Re: [ccp4bb] Refmac problem: Validation and Analysis

Dear Marian, This issue regarding validation report in refmac task has been fixed in the latest update 8.0.019. Please let us know if the problem persists. Best wishes, Martin On 05/04/2024 13:19, Jon Agirre wrote: Dear Marian, Thanks for your report. I'm sorry you're having to deal with this

Re: [ccp4bb] Refmac problem: Validation and Analysis

Dear Marian, Thanks for your report. I'm sorry you're having to deal with this problem. There is nothing wrong with your machine; this is an identified bug and we're working towards fixing it. In the meantime, the only workaround I can think of is to roll CCP4 back to a previous update, e.g. 015.

[ccp4bb] Refmac problem: Validation and Analysis

Dear list, I have a problem running the Validation and Analysis in Refmac and I would really appreciate any feed-back from your side. I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4). Last time I was using Refmac was in November 2023. At the time, I posted in the list an

[ccp4bb] refmac output query

Dear All, A quick question about Refmac on ccp4i. When refining an RNA oligonucleotide structure using the findwaters option, the pdb output labels all the atoms as HETATM (inluding the original RNA atoms which were not so labelled in the input pdb). It is of course trivial to correct this,

Re: [ccp4bb] Refmac automatically handles twinning?

I am sure you have checked this but A) is there non cryst translation? If so this can make space group selection tricky . Could it be P3 21 or P31 21 or ... B ) the twin indicators at data processing are pretty reliable and if that suggests no twinning it probably isn’t there... you could process

Re: [ccp4bb] Refmac automatically handles twinning?

The twin fraction can vary during data collection - if the beam is smaller than the crystal For example you could have crystals which are like two very short ends of pencils - with flat ends together (in your case these might pencils could be in P3) In some orientations you could have the beam

[ccp4bb] Refmac automatically handles twinning?

Just double checking that Refmac automatically handles twinning without the need for a keyword or a box click in i2.  I have a crystal in P32 21 that gives poor Rfactors and maps (Rfree mid 40s) from what should be an excellent model. I have reprocessed in P32, P1 and C2 but all give similar

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

Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

I deleted a line in the keyword file which was "pdbout format mmcif". It was my first try to convert the pdb file to an mmcif file, but it did not work! Best Marina Zitat von "Krieger, James M" : It could be good to say how you solved it for future users. Best wishes James On Aug 6,

Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

Hi, as it is often the case, the mail is out and you are able to solve the problem on your own. Thanks anyway! Best Marina Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>: Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to

[ccp4bb] refmac - use weighting term - pdb to mmcif

Hi, before I will soon finish my PhD, I have to solve one more problem. I managed to refine occupancies and tls in Refmac. I also found out that you can use pdb-extract to convert the pdb file to an mmcif file so that you can validate the structure using the validation server. However,

Re: [ccp4bb] refmac twin refinement vs resolution limit

Dear Eleanor, Thank you so much. As you said, it is a problem that the number of reflections estimated by FreeR set is different from an actual that of reflections because of the low resolution discrepancy. Moreover, twin refinement includes a problem about some overlapping of diffraction

Re: [ccp4bb] refmac twin refinement vs resolution limit

Well - I am not sure whether this has anything to do with twin refinement but resolution limits are often a bit iffy. First the low resolution discrepancy. The Free R is generated to a lower and higher resolution than any observation. The FreeR set is meant to be complete for any possible index

[ccp4bb] refmac twin refinement vs resolution limit

When I use refmac restrained refinement with intensity based twin refinement, resolution limit has been changed from 71.4519- 1.9996 to 47.392-1.986. From Log file, before refinement, Scaling and SigmaA resln: 71.4519 1.9996, seems to be correct. But in the middle of log file, around Fom and

Re: [ccp4bb] Refmac not handling microheterogeneity?

; > > > > > > In case 1 OD1 A is immediately followed bu OD1B > > > > > > In second case - all As listed then all Bs > > > > > > Eleanor > > > > > > > > > > On Wed, 2 Dec 2020 at 14:3

Re: [ccp4bb] Refmac not handling microheterogeneity?

ehalf Of Ian > Tickle > Sent: Wednesday, December 2, 2020 15:02 > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Refmac not handling microheterogeneity? > > > Dear All >

Re: [ccp4bb] Refmac not handling microheterogeneity?

his and I imagine this problem goes >> very deep into the internal representation of the model in REFMAC. That >> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a >> solution would be very welcome. >> >> Cheers, >> Robbie >> >> >

Re: [ccp4bb] Refmac not handling microheterogeneity?

t; said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a > solution would be very welcome. > > Cheers, > Robbie > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Ian > > Tickle > > Sent: Wednesday, December 2, 2020 15

Re: [ccp4bb] Refmac not handling microheterogeneity?

nal Message- > From: CCP4 bulletin board On Behalf Of Ian > Tickle > Sent: Wednesday, December 2, 2020 15:02 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac not handling microheterogeneity? > > > Dear All > > I just downloaded a PDB file (7A5V) from th

[ccp4bb] Refmac not handling microheterogeneity?

Dear All I just downloaded a PDB file (7A5V) from the EBI server, tried to run Refmac on it and got the error: ERROR: in chain A residue: 279 different residues have the same number There is an error in the input coordinate file At least one the chains has 2 residues with the same number ===>

Re: [ccp4bb] Refmac use - water addition

Hi Luca, as Eleanor mentioned, in the i2 interface there is in the option menu an add water button. That will automatically run the coot find waters script similar to the old interface. Paul did use some very sensible values to look for blobs, which might be waters. These ones are used (basically

Re: [ccp4bb] Refmac use - water addition

You don’t say quite how you are doing this. There is an option in the i2 pipeline to add waters using coot when the r factor falls below some assigned value. This is done using COOT. One can debate whether it is a useful option or whether the user would be better o open COOT and supervise the

Re: [ccp4bb] Refmac use - water addition

Dear Jon, thanks for your answer. Maybe I have been too quick in writing my last message. The point is that with the old CCP4 interface, I would have been able to run Coot-findwaters to automatically add and remove water molecules at certain DELFWT and FWT rmsd tresholds, respectively, through

Re: [ccp4bb] Refmac use - water addition

Hello, I'm not totally up-to-the minute with this but I didn't know that refmac itself added waters so maybe it's another program in an i2 pipeline, or something. However, I know another excellent refinement program that does ;-) and an excellent graphics program that does, too ;-0 In the

[ccp4bb] Refmac use - water addition

Dear CCP4 people, I am approaching in these days to the new CCP4i2 interface and, in particular, to REFMAC. Can anyone quickly explain what the factor R, that must be chosen in order to automatically add water molecules, is? How can I relate this value with the previous DELFWT and FWT map

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

[ccp4bb] Refmac Ideal Geometry Library

Hi, I'm seeking insight into some geometry outliers in my Refmac refined model. It would be nice to have confidence in the target values used by Refmac. Does Refmac use the library distributed by CCP4 in lib/data/monomers, or do it have its own library squirreled away somewhere? Dale

[ccp4bb] [refmac developers] unrestrained anisotropic

Hi Fellows, Q for the Refmac cognosci: Just curious: If I run unrestrained anisotropic refi on 1 A data, some barely supported ligands display insane and physically impossible ADPs, worthy of the ORTEP of the century. As cigars penetrate discs, it seems that Hirschfeld criteria on aniso

Re: [ccp4bb] Refmac and hydrogens -developers

The first thing you want to do when debugging hydrogens in refmac5 is to make sure it outputs whatever it was doing: MAKE HOUT Y This is not the default.  Normally, refmac will take a PDB file without any hydrogens in it, quietly add them before doing refinement, and then delete them before

Re: [ccp4bb] Refmac and hydrogens -developers

Yes - I am having problems with hydrogens in REFMAC recently - has something changed? My problem is this: Build a rough model for some residues into a lousy map. (R ~ 32% etc..) I know it is rough with clashes and bad geometry but trust refinement to improve things a bit.. However if the run

[ccp4bb] Refmac and hydrogens -developers

Hi Fellows, for an experiment, I am running 0.9 A data with unrestrained Refmac (yes I know should/could use SHELXL, but let's drop that for now). When I select 'ignore even if present in file' in a PDB that has hydrogens, I get the identical results than with 'use if present' or 'generate

[ccp4bb] Refmac per-cycle and all-cycle statistics.

I was wondering why everything appears twice in the report, as below ;-? https://www.ucl.ac.uk/~rmhajc0/percycle.jpg To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Refmac in i2

The numbers do make sense now: AaA, AbA, etc, correspond to different HETATM groups and (what was confusing me a lot) the No. atoms includes riding hydrogens.  On Thursday, 2 May 2019, 23:27:49 BST, Jonathan Cooper wrote: In the output statistics part of the GUI there is table of

[ccp4bb] Refmac in i2

In the output statistics part of the GUI there is table of mean B-factors, e.g. Chain mean B (No. atoms) AAA 23.6( 2596 )AaA 35.4( 29 )AbA 35.2( 10 )AcA 18.9( 10 )AdA 58.5( 10 )AeA 39.5( 119 )BBB 25.5( 2545 )BaB 42.0( 10 )BbB 46.9( 5 )BcB 37.3( 92 ) There is an A- and a B-chain in the structure,

Re: [ccp4bb] Refmac dictionary

Hi My apologies. This is indeed a silly question. It appears I forgot to remove the extra O when linking them together! Sam On Wed, 3 Apr 2019 at 07:21, Sam Tang wrote: > Dear all > > Hello again. > > We have another protein-RNA dataset which we are trying to refine. For > this dataset we

[ccp4bb] Refmac dictionary

Dear all Hello again. We have another protein-RNA dataset which we are trying to refine. For this dataset we have three OMU nucleotides modelled. We got the monomer from Coot 'Get Monomer'. Refmac returned the following error: ERROR : atom :OP3 OMU 2 CCC is absent in the

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

Dear Herman, On Thu, Feb 07, 2019 at 10:26:09AM +, Herman Schreuder wrote: > I did understand your question correctly and (at least for ligands) > the procedure I and also Diana Tomchick described, worked. However, > I just did a test with both Refmac and Buster and it seems that > these

[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [EXTERNAL] [ccp4bb] refmac same residue different names Herman, thanks - however, it seems like I have poorly worded my question. I do know how to generate alternate conformers, what the PDB ATOM record format is etc. The point was that when I have alternate

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

an editor and generate the alternative conformation yourself: >One of the residues gets an “A” in front of the residue name, e.g. ALEU, >and the alternative residue a “B”, say BLEU. You also have to reset the >occupancies > to 0.5 for both conformations (or different fractions which add up to

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

which add up to one). Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Edwin Pozharski Gesendet: Montag, 4. Februar 2019 22:35 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] [ccp4bb] refm

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

self: >One of the residues gets an “A” in front of the residue name, e.g. ALEU, >and the alternative residue a “B”, say BLEU. You also have to reset the >occupancies to > 0.5 for both conformations (or different fractions which add up to one). > >Good luck! >Herman > >Von: CCP4 bu

Re: [ccp4bb] [EXTERNAL] [ccp4bb] refmac same residue different names

> Good luck! > > Herman > > > > *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von > *Edwin Pozharski > *Gesendet:* Montag, 4. Februar 2019 22:35 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* [EXTERNAL] [ccp4bb] refmac same residue different names &g

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names   Belated happy 2019, everyone.   For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same residue ID.  Presented with a pdb file that has

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

ctions which add up to one). Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Edwin Pozharski Gesendet: Montag, 4. Februar 2019 22:35 An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Betreff: [EXTERNAL] [ccp4bb] refmac same residue different na

[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

Pozharski Gesendet: Montag, 4. Februar 2019 22:35 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names Belated happy 2019, everyone. For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same

[ccp4bb] refmac same residue different names

Belated happy 2019, everyone. For whatever obscure reason, I need to refine a model that has two different residue types as alternate conformers with the same residue ID. Presented with a pdb file that has such feature, Refmac fails saying this ERROR: in chain A residue: 443 > different

[ccp4bb] Refmac jelly body parameters

Dear Refmac developers, I am trying to reproduce some successful refmac runs but cannot get the previous results despite playing around with the parameters. I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have overwritten the log files in a backup. I still have the pdbs, mtz

[ccp4bb] Refmac resolution limit doesn't match data processing

Dear all, for one of my projects Refmac (ccp4i2) shows a low resolution limit lower than Aimless, which I used for scaling. How is this possible? Since this causes problems for the pdb deposition, how can I fix it? Best, Joel

Re: [ccp4bb] Refmac refinement: reduced disulfides

Hi Joel, I'm working on a similar structure at the moment. If refining in refmac, you could add a line to the pdb such as: LINKRSG ACYS A 22 SG ACYS A 96SS and tell the program to only use links defined in the pdb file. If refining in phenix, you

[ccp4bb] Refmac refinement: reduced disulfides

Dear all, I am refining structures containing disulfides using refmac. Many of the disulfides are partly broken due to radiation damage. I tried modeling alternative conformations (i.e. one cysteine pair in a disulfide and the other pair as free thiols), but after refinement the reduced form

[ccp4bb] refmac error

Hi, after updating to ccp4/7.0, I get this error when trying to run Refmac: Dictionary path has not been defined Check the environment variable CLIBD_MON Current value of CLIBD_MON is /mnt/nfs/clustersw/shared/ccp4/7.0/ccp4-7.0/lib/data/monomers It should be set to wherever_dict/dic/ ===> Error:

Re: [ccp4bb] Refmac: problem with anisotropic refinement of heavy atoms.

Sorry, I moved the image before the sending of the mail and then I was not attached. 2018-04-04 11:26 GMT+02:00 M T : > Hello, > > I am refining a structure at 2.1Å, using Refmac and manual constructions > in coot. > I have few Ca, Cl and Mg in my structure and some of them

[ccp4bb] Refmac: problem with anisotropic refinement of heavy atoms.

Hello, I am refining a structure at 2.1Å, using Refmac and manual constructions in coot. I have few Ca, Cl and Mg in my structure and some of them have a clearly anisotropic distribution, then I decided to use ANISOU line in pdb file only for these atoms. In refinement parameters of Refmac I set

Re: [ccp4bb] Refmac: removing selected ligand hydrogens after making a link

After outputting the hydrogens, delete the ones you don't want and from then on do refinement with: make hout Y make hydr Y When you do that, refmac will keep the hydrogens you put in, and also put them in the output. -James Holton MAD Scientist On 3/29/2018 2:11 PM, Phil Jeffrey wrote:

[ccp4bb] Refmac: removing selected ligand hydrogens after making a link

I've got a couple of instances where I have non-standard amino acids, nevertheless present in the monomer dictionary, that have additional non-peptide covalent linkages. I've figured out how to define these, but if I opt to output hydrogens as a diagnostic I see that Refmac doesn't delete the

[ccp4bb] refmac mixed anisotropic refinement

Dear all, How does one exclude water from anisotropic refinement in refmac5.8 under ccp4-7.0 Here is the relevant section from the com file, refi - type REST - resi MLKF - meth CGMAT - bref MIXED anisou residues from 100 A to 200 A This does not work and the logfile has the

Re: [ccp4bb] refmac-extra-params

Dear Prof Emsley That worked! Thanks Abhishek On 2017-08-24 17:42, Paul Emsley wrote: > On 24/08/17 16:29, Dr A.A. Jalan wrote: > >> I am trying to change the default refmac run parameters in coot. For this, I >> created a refmac-extra-params file in the directory from where coot is

Re: [ccp4bb] refmac-extra-params

On 24/08/17 16:29, Dr A.A. Jalan wrote: I am trying to change the default refmac run parameters in coot. For this, I created a refmac-extra-params file in the directory from where coot is launched. (set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANIS")) You can set

[ccp4bb] refmac-extra-params

Dear all, I am trying to change the default refmac run parameters in coot. For this, I created a refmac-extra-params file in the director from where coot is launched. (set! refmac-extra-params (list "MAKE HYDROGENS ALL" "REFI BREF ANIS")) But these modification are ignored through the

Re: [ccp4bb] refmac output

the CCP4 gui does just that - provides map coeffs by default.. You can seek out the full REFMAC output if needed but it is not there by default. Eleanor On 3 August 2017 at 02:04, Pavel Afonine wrote: > Hi Ed, > > your suggestion makes perfect sense to me, and it's trivial

Re: [ccp4bb] refmac output

Hi Ed, your suggestion makes perfect sense to me, and it's trivial to add an option to do what you want. This will be available in next Phenix nightly build (clearly not tomorrow given today's power outage). Command line: use "write_map_coefficients_only=True" (by default is is False).

Re: [ccp4bb] refmac output

On Wednesday, 02 August, 2017 16:12:30 Edwin Pozharski wrote: > Just to clarify, how do you use the extra columns in this scenario? My > suggestion was to have the output file that includes only the map > coefficient columns, so you still can look at the map. IIRC, FP/SIGFP > columns from refmac

Re: [ccp4bb] refmac output

Just to clarify, how do you use the extra columns in this scenario? My suggestion was to have the output file that includes only the map coefficient columns, so you still can look at the map. IIRC, FP/SIGFP columns from refmac output are actually modified from the input (scaled with Boverall),

Re: [ccp4bb] refmac output

Yes, I agree! This (“Please look at my structure, and here are my files from the last cycle of refinement") happens to me almost every week. :) Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas

Re: [ccp4bb] refmac output

As someone who uses those "superfluous" columns all the time, I would like to chime in in favor of keeping the default output columns of refmac. If only I had a nickle for every time someone asked me to "look at" a structure and only gave me the output files of refinement. Kind of ties your

Re: [ccp4bb] refmac output

> > I know space is cheap these days, but is there a reason for Refmac to > generate all those extra columns in the output mtz file? Refmac (as well > as phenix.refine and buster-tnt) output mtz file is almost always used for > only one purpose - look at the map in coot. You only need 4 columns

Re: [ccp4bb] refmac output

Perhaps a good opportunity for getting rid of (scaled) F and SIGF too? Certain pipelines need Refmac's phase estimates (Buccaneer and Crank2 off the top of my head), but I can't see how activating an 'expert mode' or 'developer mode' in order to get them would be a problem for their authors.

[ccp4bb] refmac output

I know space is cheap these days, but is there a reason for Refmac to generate all those extra columns in the output mtz file? Refmac (as well as phenix.refine and buster-tnt) output mtz file is almost always used for only one purpose - look at the map in coot. You only need 4 columns for that,

Re: [ccp4bb] REFMAC? COOT? and TER records

t; From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Eleanor Dodson > > Sent: Monday, June 19, 2017 11:42 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: [ccp4bb] REFMAC? COOT? and TER records > > > > These do seem to multiply wonderfully in the P

Re: [ccp4bb] REFMAC? COOT? and TER records

CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Eleanor Dodson > Sent: Monday, June 19, 2017 11:42 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] REFMAC? COOT? and TER records > > These do seem to multiply wonderfully in the PDB output files and > sometimees to have have strange effects/ af

[ccp4bb] REFMAC? COOT? and TER records

These do seem to multiply wonderfully in the PDB output files and sometimees to have have strange effects/ affects in COOT? As I understand there should be a TER record after a protein chain? but not after a ligand. Dont know about carbohydrate chains. Eleanor The correspondence about N linked

Re: [ccp4bb] Refmac library

On 01/05/2017 13:51, brian walker wrote: Is there a 3 letter code for D-methionine in refmac library. It is not listed in library, while all the others are? Here's the meta solution if you have Coot: File -> Search Monomer Library -> "D-methionone" -> Search gives MED Paul.

Re: [ccp4bb] Refmac library

Hi Brian, It's called MED. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > brian walker > Sent: Monday, May 01, 2017 14:52 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Refmac library > > Is the

[ccp4bb] Refmac library

Is there a 3 letter code for D-methionine in refmac library. It is not listed in library, while all the others are?

[ccp4bb] Refmac twin refine works for Amplitude based but not Intensity based

Dear CCP4bb members, I have a dataset of 3A, twinned data (twin fraction 0.15) set of space group P6222, I solved the structure by phaser (TFZ>10, LLG>1000) with space group P32 and build model to Rfree/R 30% 26%. I then tried twin refinement in Refmac, after I tried amplitude based refine the

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Christian Roth [christian.r...@bbz.uni-leipzig.de] Sent: Thursday, June 18, 2015 11:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue? Hi all, I refine

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue? update

Hi all, I looked again careful in the respective files and it turns out that all B-Factors of the protein chains which are treated with TLS are refined to the lowest possible value of 2.00 for all atoms! A workaround is to use the option to set the initial B-factor to 20.0 in the GUI and than

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

Hi Christian, I've seen this behaviour as well. I'm not an expert but I rationalized the situation as the TLS parameters for an incomplete model getting overfit as the missing/wrong parts of the model pull on the TLS parameters. REFMAC doesn't alternate between TLS and coordinate refinement, so

[ccp4bb] Refmac refinement R factors going up..... TLS issue?

Hi all, I refine a structure with TLS and restrained refinement in Refmac. After the run finished, I fixed a few outliers manually in Coot, saved that file and used that with the original TLS file from TLSMD for the next round of refinement. As soon as the restrained refinement starts the

Re: [ccp4bb] Refmac refinement R factors going up..... TLS issue?

[christian.r...@bbz.uni-leipzig.de] Sent: Thursday, June 18, 2015 11:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac refinement R factors going up. TLS issue? Hi all, I refine a structure with TLS and restrained refinement in Refmac. After the run finished, I fixed a few outliers manually

Re: [ccp4bb] Refmac fatal error with newly added ligand

] On Behalf Of Lau Sze Yi (SIgN) Sent: Monday, June 08, 2015 12:00 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac fatal error with newly added ligand Hello, I generated my new ligand using smiles string in Phenix with elbow to generate my ligand cif and pdb file. I then open

[ccp4bb] Refmac fatal error with newly added ligand

Hello, I generated my new ligand using smiles string in Phenix with elbow to generate my ligand cif and pdb file. I then open these in Coot along with my protein model and mtz and fitted this new ligand into my density. However Refmac failed with the following details in my log file:

[ccp4bb] Refmac- riding hydrogen

Dear CCP4bb, When we select 'generate all hydrogen atoms' option in Refmac5, does it use riding hydrogen model in refinement? -- Regards, Sasha Pausch

Re: [ccp4bb] Refmac- riding hydrogen

16:27 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Refmac- riding hydrogen Dear CCP4bb, When we select 'generate all hydrogen atoms' option in Refmac5, does it use riding hydrogen model in refinement? -- Regards, Sasha Pausch

[ccp4bb] refmac rigid body module in ccp4i interface

hello, could i ask the developers to check for me that the rigid body refinement module in the latest update works correctly. when i open the rigid body menu i see no possibility to neither define my own domains nor select auto. rather i see all kinds of options for auto map sharpening etc. my

[ccp4bb] REFMAC - TWIN OPTION

Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean diffraction pattern that looks like one single lattice. Very clean spots, so merohedral twinning. 2. You can use various programs to

[ccp4bb] AW: [ccp4bb] REFMAC - TWIN OPTION

Santarsiero, Bernard D. Gesendet: Mittwoch, 17. September 2014 14:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] REFMAC - TWIN OPTION Can someone point me to bulletpoint documentation on using the twin refinement in CCP4? Here's what I did. 1. I'm in space group P3, and the see a very clean

Re: [ccp4bb] REFMAC - TWIN OPTION

Hi Bernie, I agree with Herman. I think you will be all set if you simply change the no twin refinement option near the top of the Refmac interface to intensity based or amplitude based twin refinement. Refmac will determine the appropriate twin operators/fractions and refine. Best, Chris

Re: [ccp4bb] Refmac buccaneer combination

Can you send me the rest of the logfile? I think I've seen an error like this where the number of atoms built dropped to zero, in which case there is something seriously wrong with the input phases. But I expect there are other ways to trigger a refmac fail - I can't tell for sure without more

Re: [ccp4bb] Refmac buccaneer combination

Hi Ronan and Kavin, I checked the input files and found that i was assigning wrong column labels in buccaneer for which the error was popping up. I was able to fix it now. Thanks a lot. Debajyoti On Tue, 18 Mar 2014 21:09:15 +0530 wrote Hi Debajyoti,

[ccp4bb] Refmac buccaneer combination

Hi all, I am running autobuild and refinement in buccaneer/refmac pipeline. Does anybody have any idea about the following error . Refmac_5.8.0069: Check input coordinates Traceback (most recent call last): File /Applications/ccp4-6.4.0/bin/buccaneer_pipeline, line 199, in

[ccp4bb] Refmac bond restraints across special positions?

Colleagues, We have determined a structure of a palindromic DNA molecule, in which one half of the DNA is in the asymmetric unit. Is there a way to tell REFMAC that there are covalent bonds across asymmetric units? Without such LINK records in the PDB file, REFMAC treats this as a non-covalent

Re: [ccp4bb] Refmac bond restraints across special positions?

I haven’t tried this in a long time, but in the old days, we would have simply refined one strand. On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov olegtsodi...@gmail.com wrote: Colleagues, We have determined a structure of a palindromic DNA molecule, in which one half of the DNA is in the

Re: [ccp4bb] Refmac bond restraints across special positions?

: Wednesday, March 12, 2014 2:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac bond restraints across special positions? I haven't tried this in a long time, but in the old days, we would have simply refined one strand. On Mar 12, 2014, at 4:05 PM, Oleg Tsodikov olegtsodi...@gmail.com

[ccp4bb] refmac-linux-I'm out of touch question

Hi folks, I am wanting to ask for some linux help as I want to try a newer version of refmac (5.8) to test it against a refinement problem I have. My problem is that I rarely use linux these days and I'm at a loss as to how to run the latest version as my knowledge of linux has disappeared.

Re: [ccp4bb] refmac-linux-I'm out of touch question

Van: Joel Tyndall Verzonden: 10-7-2013 23:49 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] refmac-linux-I'm out of touch question Hi folks, I am wanting to ask for some linux help as I want to try a newer version of refmac (5.8) to test it against a refinement problem I have. My problem

Re: [ccp4bb] Refmac error

Dear colleagues, I have the same problems as Peer Mittl once had. Was this solved and what was the solution? Running arpWarp the job terminates with the message: Refmac_5.7.0032: Open failed: File: /software/apps/ccp4/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif However the

Re: [ccp4bb] Refmac error

- From: Alexander Batyuk [mailto:bat...@bioc.uzh.ch] Sent: den 15 maj 2013 10:34 To: Martin Moche Subject: Re: [ccp4bb] Refmac error Dear Martin, I think we solved it by changing the file's permissions (for mon_lib_list.cif) to rwxrwxrwx Best wishes, Alex On 15 May 2013, at 10:25, Martin

[ccp4bb] Refmac error

Dear Colleagues, For some reason Refmac refuses to read the file mon_lib_list.cif athough the file exists. The error message is as follows:  Open failed: Unit:   7, File: /share/prog64/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif (logical:

  1   2   3   4   >