I give MOLREP am input mtz with space group R32:H or R32 or H32
(entered as R32:H)
But MOLREP claims the SG is
default_PST_limit : 0.250 of origin peak
PST will not be used.
If you like to use PST, use keyword PST = Y
* Space group : H 3*
No: 146 Sett: 2
Cell: 185.73
Methinks this is sage reasoning on the part of Dr Dodson
Good luck
Steve
On May 27, 2017, at 6:46 AM, Eleanor Dodson
mailto:eleanor.dod...@york.ac.uk>> wrote:
no idea really - looks like a bug..
There is a limit on the Radius of gyration whch i thinks is
< 0 .5 * shortest_cell_edge..
Probably
Dear Fred,
Have you tried putting your data through the STARANISO server at
http://staraniso.globalphasing.org ?
With best wishes,
Gerard.
--
On Thu, May 25, 2017 at 07:28:50PM -0400, Dyda wrote:
> Dear All,
>
> Does anyone know by any chance
no idea really - looks like a bug..
There is a limit on the Radius of gyration whch i thinks is
< 0 .5 * shortest_cell_edge..
Probably it is chosen as 27.85, then re-adjusted to allow for anisptropy,
and not properly trapped.
You could try setting it yourself - there is a keyword - or ignore the
Dear All,
Does anyone know by any chance what to do when Molrep crashes with:
Radius of gyration : 27.85
WARNING: Radius of integration >42.40
Radius of integration : 42.40
Resolution : 29.824.00
--- rfcoef for model ---
--- rfcoef for Fobs ---
NCS (
Dear Tommi,
the molrep documentation implies to me that 'MOLREP with electron density map'
in CCP4i2 should do this. I don't have data to test it, though.
Best,
Tim
On Wednesday 18 January 2017 02:25:40 PM Kajander, Tommi A wrote:
> Hi,
>
> is the phased translation function in MolRep still wo
Hi,
is the phased translation function in MolRep still working under CCP4 - doenst
seem to go forward with the old CCP4 GUI (i cant get any coordinated out phased
or not)
and the new one (CCP4i2) doesnt seem to have that option? (in other words i
cant get any solution written out as coordinates
is absence of time to do this !
>
>
>
> Have a nice day, and good luck !
>
>
> Sacha
>
>
>
>
>
> *De :* Chen Zhao [mailto:c.z...@yale.edu]
> *Envoyé :* mardi 19 mai 2015 18:00
> *À :* Alexandre OURJOUMTSEV
> *Objet :* Re: [ccp4bb] MOLREP self-rotation matrix
>
>
>
> Dear Sacha,
>
> I am able to run the program now. Thank you so much!
>
> Have a nice day,
>
> Chen
>
>
>
A new python version will come soon I hope.
Best regards,
Sacha Urzhumtsev
De : CCP4 bulletin board de la part de Chen Zhao
Envoyé : mardi 19 mai 2015 16:11
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] MOLREP self-rotation matrix
Hi Eleanor,
Thank you so
Hah, this sounds good. I will try it out!
Thank you so much!
Best,
Chen
On Tue, May 19, 2015 at 10:22 AM, Eleanor Dodson
wrote:
> Any set of coordinates will do ..
> pdbset just converts the eulerian or polar angles to a matrix..
>
> In the example I gave
> rota euler 10 20 30
>
> corresponds
Hi Eleanor,
Thank you so much for your test! However, I am not starting with a PDB
file. What I am doing self-RF on is just the Patterson map. So my problem
is to convert the output Euler angles to orthogonal matrix.
Thanks a lot for your time,
Chen
On Tue, May 19, 2015 at 5:26 AM, Eleanor Dodso
Actually it is pretty easy:
Here is the log of pdbset
[ccp4@roo job_55]$ pdbset xyzin part.pdb
...
Logical name: XYZIN File name: part.pdb
PDB file is being opened on unit 1 for INPUT.
MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE
RF
Sorry for the spaming... Just want to correct that I plan to say covert the
MOLREP self-RF Euler angle to RESOLVE (not SOLVE) orthogonal matrix...
On Mon, May 18, 2015 at 1:44 PM, Chen Zhao wrote:
> I got some answers from the previous thread:
> https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk
I got some answers from the previous thread:
https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg36578.html
But I just want to make sure what I am doing...
Thanks a lot,
Chen
On Mon, May 18, 2015 at 1:36 PM, Chen Zhao wrote:
> Hi Eleanor,
>
> Yeah, the relationship of the XYZ with the unit c
Hi Eleanor,
Yeah, the relationship of the XYZ with the unit cell axes is tricky too.
Although I can get some clues by looking at the position of the
crystallographic symmetry axes on the XY plane, it is better if I could
find a definite answer...
Thank you,
Chen
On Mon, May 18, 2015 at 1:24 PM,
Hmm - there are programs which give you the matrix associated with Eulerian
or Polar angles. I think one is pdbset..
Or there is documentation in polarrfn or rotmat which describes how to do
it..
But remember there are conventions about which axes correspond to the
orthogonal X Y Z axes used to d
Hi all,
I am now trying to convert the NCS axis expressed by theta, phi, chi (or
alpha, beta, gamma) from MOLREP to an orthogonal matrix in order to feed
into SOLVE. Would anybody suggest me a correct way to do it?
Thank you so much in advance!
Best,
Chen
Dear all,
I recently started using CCP4i (Windows 8) software for data processing and
model building but I get the following error messages whenever I use molrep and
refmac5:
MOLREP
#CCP4I TERMINATION STATUS 0 " MOLREP(ccp4): Error in label assignments in
LABIN"
#CCP4I TERMINATION TIME 08 Oct
you can try a version from this site:
http://www.ysbl.york.ac.uk/~alexei/molrep.html
If it does not work please let me know
regards
Garib
On 15 Mar 2012, at 12:45, wrote:
> Dear All,
>
> I am trying to run MolRep with 'input fixed model' option and i am getting
> error message:
>
> At l
Dear All,
I am trying to run MolRep with 'input fixed model' option and i am getting
error message:
At line 1260 of file /usr/local/xtal/ccp4-6.2.0/src/molrep_/molrep.f
Fortran runtime error: End of record
I am using:
CCP4 6.2: MOLREP(ccp4) version 11.0.02 : 07/02/11
I found the update
PISA does just this - download pdb to ebi server; let iyt cluster molecules
and read back the assembled fcoordinates - plus lots gf useful info..
Eleanor
On Feb 24 2012, David Shin wrote:
Hi Gloria,
It depends on if you mean hard as in thinking up a slick trick, or hard as
in maybe 20-30 min
Hello Gloria,
I usually let Coot display the nearest symmetry molecules (as CA) and save
those that fit: Option "Save Symmetry Coordinates..." and pick the
molecule to save.
Best regards, Daniel
--
Daniel Schlieper email: daniel.schlie...@tuxomania.net
Biochemische Pflanze
Hi,
There is an option in the molrep interface (in the search parameters
tab) to output all models closest to the input coordinate file With a
bit of luck, that should do it.
Johan
On 24 February 2012 00:07, Gloria Borgstahl wrote:
> Hello all,
> We are solving a superstructure of a protein com
Hi Gloria,
It depends on if you mean hard as in thinking up a slick trick, or hard as
in maybe 20-30 mins of tedious work. I had the same problem with 18 in the
ASM, where the solution had scattered models, but didn't want to think
about it, so just used pymol.
1) open the first model with the or
Hello all,
We are solving a superstructure of a protein complex with 2 parts.
Built 6 of the first part and they are all sensibly stacked next to each other.
Then we read this into molrep as the "fixed" model and solved for the
second part.
The solution was found but the 6 for the second model are
When using a multi-copy search/fitting two models in Molrep, I encounter a
fortran runtime error. This happens at the stage where the second model is
being read in. I see that there are some previous posts concerning this. I did
try using a different version (as previous posters reported working
Sorry,
I should have had a look also at the CCP4 site:
updated version of molrep from Aug 8.
http://www.ccp4.ac.uk/updates/linux/ccp4-6.2.0/bin/
Cheers
Guenter
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Dear Zhong Chen and CCP4 users,
I get the very same error on a Centos 5 box. Is there a solution yet?
Best regards,
Guenter
Dear all,
Recently, I used MOLREP to molecular replacement.
My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
When I run a pdb file and mtz by MOLREP w
Dear all,
Does anyone know the definition of the "TFcntrst" value in MOLREPv10.2.35 and
the difference of "TFcntrst" to "Cntrst"?
an example from a MOLREP log-file:
Time_elapsed: 0h 0m 18s Remained: 0h 0m 40s
Sol_ RF TF Tf/sig TFcntrst PFind PFPFmin wRfac Scor Scor_max Cn
Dear all,
I'm using MOLREP in CCP4 for MR. The problem is that it doesn't output a pdb
file although the last contrast value written in the log file is 3.13! Are
there certain criteria which have to be fulfilled before it gives a pdb file or
is it a bug?
Thanks for your help!
Eric
Dear all,
Recently, I used MOLREP to molecular replacement.
My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
When I run a pdb file and mtz by MOLREP without input fixed model, everything
is right.
However, when I run it by MOLREP when using "input fixed model".
The erro
Dear all,
Recently, I used MOLREP to molecular replacement.
My OS is fedora 14 and CCP4 version is the newest one ccp4-6.2.0 .
When I run a pdb file and mtz by MOLREP without input fixed model, everything
is right.
However, when I run it by MOLREP when using "input fixed model".
The e
Hello all-
(Paging Paul and Alexei)
I recently came across a difficulty in Coot and Molrep in parsing PDB
files containing insertion residues of the type where the residue
number is the same but with an A, B, etc appendage.
Hello Stephen,
Thanks for your comment - you remind me to add a
Hello all-
(Paging Paul and Alexei)
I recently came across a difficulty in Coot and Molrep in parsing PDB
files containing insertion residues of the type where the residue number
is the same but with an A, B, etc appendage.
For example, PDB file 2CMR has several instances of the following type:
I guess the only real choice is P2 21 21 or P21 21 21 - the absences
alng h00 could be a result of the pseudo-translation.
I cant explain the score - maybe there is something in the documentation?
But I am afraid after refinement in P212121 the resultant model is sure
to give the best score in
Hi all
I'm checking all space groups under P222 for data that contains a
pseudotranslation. The data integrates in P222 but a 26% PST peak
(0.500, 0.000, 0.23) makes this look like a C2221 cell (see previous
CCP4bb post subject: Let's talk pseudotranslational symmetry (or
maybe it's bad
The molecular replacement program does not know about your molecule
being a single polypeptide chain. The problem is "fit two bodies"
therefore the program fits two bodies. The centre of mass of whatever
you wish to position is placed the "standard asymmetric unit" used by
the program. If it ha
http://www.ysbl.york.ac.uk/~alexei/molrep.html#stick
On Thu, 2011-02-17 at 19:32 +0100, Christian Roth wrote:
> Dear all,
>
> I tried MolRep with a two domain protein. I have cut the two domain as one
> domain rotates which prevent a search with the complete model. After I
> finished
> the fir
Dear all,
I tried MolRep with a two domain protein. I have cut the two domain as one
domain rotates which prevent a search with the complete model. After I finished
the first run. I put this solution as fixed input model in the second molrep
run
with the second domain. The resulting solution p
Molrep 11.0 is available from here:
http://www.ysbl.york.ac.uk/~alexei/molrep.html
Several improvements recently, but the main news is
a new algorithm of Multi-copy search.
Instead of searching for two copies and then for the next two etc.
the program constructs larger multimers (3mers,4mers,5
Dear Jonathan
this sounds like a known issue with the version on molrep that was
released with ccp4 version 6.1.1 (so if you are having the problem
with 6.1.3 then it has got back in). For some reason we did not get
to the bottom of the file path gets doubled up, /home/caruthej/bo3/
ccp4
Dear Jon --
it looks to me that it is trying to open a file that does not exist
because of the path name... I'm not an expert in MolRep, but you
defined PATH_SCR and PATH_OUT with the same names; the problem might
then be that it tried to open a file located in the PATH_SCR/
PATH_OUT... (o
Often times these types of errors arise from the lack of write
permissions to the directory in question or the lack of a directory
altogether. The clue is here/The clue is here:
/home/caruthej/bo3/ccp4/bo3P1_11_molrep_/home/caruthej/bo3/ccp4/
James
On Feb 26, 2010, at 11:31 AM, Jonathan
All:
Can anyone help me out here? I'm trying to get Molrep to run but it seems to
be crashing while trying to open some file after it's done the rotation
function search. I'm getting the following error:
**
Number of RF peaks :
Then I suspect the sequence is overriding the model.
My preferred approach.
Get a sequence alignment from somewhere and use CHAINSAW to edit the
model you want to use. That is documented! And it will edit both
monomers in turn I believe..
Then you will have a dimer with the appropriate seque
How can that be! Are you also providing a sequence?
Eleanor
Tommi Kajander wrote:
Hi,
I have been using a dimer as a search model in MOLREP (there will be
several in AU),
for some reason the program tends to break the dimer into monomers
wihtout asking me..
how is this determined in the prog
Hi,
I have been using a dimer as a search model in MOLREP (there will be
several in AU),
for some reason the program tends to break the dimer into monomers
wihtout asking me..
how is this determined in the program... a more detailed manual would
be nice, also on the output
as the different c
t: 29 June 2009 18:15
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] molrep can't find *_trfn_scr.crd
When doing a multi-copy search, after the first rotation is done it
seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp
directory that it can't find just prior to doing the
reyes/
Andrea__121_molrep_/tmp/francisreyes/
Andrea_121_molrep_trfn_scr.crd "
#CCP4I TERMINATION TIME 29 Jun 2009 11:10:51
#CCP4I MESSAGE Task failed
Thanks
FR
Begin forwarded message:
From: Francis E Reyes
Date: June 29, 2009 11:15:14 AM MDT
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mo
When doing a multi-copy search, after the first rotation is done it
seems to be looking for a _121_molrep_trfn_scr.crd file in my /tmp
directory that it can't find just prior to doing the "first monomer
search".
Anyone have any ideas?
thanks
FR
MR on CCs is generally a pain. The problem is that sliding any CC along
its own supertwist (say by one heptad) will give you a solution that
lines up very well with the "right" model. There are a lot of solutions
of this type, so you basically have a multitude of models that are all
"okay" an
ation Laboratory,
Menlo Park, CA.
-Original Message-
From: CCP4 bulletin board on behalf of Thomas Edwards
Sent: Fri 3/28/2008 5:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] MolRep of coiled coils
Dear BB,
I am attempting molecular replacement with a 2.8A data set from crystals of a
coiled
My short experience with coiled-coil is that molecular replacement can
be difficult for "classical software" (due to the very anysotropic
shape of the protein).
In our case (a short parallel dimeric coiled-coil), molecular
replacement trials using AMoRe or MOLREP were unsuccessful. We solved
the st
Sorry - I should have added that, yes, there are 2 identical peptide chains
that should be parallel coiled-coil.
Any advice gratefully received.
Ed
-Original Message-
From: cockburn [mailto:[EMAIL PROTECTED]
Sent: Fri 3/28/2008 1:35 PM
To: Thomas Edwards
Subject: Re: [ccp4bb] MolRep of
Dear BB,
I am attempting molecular replacement with a 2.8A data set from crystals of a
coiled coil of about 150 residues.
Probably p21212 but maybe p2221.
So far, Phaser, MolRep, Amore, Mr Bump, have not provided a good solution as
judged by Z-scores, CCs, Rfactors, and whether there is any den
output.
Norman Stein
CCP4
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Mike Xishan
Sent: 25 February 2008 11:28
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Molrep fails to run
Dear all
sorry if this query has already been asked. Whenever, I
Dear all
sorry if this query has already been asked. Whenever, I run a job for
molecular replacement in Molrep program using ccp4i, it fails to run and
shows the following error.
Child killed: segementation violation
I would appreciate for suggestions to fix this eror.
xishan
In the previous email I missed index.jsp. Here is the correct url for
programs (including molrep). So again
In newer version of molrep cubic space groups are handled much
faster. Here is the url where you can download molrep
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
regards
Garib
I think it is now much faster. If you take the version from Alexei's
home page it should be faster and may be better also.
You should be able download it from this site:
http://www.ysbl.york.ac.uk/YSBLPrograms
Garib
On 17 Sep 2007, at 10:10, Manfred S. Weiss wrote:
Dear CCP4ers,
has anybod
Dear CCP4ers,
has anybody ever noticed a strange behaviour of MOLREP in space
group F432 (no. 209)? It seems as if the rotation function works
ok, but translation functions take about 100 times the time they
should.
Cheers, Manfred.
***
Hi all,
I'm using molrep with an MTZ file as input, so according to the manual I
should end up with a formatted CIFF file with the F_observed, but I only get
a pdb file for the coordinates. Any idea of what I'm doing wrong?
Thanks in advance,
Cynthia
Hi Jay,
Maybe try to use the the rhombohedral setting (space group R32:R, with
unit cell 229,229,229,81,81,81 ) rather than the hexagonal one used now.
Depending on the fft algorithm used to compute structure factors for
your partial model, this can save you a chuck off memory/time.
You can
The cell is quite big. 300 x 300 x 450 A, 90, 90, 120 (R32). I'm using the
entire resolution range at the moment, but I've just set up another job with
a reduced resolution range. So we'll see how this goes. I only get this
error message when I do a run with Phaser with this partial known solu
Jay Thompson wrote:
Hi,
I have a question with molecular replacement using Phaser. I'm trying
to solve a complex and I have a partial molecular replacement solution
solved using another program. This solution is correct and makes up
~50% of the entire complex. I wanted to fix this solution
Hi,
what resolution range do you use? You can try reducing it a little.
How big is your cell?
Tim
On Friday 18 May 2007 13:46, Jay Thompson wrote:
> Hi,
>
> Thanks for the suggestions and quick reply. Suggestions work great!
>
> But I have another problem and looking back at the ccp4bb, I see t
Hi,
Thanks for the suggestions and quick reply. Suggestions work great!
But I have another problem and looking back at the ccp4bb, I see that Elenor
had a similar problem late last year. The error message is as follows:
--
OUT OF MEMORY ERROR: St9bad_alloc
--
Hello,
you could try to let phaser search for the first fragment, too. That way it
should produce a file ending with '.sol' which you can pass to phaser for the
second search (bottom at the ccp4-gui, "Define search sets...").
Otherwise, if you do not want to move the first fragment, both the Eu
What about giving the correctly positioned partial solution,
and fixed angles/translation of 0,0,0,0,0,0 for that part?
Jay Thompson wrote:
Hi,
I have a question with molecular replacement using Phaser. I'm trying
to solve a complex and I have a partial molecular replacement solution
solved
Hi,
I have a question with molecular replacement using Phaser. I'm trying to
solve a complex and I have a partial molecular replacement solution solved
using another program. This solution is correct and makes up ~50% of the
entire complex. I wanted to fix this solution and search for another
Is the result clearly better in one space group than all the others?
ie Are you sure you have a correct solution?
Eleanor
shivesh kumar wrote:
Dear all
I am trying MR in molrep(CCP4) with P21212.mtz.I have tried nearly all
space group.Rfact and corr.coeff is 57-59% and 23-25% resp.what shoul
Dear all
I am trying MR in molrep(CCP4) with P21212.mtz.I have tried nearly all space
group.Rfact and corr.coeff is 57-59% and 23-25% resp.what should I try to
lower the Rfact.The data is at 2.2A.Any suggestions are welcome.Thanx in
advance.
Shivesh
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