paul (Emsley) is better qualified to answer to this question. However 1) coot uses 2mFo-DFc maps 2) you should be able to feed any map you want to coot so it is nice place for experimenting this kind of calculation 3) You may try to relax gemetry 4) Usually if the model does not

Re: [ccp4bb] Can some utilities of CCP4 do the real-space refinement locally with the residue range explicitly specified?

But equation given in slide #4 is exactly least-square equation with some modified maps. Just use Pareval's theorem, then for case of 2mFo- Dfc you will have sum_{reflection used) (2mFo-DF_{c current) -k F_{model})^2 F_model is equal to F_{c current} at the point of calculation. All

Re: [ccp4bb] A strange case of MR

I would be careful with Rfactors at the early stages of refinement, especially in the presence of twinning (apparent or real). You can see weird behaviour of Rfactors in this presentation: www.ysbl.york.ac.uk/refmac/Presentations/Refmac_Erice_workshop.ppt, slides 18-20. In short if you

Re: [ccp4bb] how to tie water mols in refmac

You can use harmonic restraint. There is no option on the interface. However you can create and use keyword file on the interface. In the keywords file you need to give instruction where you want to put harmonic restraints. Syntax is: for particular atom: external harmonic chain [ch]

Re: [ccp4bb] How will I know if covalent has been formed between ligand and protein?

Hi As far as I know Paul and Eugene are working very hard to make this option painlessly available to users. With the current versions of refmac and coot I would check carefully at every stage. In coot I would look at the distance berween atoms supposed to be linked (even if they are not

Re: [ccp4bb] covalent bond

Better link with nice tutorial from Andrey is: www.ysbl.york.ac.uk/mxstat/ In the JLigand section there are some tutorials from Andrey to demonstrate how covalent links can be generated and used. Garib On 14 Jul 2010, at 14:35, Paul Emsley wrote: On 14/07/10 12:56, Vandana Kukshal wrote:

Re: [ccp4bb] differences Rfactor calculations

There may be several reasons: It looks strange. Something seems to be wrong in protocols 1) Check free R flags. I have seen in few cases wrong free R. Generally number of reflections for free should be less than for work reflections 2) Check TLS refinement. You may need to restart TLS

Re: [ccp4bb] LINK option during refinement

In your run with the option residues are close only refmac also should generate a pdb file with link records added. In very simple form you can edit this pdb file and remove all unnecessary links and leave link you want. Then you can rerun with normal options and generated library. Better

Re: [ccp4bb] creating new ligand cif file

Prodrg does very good job in guessing atom types and bond orders. Once it guessed things right it does extremely good job in generating bond lengths, angles etc. But it still depends on accuracy of coordinates. You need to check carefully bonding orders before using them in refinement. You

Re: [ccp4bb] Twin fractions vs. twin domains

I guess you are using version 5.5. In that version in the beginning the program finds all possible twin operators and assigns twin fraction for each of them. Then it tries to filter out smaller twin domains and takes only significant domains. I.e. when twin fractions are higher than 0.05

Re: [ccp4bb] sketcher

Perhaps you could try to use JLigand. It may do a better job. it is available from: www.ysbl.york.ac.uk/mxstat/ In the jligand session there are two tutorials also. they may help you to run and generate your ligand description. If any problem please let me know. In general refmac is not

Re: [ccp4bb] JLigand Coot link

In the latest, latest version refmac writes LINK instead of LINKR. It is a temporary solution. We need a better solution and hopefully we will have one soon This version of refmac is available from: www.ysbl.york.ac.uk/refmac/data/refmac_experimental/ regards Garib P.S. This version also

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

Thank you, Frank, for pointing this out Here is the link to that presentation again: www.ysbl.york.ac.uk/refmac/Presentations/Refmac_February.ppt Garib On 24 Apr 2010, at 12:05, Frank von Delft wrote: Hi Garib, the link you sent doesn't work from here, phx. On 24/04/2010 00:17, Garib

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

You may be using output reflection data from the previous cycle of refinement for the next session. After twin refinement output Fobs (confusingly) may be detwinned. You can try to use original reflection data file (e.g. after scala/truncate/freerflag) and for refinement and it may

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

And another (not so) minor point: Defferences between R/Rfree with twin on and off suggest that there is strong correlation between twin and NCS. For this cases better dealt with if you use twin refinement with sufficiently strong NCS restraints. In new refmac (www.ysbl.york.ac.uk/refmac/

Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates

I hope Kevin will respond soon. I think he has done (or is planning to do) to twinning and ncs in his pipeline of model building. I think something like that may already be in new ARP/wARP (Victor and Tasos will correct me if I am wrong) regards Garib On 23 Apr 2010, at 23:16, Ethan Merritt

Re: [ccp4bb] YATQ (yet another twinning question) - may involve pirates

I am getting in habit of writing double emails. I would say that refmac overestimates at early stages and truncate underestimates (it is just an intuition, not based on theoretical or empriical results) Garib On 23 Apr 2010, at 23:16, Ethan Merritt wrote: In a nutshell =

Re: [ccp4bb] Shifting twin fraction with refinement - finally zero

I think your procedure is good with current technology. At early stages twin refinement may give misleading results. An intuitive resoning for low R factor would be: Twin is summation of intensities. As you sum intensities two things happen: 1) distribution of intensities become more

Re: [ccp4bb] geometry problems with sugars

As I see there is no chirality definition for NAG-ASN link (perhaps there should be but then people will be unhappy even more). Only reason i can see for this flattening is conflict between geometry and electron density. Your example shows that even if electron density is weak it may play a

Re: [ccp4bb] geometry problems with sugars

. Here you have only two orientations. Garib On 21 Apr 2010, at 14:20, Paul Emsley wrote: Garib Murshudov wrote: As I see there is no chirality definition for NAG-ASN link (perhaps there should be but then people will be unhappy even more). Only reason i can see for this flattening is conflict

Re: [ccp4bb] CAQ

It is part of the new dictionary we are preparing. Please find attached dictionary. It was not in the distributed dictionary. Garib CAQ.cif Description: Binary data On 2 Apr 2010, at 22:53, Vin Purp wrote: Does anyone know what happened to the monomer CAQ? There are several structures

Re: [ccp4bb] Refmac remove restraints on targeted atoms

Hi Waters are not restrained in any case. There are only antibumping restraints for waters. If you want to remove them then please let me know and I will send you instructions how to do it. If you want to remove (or relax) restraints from ligand you need to edit your dictionary for this

Re: [ccp4bb] 3D fitting

One option would be molrep molrep -m model1 -mx model2 Of course it assumes that your two structures have overall similar structures and no substantial conformational changes. As the question posed, I think, it does not have solution (only approximations). Almost all programs assume

Re: [ccp4bb] PDB 3.2 Nomenclature

If you want dictionary, atom naming and everything else about new compound names you can copy all monomers (in our definition) from: ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/data/monomers/components.cif.gz It has all compounds used in pdb with idealised coordinates, compound

Re: [ccp4bb] Refmac and links between ligands

Can you check your input file. It may contain contain link record already regards Garib On 1 Feb 2010, at 13:52, Jan Dohnalek wrote: Dear all I understand that when I use the Refmac keyword make link no Refmac should not apply found links. It keeps finding links between ligands (Na+ and

Re: [ccp4bb] refmac resolution limit vs twin refine

I thought this problem is fixed. Could you please try the version from: www.ysbl.york.ac.uk/refmac/latest_refmac.html Problem was that when refmac starts twinning analysis it uses generous tolerance and then filters out unlikely twin operators. When large deformation is needed merohedral

Re: [ccp4bb] Refmac refinement

What are the versions of refmac you are using. Differences (as Pavel mentioned) could be scaling and different scaling parameters. If you would send your log file to me I can try to find out and try to sort out this problem. regards Garib On 4 Jan 2010, at 17:35, Feng Guo wrote: Hi, I

Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5

Could you please try the version from York: www.ysbl.york.ac.uk/refmac/latest_refmac.html I think probkem you mention is related with compilation or something. At least I cannot repat it on my computer regards Garib On 25 Nov 2009, at 16:18, John Pascal wrote: Hello All, We are trying

Re: [ccp4bb] Alterate conformers destroyed by Refmac!

Few people had complains about this. It seems to be related with compilation. If you take the version from York's website then it should work fine. www.ysbl.york.ac.uk/refmac/latest_refmac.html I have compiled it for mac 10.5 and it does not seem to work on mac 10.4. I am trying to make

Re: [ccp4bb] Question about the covalent Link between PLP Lysine

You can try JLigand from http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html to create link and then add link record on your pdb Garib On 9 Oct 2009, at 03:40, Sampath Natarajan wrote: Dear All, I’m currently refining the structure (2.0 A) with a cofactor PLP. The PLP density is

Re: [ccp4bb] cif file for NAD

Dear RajeshCould you please try the attached dictionary. Please let me know if it still has a problem.What are the issues around O1N-PN-O2n and O3N-PN-O5?regardsGarib nad_exp.cif Description: Binary data On 8 Oct 2009, at 15:11, RK Singh wrote:Dear All,I would like to request to send me a working

Re: [ccp4bb] gpp4 version 1.2 released

Same goes for refmac 5.6 series. It should be stable enough for general use in a few months time Garib On 2 Oct 2009, at 14:10, harry powell wrote: Hi I'd like to point out that anyone trying to do anything with Mosflm 7.0.6 does so at their own risk - I don't anticipate it being

Re: [ccp4bb] Rfactor got stuck with a data having alternate strong and weak reflections.

You may try Andrey Lebedev's Zanuda program from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp If the problem is related due to false origin related with the presence of strong pseudo-translation then this program may be able to sort this out. In some cases it may also correct space group (if

Re: [ccp4bb] LINKR in refmac

...@jiscmail.ac.uk [mailto:owner- ccp...@jiscmail.ac.uk] On Behalf Of Garib Murshudov Sent: 16 August 2009 22:09 To: Tim Fenn Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] LINKR in refmac Tim is right. The link you want is TRANS. And if you want link between alternative position then you need

[ccp4bb] YSBL server

Dear all Since last announcement the number of usage of YSBL server was more than our server could cope. That is why we had to close it for few days and upgrade the sfotware on the server. Now YSBL programs server is open again and it should be able to cope (at least for a while). All

[ccp4bb] new version of automatic molecular replacement system - BALBES

or suggestions please do not hesitate to contact with one of us. Your suggestions, complains and questions were instrumental in developing this system. Fei Long - f...@ysbl.york.ac.uk Alexei Vagin - ale...@ysbl.york.ac.uk Garib Murshudov - ga...@ysbl.york.ac.uk regards Garib

Re: [ccp4bb] problem of Refmac refinement on twinning data

This case would happen if the program first decides that the number of twin operators are several. But them to be twin cell should be deformed. This deformation makes some of the reflections to be equivalent to higher resolution reflections than they are. After calculating Rmerge and twin

Re: [ccp4bb] Follow up to twinning question

It is in general matter for debate what to do in these extreme cases. When NCS rotation is parallel to the potential twin operator even if twin is present electron density does not change much (at least not as much as we would like). There are many cases where because of this twinning was

Re: [ccp4bb] images

Dear all Before going into and trying to find a technical solution to the problem it would be good if decide if we need images. As far as I know if we face with a problem to solve and we know that it is necessary to solve then we find technical solution to the problem (either from other

Re: [ccp4bb] map coefficients for padded reflections Fobs=absent

On 18 Mar 2009, at 01:47, Bernhard Rupp wrote: I mean *absent* reflections here with fobs=0 Dear All, during processing some mtz files I noted that some programs complete the reflection list by padding missing reflections. a) for Refmac (which did not pad

Re: [ccp4bb] AW: [ccp4bb] Twinned data and maps

As far as I know map coeffiicient correspond to detwinned data. But using detwinned data may not be a good idea. It would be good to see what are R factor. Another thing to consider is that different program may use different flags for free R and it may cause some problem. What are Rfactors,

[ccp4bb] images

Dear Gerard and all MX crystallographers As I see there are two problems. 1) Minor problem: Sanity, semantic and other checks for currently available data. It should not be difficult to do. Things like I/sigma, some statistical analysis expected vs observed statistical behaviour should

Re: [ccp4bb] Refmac5 and Pseudo-merohedral twinning

Current version does not expand data or model. C222 twinned in P2 will not be handled if data are in C222. Overmerged data are a bit tricky to deal with. And model in higher space group would not fit into the asymmetric unit in general. In short: in the current version space group should be

Re: [ccp4bb] TLS refinement in Refmac gets stuck

Child killing and/or wrong bus seems to be related with static compilation on Mac intel OS 10.5. Existence of this bug is the reason why the version with bug fixes was not announced. If you build from source code then this bug can be overcomed Download source files and copy them to ccp4

Re: [ccp4bb] fix atomic positions in REFMAC5

There is an option to do harmonic restraints: external harmonic chain [ch] residue [res] insertion [ins] atom [n] [altcode [a]] [sigma [value]] or external harmonic residues from [residue_number] [chain_name] to [residue_number] [chain_name] sigma [value] sigma 0.1 For example:

Re: [ccp4bb] Problem during refinement

IT could be miscommunication between refmac and coot. Try to remove cispep lines from your pdb and refine again. Then it may work. After model building info about cispep and/or ssbridge should be removed from the pdb file (unless you are confident about them) regards Garib On 25 Jan 2009,

Re: [ccp4bb] Secondary structure restraints: Oops

If top/par file could be converted to the following type of instructions then you do not need to define everything in cif file (these are for torsion angles, all other restraints can be defined similarly) General torsion angle restraints for any quartet of atoms: external torsion first

Re: [ccp4bb] NCS restraints of domains

Dear Nick Using TLS sometimes improves behaviour of NCS restraints (it makes sense since remaining B values should be similar). However in other cases it does not improve. Perhaps removal of B value restraints for these domains may improve NCS restrained refinement. I have not done tests

[ccp4bb] New ligand and link interface

Dear All Happy new year to you all!! JLigand is a java application which allows ligands to be linked on- screen and a link description to be created. JLigand 0.1 Beta is now available at http://www.ysbl.york.ac.uk/~pyoung/JLigand/JLigand.html There is a documentation how to use JLigand

Re: [ccp4bb] PDB atom names in Coot Refmac

/ * ** * Garib Murshudov http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Erice 2010: Structure and Function from Macromolecular Crystallography: Organization in Space and Time http://www.crystalerice.org/erice2010/2010.htm

Re: [ccp4bb] PDB atom names in Coot Refmac

Garib Murshudov http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Erice 2010: Structure and Function from Macromolecular Crystallography: Organization in Space and Time http://www.crystalerice.org/erice2010/2010.htm

[ccp4bb] announcement: balbes linked wit arp/warp

development team: Fei Long, Paul Young, Andrey Lebedev, Alexei Vagin and Garib Murshudov in collaboration with ARP/wARP development teams in Hamburg and Amsterdam Garib Murshudov http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp Erice 2010: Structure and Function from Macromolecular

Re: [ccp4bb] refmac, twin - really low Rfactors

Hi all One should be aware of some stats about twinning (and in general): 1) If you have perfect hemihedral twinning and no correlated rotational NCS then random R factors are around 40 instead of Luzzati's 58. 2) If you have perfecthemihedral twinning and you are not modelling twin then

Re: [ccp4bb] Preventing close contact between protein and ligand

Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero occupancy are considered as absent and there are not restraints on them 2) symm y at the end of instructions means that the program check all possible symmetry operators and finds minimal

Re: [ccp4bb] Preventing close contact between protein and ligand

[mailto:[EMAIL PROTECTED] On Behalf Of Garib Murshudov Sent: Wednesday, July 30, 2008 5:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Preventing close contact between protein and ligand Dear Snageetha 1) Could you check please if specified atoms have zero occupancy. Atoms with zero

Re: [ccp4bb] Preventing close contact between protein and ligand

There should be something like: loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd MAN-b-D O1 C1single 1.4100.020 MAN-b-D C2 C1single 1.524

Re: [ccp4bb] Preventing close contact between protein and ligand

in order to have the well behaving refinement I will have to change these occupancies to 50-50, right? And just pay the price with the higher B factors? Or is there any other way to deal with this situation? Aleks On 30 Jul 2008, at 16:15, Garib Murshudov wrote: If sum of occupancies of atoms

Re: [ccp4bb] Definition of Fourier coefficients

it was there for some time. Info about this and some other new and not so new features can be found here: http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html Some of the features like n mfo-l dfc map was there for 5.3 and may be even earlier. regards Garib On 8 Jul 2008,

[ccp4bb] new version of refmac (v5.5)

Dear all New version of refmac (v 5.5) is now available for use. Please have a look: www.ysbl.york.ac.uk/refmac/latest_refmac.html Major new developments are: 1) Maximum likelihood refinement against data from twinned crystals. Current version allows only one instruction: twin All

Re: [ccp4bb] angle restraint refmac etc

On 23 May 2008, at 02:03, Bernhard Rupp wrote: Dear All, I have a 3 minor questions re refmac internals: 1) does refmac use angle values directly or restrain 1-3 distances for angle restraint setup? Yes. Angles are angles in degrees. 2) the ML coefficients FWT and DELFWT - are they the

Re: [ccp4bb] Refmac 5.4 monomer dictionary mirror?

It will be available tomorrow (hopefully) afternoon. Garib On 19 May 2008, at 19:50, Thomas J Magliery PhD wrote: I am trying to upgrade Refmac from 5.2 to 5.4. I didn't download the monomer library (refmac5.4_dictonary.tar.gz) when I downloaded the executables, and I can't access the

Re: [ccp4bb] Refmac

If you are using new version of refmac from www.ysbl.york.ac.uk/YSBLPrograms/index.jsp then you can use harmonic restraints. Have a look for instructions: www.ysbl.york.ac.uk/refmac/data/refmac_news.html I hope it helps. regards Garib On 6 May 2008, at 16:39, Debasish Chattopadhyay wrote:

[ccp4bb] balbes with space group checks

Dear all After announcing molecular replacement server with all allowed space group checks because of rapid increase of the usage our system could not handle it and we had to turn off this option. Now we have upgraded the system and it is ready for to use. Note that the new option of the

Re: [ccp4bb] fixing position in the refinement: Shelx, refmac5

(In my view of course, which is debatable) Garib On 4 Apr 2008, at 06:56, Frank von Delft wrote: Is that also how you would restrain refinement at low resolution when using a high-resolution model? (e.g. a 1.8A model into 4A data) phx. Garib Murshudov wrote: In newer version of refmac

Re: [ccp4bb] modified amino acid connection to protein

Dear Catherine Is your SUU an amino acid modified on the side chain side? If yes then you can use standard peptide links. For this your SUU should be declared as L-peptide in the description. Can you send description of your SUU and I can try to sort out what is going on. Garib On 26

  1   2   >