That result looks really bizarre but it is hard to make a sensible comment
without more details..maybe you could attach the whole log file for the
refmac run.
What input reflection dAta are you using ? You couldn’t have picked up a
Sharpened set by any chance? (It is always good practice to make
Dear Martin,
one suspicion comes to my mind: could it be a "computer problem" in the sense
that you are using different computing environments for the two calculations
(arpWarp vs standalone refmac5)? That could lead to different decimal
separators ("." versus a ","; see
https://en.wikipedia.o
Maybe this will help?
https://bl831.als.lbl.gov/~jamesh/scripts/refmac_occupancy_setup.com
Make a pdb file of the residues you want to occupancy-refine and put it
on the command line of this script, along with the word "allatoms".
This will generate a file called "refmac_opts_occ.txt" that you
Dear CCP4 community,
I am refining several structures of multimeric protein-ligand complexes and I
wanted to refine occupancy of the ligand. Manual definition of groups would be
tedious and error prone considering that ASU contains 10 protein chains and 1-8
bound ligand molecules. Hence my ide
Well - I would look at the deviants in COOT and see if there is a proper
reason for the angels - water molecules too close? alternate conformation
for some near by sidechain? Any refinement program wants to get good
geometry unless there is an obstacle. If there is nothing obvious to fix
you could
Hello Pradeep,
Have you visually checked the model at these locations? Is this non-ideal
geometry of the DNA supported by the map? At 2.3 A resolution, the DNA should
be well resolved (both backbone and nucleic bases planes). Some (most?)
DNA-binding proteins distort DNA when binding to it, so
REFMAC5 refinement: nucleic acid residues with bad geometry
Hi All,
I am in the final refinement stage of an X-ray structure of a protein-DNA
complex,
2.3 A resolution, using Refmac5 (REFMAC 5.8.0267, CCP4Interface 7.1.018, Linux
platform).
I am confident about the space group, refinement steps,
nal Message-
> From: CCP4 bulletin board On Behalf Of Joern
> Krausze
> Sent: Tuesday, February 4, 2020 10:24
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac5 question
>
> Dear all,
>
> I've got a Refmac5 question. When I refine my protein structure
> On 4 Feb 2020, at 09:24, Joern Krausze wrote:
>
> These hydrogen atoms were present in the input file with their occupancies
> matching that of the residues they are attached to.
What happens with make hydrogen YES?
That should keep all hydrogens present in the input file
(http://www.ccp4.
Dear all,
I've got a Refmac5 question. When I refine my protein structure in
Refmac5 with the options make hydrogen ALL and make hout yes, some of
the hydrogen atoms in the output file have zero occupancies. At a first
glance, only the the H-atoms attached to OG1 of Ser, ND2 of Asn, and NE2
o
erman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
Im Auftrag von "Deniz Üresin"
Gesendet: Mittwoch, 3. April 2019 13:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid
Hello,
I'm trying to refine the structure
uot;Deniz Üresin"
Cc: "CCP4BB@JISCMAIL.AC.UK"
Betreff: Re: [ccp4bb] refmac5 problems with unnatural amino acid
Qs..
1) You are using the same dictionaries for both REFMAC and COOT?
2) What happens in refmac if you just use REFI IDEALISE?
And turn on the option for REFMAC to
M
f file.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *"Deniz Üresin"
> *Gesendet:* Mittwoch, 3. April 2019 13:15
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] refmac5 prob
internal cif file.
Best,
Herman
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von "Deniz
Üresin"
Gesendet: Mittwoch, 3. April 2019 13:15
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac5 problems with unnatural amino acid
Hello,
I'm trying to refin
Qs..
1) You are using the same dictionaries for both REFMAC and COOT?
2) What happens in refmac if you just use REFI IDEALISE?
And turn on the option for REFMAC to
MONITOR MANY - it might tell you if there is some clash which is overriding
the geometry restraints..
Eleanor
On Wed, 3 Apr 2019 at 1
Hello,
I'm trying to refine the structure of a protein mutant that has an unnatural amino acid in it. I created a restraint file for the AA and the mutation worked fine in COOT. But when I use refmac5 for refinement, it always changes the bond angle in the sidechain (an azide group, which should h
Hi Ray,
Not necessarily close to 1.00 but rather 1.00 or lower.
Cheers,
Robbie
-Original Message-
From: Raymond Brown [mailto:ray-br...@att.net]
Sent: Tuesday, March 12, 2019 15:56
To: Robbie Joosten
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 refinement question
Hi Robbie
Joosten wrote:
Subject: Re: [ccp4bb] Refmac5 refinement question
To: CCP4BB@JISCMAIL.AC.UK
Date: Tuesday, March 12, 2019, 4:58 AM
Hi Ray,
This is how I see it: Because different bond
length and angle target tolerances/sigmas you cannot compare
them on an absolute scale. What is less
with the geometric
restraint weights.
HTH,
Robbie
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raymond
Brown
Sent: Monday, March 11, 2019 17:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac5 refinement question
Hi folks,
What are accepta
Hi folks,
What are acceptable values for RMS Bond length, RMS Bond angle and RMS Chiral
volume?
The tutorial suggests RMS Bond length of 0.0200?
I would like to hear your suggestions and/or rationale.
Many thanks
Ray Brown
#
Hi Jon & Robbie,
Yes, that did the trick. I must have missed the whole discussion on how
treatment of carbohydrates has changed since I refined this glycosylated
protein. Strangely, Refmac still complains that OXT is missing from every
residue in the structure, but at least it doesn't bomb out
Hi Derek,
Try removing any MODRES records in your PDB file. This might solve the
carbohydrate related issues.
Cheers,
Robbie
On 28 Nov 2018 17:24, Derek Logan wrote:
Hi,
I'm trying to finish off refinement of a structure I last refined in 2009, but
Refmac5 is crashing with very odd problems.
Hi,
I'm trying to finish off refinement of a structure I last refined in 2009, but
Refmac5 is crashing with very odd problems. I list some relevant lines from the
log files below. Essentially refmac seems to think that every residue is a
terminal one, as it complains that OXT is missing for eve
Hi,
I am getting a "non-positive definite" error when following the mrc refmac5
Tutorial:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/tutorials/refmac_tutorial/files/part_2.html#prepare_tls
I'm using the same data recommended by the tutorial and am following the
tutorial with no de
gt; ---------
>
>
> TWINNING SUMMARY
>
>
> Twinning fraction from H-test: 0.42
>
> Twinning fraction from L-Test: 0.18
>
>
> It is highly probable that your crystal is TWINN
his (if not, then not
>> a “good reviewer.”)
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Alex Lee
>> *Sent:* Friday, April 14, 2017 11:50 AM
>>
>> *To:* CCP4BB@
not a “good
reviewer.”)
JPK
From: CCP4 bulletin board
[mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Alex
Lee
Sent: Friday, April 14, 2017 11:50 AM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Refmac5 twin refinement pushing
eviewer will have you do this (if not, then not
>> a “good reviewer.”)
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
>> *Alex Lee
>> *Sent:* Friday, April 14, 2017 11:50 AM
>
017 11:50 AM
>
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
> surprisingly down
>
>
>
> Thanks Eleanor, I tried MR for P32 21 and P32 12.
>
> SG P3221: SOLU SET RFZ=5.3 TFZ=8.8 PAK=0 LLG=121 TFZ==11.2 LLG=944
> TFZ==29.2 P
@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down
Thanks Eleanor, I tried MR for P32 21 and P32 12.
SG P3221: SOLU SET RFZ=5.3 TFZ=8.8 PAK=0 LLG=121 TFZ==11.2 LLG=944 TFZ==29.2
PAK=0 LLG=944 TFZ==29.2
SOLU SPAC P 32 2 1
SG P3212:
Solution #1 annotation
just try with the
>> higher-symmetry point group first, see what happens.
>>
>>
>>
>> JPK
>>
>>
>>
>> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
>> *Sent:* Thursday, April 13, 2017 11:32 PM
>>
>> *To:* Keller, Jacob
>> *Cc:*
;
> *To:* Keller, Jacob
> *Cc:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
> surprisingly down
>
>
>
> Hi Keller,
>
>
>
> Thanks for the suggestions! I only have two copies in ASU at SG P32.
> Zanuda also suggests P32 i
-symmetry point group first, see what happens.
JPK
From: Alex Lee [mailto:alexlee198...@gmail.com]
Sent: Thursday, April 13, 2017 11:32 PM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down
Hi Keller,
Thanks for the suggestions
hese types of
> things!
>
>
>
> JPK
>
>
>
> *From:* Alex Lee [mailto:alexlee198...@gmail.com]
> *Sent:* Thursday, April 13, 2017 9:08 PM
> *To:* Keller, Jacob
> *Cc:* CCP4BB@JISCMAIL.AC.UK
>
> *Subject:* Re: [ccp4bb] Refmac5 twin refinement pushing Rfree
&g
works out—I am interested in these types of things!
JPK
From: Alex Lee [mailto:alexlee198...@gmail.com]
Sent: Thursday, April 13, 2017 9:08 PM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down
Hi Keller,
I do not how to check
://doi.org/10.1107/S2059798316019318
>
>
>
> Jacob
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of
> *Eleanor
> Dodson
> *Sent:* Thursday, April 13, 2017 3:11 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Refmac5 twin refinem
f Of Eleanor
Dodson
Sent: Thursday, April 13, 2017 3:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down
Twin refinement cannot be compared directly to untwinned - the R factors are
between different parameters - without twinning it is assumed
ac log file, it would warn you of potential space
> group errors. Refmac will also give you a refined estimate of the twin
> fraction.
>
>
>
> Cheers,
>
> Robbie
>
>
>
> Sent from my Windows 10 phone
>
>
>
> *Van: *Alex Lee
> *Verzonden: *donderdag 1
fraction.
Cheers,
Robbie
Sent from my Windows 10 phone
Van: Alex Lee<mailto:alexlee198...@gmail.com>
Verzonden: donderdag 13 april 2017 19:19
Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Onderwerp: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down
Dear Al
Dear All,
I have a protein/dna complex crystal and data collected at 3A and another
set at 2.8A, space group P32. L test shows twinning (fraction around 0.11).
The structure solved by MR and model building of the complex finish (no
solvent built yet, I do not think it's good to build solvent in su
The main issue is that carboxyls seem to be invisible and Coot tries to fit
them as though the map had them there
Well, if the atoms are part of the model, then Coot will try to fit them to
the "data." I routinely chop off GLU and ASP side-chain when modelling into
cryo-EM maps (that's what th
On 01/02/2017 17:11, Trevor Sewell wrote:
I have a 3.4 A (enzyme – protein only) map that I have fitted manually using
Coot and
automatically with Rapper. It all looks very nice – I can fit all but 13 of the
330
residues. I have the following questions:
Is there a way of having Coot know tha
[trevor.sew...@uct.ac.za]
Sent: Wednesday, February 01, 2017 12:11 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Refmac5 and Coot for refining cryo-EM structures
I have a 3.4 A (enzyme – protein only) map that I have fitted manually using
Coot and automatically with Rapper. It all looks very nice – I
I have a 3.4 A (enzyme – protein only) map that I have fitted manually using
Coot and automatically with Rapper. It all looks very nice – I can fit all but
13 of the 330 residues. I have the following questions:
Does refmac5 have a way of refining the scale of the map? – I did my best to
calibr
Got it. Thank you very much Christian!
On Fri, Dec 16, 2016 at 12:14 PM, Christian Roth wrote:
> Hi,
>
> the adding water option is basically a COOT script to find waters, which
> get subsequently refined. There is no automatic evaluation and deletion of
> waters based on certain criteria. That
Hi,
the adding water option is basically a COOT script to find waters, which
get subsequently refined. There is no automatic evaluation and deletion
of waters based on certain criteria. That you have to do manually. You
can always try to automatically add new waters, which is done by this
opt
Dear CCP4bb members,
Does Refmac5 in CCP4i have an option of adding waters to the refined
structure (the input coordinate does not have any water)? I see in Phenix
refine there is an option of "update water", I tried to look for this
option in Refmac5 but I could not find it. I am using CCP4i 7.0
Dear all,
refinement of my protein structure involves a C-terminal amide. Looking
through the monomer/link library files mon_lib_list.cif and
mon_lib_ind.cif I could not identify a modification or link suitable
for amide restraints. I know I could construct a proper .cif myself,
however I a
density and you
> will have to manually fit the sugar as good as possible. Some of the older
> files in the PDB may have distorted carbohydrates, so here it is probably
> best to build the carbohydrates again from scratch (get monomer, delete
> linking oxygen) etc.
>
> Go
he carbohydrates again from scratch (get monomer,
> delete linking oxygen) etc.
>
> Good luck!
> Herman
>
>
>
>
>
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Remie Fawaz-Touma
> Gesende
treff: [ccp4bb] Refmac5
Hello everyone,
When I refine in CCP4 a structure with Glc units attached every few of them as
a ligand and there are several of them in the same file, I start off with a PDB
that shows the LINK records between the GLC units as LINKR because I add the
links by > Ex
Hello everyone,
When I refine in CCP4 a structure with Glc units attached every few of them as
a ligand and there are several of them in the same file, I start off with a PDB
that shows the LINK records between the GLC units as LINKR because I add the
links by > Extensions > Modelling > Make Li
For REFMAC, I think you need to alter the cif file for the modified residue -
such that the residue type is L-peptide rather than anything else.
Tony.
Sent from my iPhone
On 2 Aug 2013, at 17:08, "Arnon Lavie" mailto:la...@uic.edu>>
wrote:
Hi:
Despite Google and several attempts, I am still
la...@uic.edu]
Sent: Friday, August 02, 2013 12:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] REFMAC5: linking a modified amino acid to adjacent residues
Hi:
Despite Google and several attempts, I am still having no success in getting
Refmac5 to link a modified amino acid to its adjacent r
Hi:
Despite Google and several attempts, I am still having no success in
getting Refmac5 to link a modified amino acid to its adjacent residues.
Using sketcher, a cif file for the modified amino acid was generated.
This cif file was used an input to Refmac5.
The relevant part from the Refmac5
On 06/27/2013 05:34 PM, Ben Eisenbraun wrote:
Howdy Y'all,
Howdy.
It looks like REFMAC is trying to open
$CLIBD_MON/list/mon_lib_list.cif read-write and then read-only,
Yes, it does... curious. In libcheck.f's WRT_LIB_LIST_NEW_STYLE, should
be OPENFR(), I imagine.
but
with the flag t
Howdy Y'all,
I have a lab where REFMAC jobs are blowing up trying to access the
monomers database. The logfile looks like this:
Open failed: Unit: 7, File:
/programs/x86_64-linux/ccp4/6.3.0/ccp4-6.3.0/lib/data/monomers/list/mon_lib_list.cif
(logical:
/programs/x86_64-linux/ccp4/6.3.0/ccp4-6.3.
acid naming problem). So I
prefer causing an error message.
Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Ed Pozharski
> Sent: Monday, February 11, 2013 15:07
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4b
On Mon, 2013-02-11 at 09:56 +0100, Robbie Joosten wrote:
> This is a 'compatability' option in Refmac that internally renames
> atoms. If you comment out 'MMA .C7 CM' in your
> mon_lib_list.cif file, the problem will disappear.
>
Robbie,
thanks a lot - this fixes it.
Is th
..@umaryland.edu
> Subject: [ccp4bb] refmac5 MMA bug
> To: CCP4BB@JISCMAIL.AC.UK
>
> I see a strange issue with a model that includes O1-methyl-mannose
> (three letter code MMA). Basically, refmac fails and says that C7 is
> missing in the model while "CM" is absent from th
I see a strange issue with a model that includes O1-methyl-mannose
(three letter code MMA). Basically, refmac fails and says that C7 is
missing in the model while "CM" is absent from the library. The problem
is that there is no CM atom in the pdb file, while C7 is right there.
This happens wi
On Fri, Jan 25, 2013 at 2:24 AM, Robbie Joosten
wrote:
> Phenix however needs to deal with the CCP4 type reflection binning. Now the
> size of the sets cannot be used which means that you have find a smarter
> solution. So I wonder how this is implemented. Does Phenix use the
> (reasonable) assump
is labeled 1.00 or 0.00? Or does it also check the
sets with other labels?
Cheers,
Robbie
Sent from my Windows Phone
From: Garib N Murshudov
Sent: 2013-01-25 10:46
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] refmac5 vs phenix refine mixed up
Dear Tim
In
Dear Tim
In principle if a user defines freer flag then refmac knows about that (unless
freer flag is 0 then refmac assumes that it is default). In this case (if freer
defined by user) then it is not altered.
regards
Garib
On 25 Jan 2013, at 09:14, Tim Gruene wrote:
> -BEGIN PGP SIGNED M
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Pavel, dear Garib,
how do you figure out automatically the correct flag? (I hope both
phenix and refmac will allow to manual overwrite the software's decision)
Cheers,
Tim
On 01/24/2013 07:47 PM, Pavel Afonine wrote:
> Hi,
>
> It would be nice
Yes, Nat is right. Starting with the latest version 5.7 (that is part of ccp4)
refmac makes sure that it uses correct set for free reflections. Hopefully it
will remove some of the confusions when switching from one software to another.
refmac 5.8 version should definitely have this feature. Thi
Hi,
It would be nice if default setting was the same in different suites.
it's a nice idea of course, but I feel it is impractical as it would
require changing a lot of software, both modern and legacy.
However, given array of flags it is algorithmically trivial to figure out
what is test and wo
On Thu, Jan 24, 2013 at 10:34 AM, Leonid Sazanov
wrote:
> Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
> ccp4/refmac - as 0.
> That would explain your Rfree going down - because your Rfree reflections
> were refined by refmac.
According to Garib, the current ver
Most likely scenario is that Phenix by default assigns Rfree flag as 1, while
ccp4/refmac - as 0.
That would explain your Rfree going down - because your Rfree reflections were
refined by refmac.
It would be nice if default setting was the same in different suites.
Best wishes.
Dear all
As it was already stated it is essential to use the same input file (after
scaling and trancating) for all refinement sessions.
Output mtz file in the absence of twinning has been scaled to account for
anisotropic overall B values. It is modification of the data. In the twinning
case
PS just checked an example, and the the refmac input and output F and SIGF are
in fact NOT the same and have been subjected to something more than linear
scaling.
This was using refmac version 5.5.0109, admittedly not the newest one.
So using the refmac output mtz as input for the next run is wro
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear,
of course you could ask Garib whether or not the output data were
modified by refmac5 - often they are, at least linearly scaled (which
would certainly do no harm), and unless you have read the refmac5 code
or Garib assures you I would not r
if they are the same, there is in principle no problem.
(you can quickly check using "mtzdump")
but, just to make sure, I always use the exact same scaled and truncated
mtz-file for all refinements of any particular structure. Then there is no
doubt at all...and it is in fact easer, i.e. one less
Dear Rajesh,
In addition to the R/Rfree, you also need to look at issues like
stereochemistry, bad contacts, clashes, the general fit into density,
unmodelled ligands/waters, Ramachandran outliers, correct side chain
rotamers etc etc. I would advice you to spend (a lot of) time visually
inspe
Dear Tim Gruene,
2013/1/24 Tim Gruene
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Rajesh,
>
> first of all, a model is not "true" or "false", it can only be
> "better" or "worse".
>
> The explanation of what you observe depends on what you did:
> - - did you use the identical an
Yes, the wilson B-factor is comparable which is 53.6.
And also same MTZ was used for refmac5 and phenix refine, which is
processed one (original one). And also the reflections used in the
refinement was: Phenix (46793 reflections) and refmac5 (44431 reflections).
I do not know whether I answered y
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Rajesh,
first of all, a model is not "true" or "false", it can only be
"better" or "worse".
The explanation of what you observe depends on what you did:
- - did you use the identical and very same mtz-file as input to all
three scenarios? Some p
Well I am not answering your question. What is the (Wilson) B-factor of
the diffraction data ? I would personally compare the average isotropic
temperature factor of the model to that of the diffraction data.
And further the aim of refinement is not to reduce the B-factor. The aim
of refinemen
Dear All,
I am working on a perfectly twinned data in space group P31. when I
refine this data with phenix refine the R/Rfree is 26.6/29.4 and average
B-factor is 38.
I did one test now.
I used phenix refined pdb and refine with refmac5 and got R/Rfree of
26.2/29.7 and average B-factor
Thank you very much for the help from all of you.
I used "no prior phase information", and got R/Rfree = 0.2202/0.2544.
I used "SAD data directly" and got R/Rfree = 0.2066/0.2302.
I used "Hendrickson-Lattman coefficients" and got R/Rfree = 0.2255/0.2539.
It seems that the "SAD data directly" gets
>
> I am not sure how you would fare with SAD data directly..
>
>
If you would like a comparison, check out the refmac paper.
http://journals.iucr.org/d/issues/2011/04/00/ba5152/index.html
See Figure 1 - this shows model building with ARP/wARP on over 100 data
sets using
the different Refmac func
I don't know what exactly the phenix.autosol output is.
If you are satisfied with the solution and have a mtz file containing F sigF
HLA etc, then use Hendrickson Lattmann coefficients.
If there is only Phase/Fom then use that.
I am not sure how you would fare with SAD data directly..
But bewa
Dear Cai
On 5 Nov 2012, at 09:46, Qixu Cai wrote:
> Dear all,
>
> What's the difference between "no prior phase information", "phase and FOM",
> Hendrickson-Lattman coefficients", and "SAD data directly" in the refmac5 GUI
> of CCP4i?
I would use SAD data directly if you have SAD data set. I
Dear all,
What's the difference between "no prior phase information", "phase and
FOM", Hendrickson-Lattman coefficients", and "SAD data directly" in the
refmac5 GUI of CCP4i?
I have a SAD dataset and solve the phase by phenix.autosol. Now I want to
refine the structure by refmac5, which kind of i
, 2012 9:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refmac5, SIGF/SIGIMEAN labels
Hi all,
we noticed a strange behaviour of refmac5.7.0029 that comes with CCP4-6.3.
We run a most basic script: 5 rounds of restrained refinement with all default
parameters. The input mtz file contains
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Jan,
could you attach or include the refmac script, please?
Cheers,
Tim
On 07/27/12 08:10, Jan Abendroth wrote:
> Hi all, we noticed a strange behaviour of refmac5.7.0029 that comes
> with CCP4-6.3. We run a most basic script: 5 rounds of restr
Hi all,
we noticed a strange behaviour of refmac5.7.0029 that comes with CCP4-6.3.
We run a most basic script: 5 rounds of restrained refinement with all default
parameters. The input mtz file contains besides H/K/L and FreeR_flag,
IMEAN/SIGIMEAN, and F/SIGF.
Refmac 5.6.0117 outputs F/SIGF, whil
edu]
Sent: Tuesday, March 27, 2012 5:14 PM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> >phenix.refine allows any number of alternate c
On Tuesday, March 27, 2012 04:35:40 pm Bernhard Rupp (Hofkristallrat a.D.)
wrote:
> >phenix.refine allows any number of alternate conformers.
>
> Hmm. quoting our old friends from the validation circuit: Where freedom
> is given, liberties will be taken
True, but...
[warning: back of t
>phenix.refine allows any number of alternate conformers.
Hmm. quoting our old friends from the validation circuit: Where freedom
is given, liberties will be taken
BR
Hi James,
my understanding is that phenix.refine allows any number of alternate
conformers. There may have been a limit of 4 some time in the past, but no
longer. So your idea could be tested.
Cheers,
Paul
On Mar 27, 2012, at 12:33 PM, James Holton wrote:
> Try this:
>
> 1) tak
Try this:
1) take your favorite PDB file and set all the B factors to ~80 (reduces
series-termination errors)
2) use sfall/fft in CCP4 to calculate structure factors to 4A resolution
3) use sftools to add a "SIGF" column (0.1 will do) to make refmac5 happy
4) refine the "perfect" model against
here the missing
> residues are. They may even have been removed by a protease.
>
> Cheers,
> Herman
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ed
> Pozharski
> Sent: Monday, March 26, 2012 4:50 PM
> To: CCP4B
: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
On Mon, 2012-03-26 at 16:30 +0200, herman.schreu...@sanofi.com wrote:
> It is like with Heisenbergs uncertainty principle. Either one has a
> complete model with a number of atoms having a coordinate uncertainty
On Mon, 2012-03-26 at 16:30 +0200, herman.schreu...@sanofi.com wrote:
> It is like with Heisenbergs uncertainty principle. Either one has a
> complete model with a number of atoms having a coordinate uncertainty
> of 4-6 Å, or one has a model where the uncertainty of all atoms is
> below say 0.5 Å,
On Mon, 2012-03-26 at 10:17 -0400, Gregory Bowman wrote:
> But what about the issue of resolution? As was previously pointed out,
> at say 3.2 Å resolution, many side chains will fail to fit, but it
> doesn't seem appropriate to trim them all down.
Why is it inappropriate to trim them down? Some
: Monday, March 26, 2012 4:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] REFMAC5 residues with bad geometry
But what about the issue of resolution? As was previously pointed out,
at say 3.2 Å resolution, many side chains will fail to fit, but it doesn&#
This is a personal preference. I do model at low sigma levels if there IS
some indication of where to put atoms, always try to keep the correct
sequence even if some atoms are missing, and just for coot convenience keep
atoms with occ = 0, rather than delete them altogether. (COOT will refine a
But what about the issue of resolution? As was previously pointed out, at say
3.2 Å resolution, many side chains will fail to fit, but it doesn't seem
appropriate to trim them all down. The users need to also be aware of the
quality/resolution of the structures that they are looking at.
Greg
I agree with Eleanor 100%...
In my biased opinion, only the atoms supported by electron density
should be included in deposited models. To satisfy the "but this will
mess up the electrostatic potential coloring" argument (a valid one, of
course), the "projected model" can be deposited alongside w
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