[ccp4bb] MOLREP bug..

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:

Re: [ccp4bb] Molrep

Methinks this is sage reasoning on the part of Dr Dodson Good luck Steve On May 27, 2017, at 6:46 AM, Eleanor Dodson > wrote: no idea really - looks like a bug.. There is a limit on the Radius of gyration whch i thinks is < 0 .5 *

Re: [ccp4bb] Molrep

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

[ccp4bb] Molrep

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

[ccp4bb] MOLREP phased translation function

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

Re: [ccp4bb] MOLREP self-rotation matrix

...@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

Re: [ccp4bb] MOLREP self-rotation matrix

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

Re: [ccp4bb] MOLREP self-rotation matrix

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

Re: [ccp4bb] MOLREP self-rotation matrix

Re: [ccp4bb] MOLREP self-rotation matrix

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 eleanor.dod...@york.ac.uk 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

Re: [ccp4bb] MOLREP self-rotation matrix

version will come soon I hope. Best regards, Sacha Urzhumtsev De : CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK de la part de Chen Zhao c.z...@yale.edu Envoyé : mardi 19 mai 2015 16:11 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] MOLREP self-rotation matrix Hi

Re: [ccp4bb] MOLREP self-rotation matrix

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,

Re: [ccp4bb] MOLREP self-rotation matrix

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

Re: [ccp4bb] MOLREP self-rotation matrix

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 c.z...@yale.edu wrote: Hi Eleanor, Yeah, the relationship of the XYZ

Re: [ccp4bb] MOLREP self-rotation matrix

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 c.z...@yale.edu wrote: I got some answers from the previous thread:

[ccp4bb] MOLREP self-rotation matrix

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

[ccp4bb] Molrep and Refmac5 errors

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

[ccp4bb] MolRep error

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

Re: [ccp4bb] MolRep error

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, Justyna Wojdyla jw...@york.ac.uk wrote: Dear All, I am trying to run MolRep with 'input fixed model' option and i am

Re: [ccp4bb] molrep question - how get our ducks in a row?

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

Re: [ccp4bb] molrep question - how get our ducks in a row?

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

[ccp4bb] Molrep - Fortran runtime errors

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

[ccp4bb] molrep question - how get our ducks in a row?

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

Re: [ccp4bb] molrep question - how get our ducks in a row?

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

Re: [ccp4bb] molrep question - how get our ducks in a row?

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 gborgst...@gmail.com wrote: Hello all, We are solving a

Re: [ccp4bb] MOLREP fails when using input fixed model

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

[ccp4bb] Solved: [ccp4bb] MOLREP fails when using input fixed model

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,

[ccp4bb] MOLREP TFcntrst

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 Cntrst

[ccp4bb] MOLREP no output!

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

[ccp4bb] MOLREP fails when using input fixed model

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 error

[ccp4bb] Molrep and Coot bugs

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

Re: [ccp4bb] molrep NOSG=-1 (space group checking)

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

[ccp4bb] molrep NOSG=-1 (space group checking)

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

[ccp4bb] Molrep with two models

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

Re: [ccp4bb] Molrep with two models

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 first

Re: [ccp4bb] Molrep with two models

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

[ccp4bb] Molrep 11.0

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

Re: [ccp4bb] Molrep error - bug 3790

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/

Re: [ccp4bb] Molrep error -

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...

[ccp4bb] Molrep error -

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 :

Re: [ccp4bb] Molrep error -

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

Re: [ccp4bb] MOLREP

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

Re: [ccp4bb] MOLREP

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

[ccp4bb] MOLREP

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

Re: [ccp4bb] molrep can't find *_trfn_scr.crd

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 first monomer search

[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 first monomer search. Anyone have any ideas? thanks FR -

Re: [ccp4bb] MolRep of coiled coils

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

Re: [ccp4bb] MolRep of coiled coils

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

Re: [ccp4bb] MolRep of coiled coils

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 coil

Re: [ccp4bb] MolRep of coiled coils

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 and

[ccp4bb] Molrep fails to run

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

Re: [ccp4bb] Molrep fails to run

the 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

[ccp4bb] MOLREP for space group F432

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.

Re: [ccp4bb] MOLREP for space group F432

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

[ccp4bb] Molrep question

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

[ccp4bb] MolRep with Phaser using a partial existing solution

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

Re: [ccp4bb] MolRep with Phaser using a partial existing solution

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

Re: [ccp4bb] MolRep with Phaser using a partial existing 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 that