[ccp4bb] artificial tetramer

2011-12-12 Thread Fred
be at a certain distance of the molecule. This sounds conceptually simple, but I would like to do that in batch mode for hundreds of PDB's. Could someone, please, tell me the easiest way/program to do that? Thanks in advance, Fred

Re: [ccp4bb] artificial tetramer

2011-12-12 Thread Fred
lecule into the cell and give it the 4-fold propriety. Quite simple, but don't which program to use. Regards, Fred Em 12-12-2011 18:23, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Fred, if you know the rotation matrix, you can use pdbset with its 'rotate

Re: [ccp4bb] artificial tetramer

2011-12-12 Thread Fred
at few Angstrons of the protein. Em 12-12-2011 19:01, Jacob Keller escreveu: How do you know where to put the axis? JPK On Mon, Dec 12, 2011 at 2:34 PM, Fred wrote: Hi Tim, Thanks for your message and sorry if I wasn't clear. I don't have neither the axis orientation nor the rotat

Re: [ccp4bb] artificial tetramer

2011-12-12 Thread Fred
y distance of the origin, pass a vector/axis through it and take the 3 others molecules by symmetry. That's trivial, given the point, the orientation and the property of the rotation. Don't know which program to use. Regards, Fred Em 12-12-2011 19:18, James Stroud escreveu:

Re: [ccp4bb] artificial tetramer

2011-12-12 Thread Fred
I only want to produce an artificial tetramer. Em 12-12-2011 19:41, Jacob Keller escreveu: Can you clarify your reason for doing this? JPK On Mon, Dec 12, 2011 at 3:36 PM, Fred wrote: Hi James, In my first post "arbitrary orientation into the cell" only means not paral

Re: [ccp4bb] artificial tetramer

2011-12-13 Thread Fred
uence region, which also will be part of the tetramer interface. I'll try to make things work. Once more, sorry for any inconvenience and thank you very much. Kind regards, Fred

Re: [ccp4bb] artificial tetramer

2011-12-14 Thread Fred
trace vectors inside a cell and give it rotation properties. However, Xfit seems to be frozen and integration with pdbset would be painful. Regards, Fred Em 14-12-2011 07:32, Tim Gruene escreveu: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Fred, this sentence of yours, "All pdb's

[ccp4bb] [RESUME]: [ccp4bb] artificial tetramer

2011-12-19 Thread Fred
it and apply the desired symmetry. However, unless XFIT, I don't know which program else has these capabilities. So the steps described here in are not of general application, but has solved my problem. Best wishes and Marry Xmas, Fred

[ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

2012-02-03 Thread Fred
tension time up to 9 min. Is there anything else I can try? Any help is appreciated! Regards. Fred P.S.: Agilent's e-mail support is not working. P.P.S.: this might not be of other's interest, address the answers, please, to my e-mail only.

Re: [ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

2012-02-03 Thread Fred
) Purify your PCR product before transformation if possible or use 3 of 4 microL of it. This is more or less the amount of DNA showed in the uploaded image. Kind regards, Fred P.S.: I'll let you know the results.

Re: [ccp4bb] [RESUME] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

2012-02-07 Thread Fred
7;t want start another discussion but, is there any reason for differences in the transformation efficiency between the parental and the mutated (cleaned) plasmids? All the Best, Fred Em 03-02-2012 16:14, Fred escreveu: Hi CCP4 list, Thanks everyone who have answered my post concerning to mutagene

[ccp4bb] non-symmetric tetramer ?

2010-07-28 Thread Fred
Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tetramer composed by 4 identical subunits, it'll always have a P4 point group symmetry? Thank in advance, Tomb

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

2010-07-29 Thread Fred
ental envelop does have a 4-fold axis. I appreciate if you could add some more comments on this. Thanks in advance, Fred On Wed, 28 Jul 2010 15:31:45 -0300 Fred wrote: Dear CCP4bb, Could someone please, point me to some references about non-symmetric tetramers? If I have a tet

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

2010-07-29 Thread Fred
uprising, a particle with 222 symmetry does not have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes that intersect at the origin (of the "particle", of the molecule) [and for the nomenclature, these axes are named the P Q and R axes]. Fred. Fred wrote: Thanks all

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

2010-07-29 Thread Fred
ee mutually perpendicular twofolds than a fourfold (e.g. the favorite classic hemoglobin has no fourfold anywhere). And there is no fundamental reason that a tetramer has to have any particular symmetry. Phoebe Original message Date: Thu, 29 Jul 2010 13:04:02 -0300 From: Fred

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

2010-07-29 Thread Fred
So, that was my previous question. Em 29-07-2010 14:14, Phoebe Rice escreveu: You don't have to keep the same number of symmetrical contacts. Original message Date: Thu, 29 Jul 2010 14:13:56 -0300 From: Fred Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round To: C

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

2010-07-29 Thread Fred
07-1r.pdb !! NSD = 1.213 egp5S214-1r.pdb !! NSD = 1.270 egp5S208-1r.pdb !! NSD = 0.710 Em 29-07-2010 13:11, Kushol Gupta escreveu: Fred, Two cents - I think the P1 SAXS solution should strongly guide your choice of symme

[ccp4bb] [OFF TOPIC] his-tag doesn't bind

2009-01-27 Thread Fred
ny help is appreciated. Fred

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

2009-01-28 Thread Fred
enced the same problem before, which I solved just increasing urea from 6M to 8M. Now, I have reached GndHCl 6M and no binding at all. I'm currently running a SDS-PAGE with samples eluted from Talon and let you know the results. All the Best, Fred --- Fred // schrieb am *Di,

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

2009-01-28 Thread Fred
Just to let you know. No way, Talon also don't work. I am gonna try the GE His-trap column. Fred wrote: > Hi everyone, > Thanks for answer my question. Just to add some more notes regarding to my expression system. The insert-vector (pET28) has been sequenced and the his-tag is

[ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

2020-01-23 Thread Fred Vellieux
x) ? Just launch the executable and it runs, no questions asked... Thank you, Fred. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Summary: MD program suitable to compute trajectories of a very small molecule in a protein

2020-01-23 Thread Fred Vellieux
Desmond - their installation is simple and they work reasonably well. ---> Jack Tanner (U. Missouri-Columbia): "You might want to review the literature on using MD to study diffusion of O2/CO in myoglobin." (I had started in fact) [---> Lorenzo Briganti: the reply seems t

[ccp4bb] current location for the Superimposé web server ?

2020-02-27 Thread Fred Vellieux
*Hello, I am looking for the Superimposé web server (from Charité, Berlin). * *This web server must have moved from the place where it is supposed to reside, farnsworth.charite.de , not found. Does anyone know where this web server resides now ? TIA, Fred

Re: [ccp4bb] current location for the Superimposé web server ?

2020-03-01 Thread Fred Vellieux
Hello, Follow up concerning my query to the bb (in case anyone is interested), reply received from Robert Preissner through Philip E. Bourne and Joel Sussman: The Superimposé server was stopped in May 2018. Fred. Vellieux On 2/28/20 7:47 AM, Fred Vellieux wrote: *Hello, I am looking

[ccp4bb] superimposition of 3D structures with the DNA part only

2020-04-24 Thread Fred. Vellieux
s the "best" way of doing this. Your suggestions will be appreciated, thanks. Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, clic

[ccp4bb] summary of replies, superimposition of 3D structures using the dsDNA part only

2020-04-27 Thread Fred Vellieux
Thanks to all who replied. Superposition using the nucleid acid part of complexes can be very informative. Have a nice day further, Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic

[ccp4bb] Help needed (input files)

2020-08-04 Thread Fred Vellieux
ology files for each component separately merge these into global parameter and topology files for the system run initial Energy Minimization run M.D. simulations analize the trajectories of the small molecules. Thanks in advance. Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, V

Re: [ccp4bb] 3 letter code for the Ligand

2007-01-26 Thread Fred. Vellieux
file format. Contains h, k, l, Fobs, Sigma F etc dsn6 is a map file (density, such as electron density, Patterson density). Hence you cannot convert between the two. You use the mtz file to compute a map, then use mapman from Uppsala to convert the map to a dsn6 file. Fred. -- Fred. Vellieux, es

[ccp4bb] CNS v1.2 and unwanted introduction of OXT

2007-03-05 Thread Fred. Vellieux
(no harm meant there, this is not targetted at anyone). Please note that I have also posted to cnsbb in order to get more replies. Help is really needed since I do not know why I get these extra OXT atoms introduced in the model. Please read on further: Date: Mon, 5 Mar 2007 13:34:54 +0100 (CET

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

2007-03-05 Thread Fred. Vellieux
On Mon, 5 Mar 2007, James Irving wrote: > Hi Fred, > > From memory, this can occur due to long bond lengths in the model being > interpreted as chain breaks, try editing the generate.inp or > generate_easy.inp script and increase the value for "break_cutoff": &

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

2007-03-05 Thread Fred. Vellieux
On Mon, 5 Mar 2007, Fred. Vellieux wrote: > Hi James, > > I tried to increase the parameter value to 3.0 A. The resulting file gives > the same behaviour (and the newly introduced OXTs are within 0.05 A of the > N atom of the following residue) so I think the distances are reas

Re: [ccp4bb] Highest shell standards

2007-03-26 Thread Fred. Vellieux
e true phases. Since F's are phased quantities and since phases are more important than amplitudes, non random amplitudes plus non random phases (both from map inversion of averaged maps) lead to better electron density maps. Fred. -- Fred. Vellieux, esq. ===

[ccp4bb] looking for test data

2007-07-09 Thread Fred. Vellieux
guarantee at this stage that there will be a publication however! Thank you all in advance, Fred. -- Fred. Vellieux, esq. = IBS J.-P. Ebel CEA CNRS UJF / LBM 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: (+33) (0) 438789605 Fax: (+33) (0) 438785494 =

Re: [ccp4bb] Phaser question !!!

2007-07-12 Thread Fred. Vellieux
gt; phaser.out << EOI MODE MR_AUTO HKLIN rescut.mtz LABIN F = FP SIGF = SIGFP PACK 6 ENSEMBLE TET1 PDBFILE trimer.pdb IDENTITY 0.221 COMPOSITION PROTEIN MW 168960 NUM 2 SEARCH ENSEMBLE TET1 NUM 1 ROOT phaser_trimer SOLU 6DIM ENSE TET1 EULER 327.076 56.322 181. FRAC 0.12840 -0.

Re: [ccp4bb] Backup of whole synchrotrons

2019-04-01 Thread Fred Vellieux
Hi, We already have problems with the volume taken by our standard backups (they take too much space and we haven't been able to push the walls outwards in the Institute - I don't know why they keep telling us that our data should be in some clouds up in the sky). Hence I was wondering about

[ccp4bb] Current "best" software for computing volumes of active sites

2019-04-03 Thread Fred Vellieux
use Voidoo however I do not know where to download an initial (and fairly comprehensive) cavity.lib file which I'd modify if need be. The links on the USF web site appear to be broken. I am running Linux. Thanks for the advice,

[ccp4bb] summary: how to define connectivity, bond types... in PDB files

2019-10-14 Thread Fred Vellieux
found at the cmake stage, although it is present on my system) Thank you for the prompt responses. Fred. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Absence of contact between layers in a crystal

2015-02-06 Thread Kerff Fred
ce of contacts between layers in the crystal. Is it something that has already been observed in other crystals? Best regards, Fred - Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Ba

Re: [ccp4bb] Absence of contact between layers in a crystal

2015-02-06 Thread Kerff Fred
Thanks for all the replies and sorry for rerun of a thread. I however have two additional questions: - Why is the pdb still available without any obvious sign of the fraud? - Why is the paper stil available ? Fred - Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des

Re: [ccp4bb] Various OSes and Crystallography

2012-08-09 Thread Fred. Vellieux
Hi, To make it short: If you want a computer you wish to bring home so that you can do plenty of things (i.e. not crystallography-related in addition to crystallography): Windows because you can edit videos easily, or play games, or (I don't) because there is plenty of (free) software available.

Re: [ccp4bb] NADP binding protein without Rossmann fold.

2012-08-12 Thread Fred. Vellieux
Hello, You could look at this family of enzymes, http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.jc.b.b.html [the sulfolactate dehydrogenase-like family] No Rossman fold there. HTH, Fred. > Dear all, > > I have biochemically characterized one enzyme that can dephosphorylate > N

[ccp4bb] two Postdoctoral positions at YSBL

2012-08-20 Thread Fred Antson
Two Wellcome Trust funded postdoctoral positions are available at York Structural Biology Laboratory, to work with Dr Fred Antson. Both posts are available for 3 years, with potential to extend for a further 2-years. One project focuses on investigating protein-nucleic acid interactions within

Re: [ccp4bb] Changing HETATM to ATOM record

2012-08-20 Thread Fred. Vellieux
An alternative: vi my_pdb.pdb (carriage return) :%s/HETATM/ATOM /g (carriage return) :wq! (carriage return, or ZZ i.e. shift zz) This does the trick. Simple operations like this can be done easily with an editor. I don't know Windows editors (because I don't use Windows). F. > Dear all > > Is

Re: [ccp4bb] diagram of dsDNA

2012-09-16 Thread Fred. Vellieux
Wow, an email from the future ! [Sorry...] > Subject: [ccp4bb] diagram of dsDNA > From: "cuisheng2007" > Date: Mon, October 1, 2012 9:33 am > To: CCP4BB@JISCMAIL.AC.UK > Dear all > > When I was playing around with Nucplot to generate diagram for > dsDNA/Protein > complex,

[ccp4bb] Which Coot for Scientific Linux 6.3

2012-09-20 Thread Fred. Vellieux
Hi all, The question is in the Subject line of this email: which version of Coot should I download and install on a Scientific Linux 6.3 box ? Ta very much in advance, F.V. -- F.M.D. Vellieux (B.Sc., Ph.D., hdr) IBS / ELMA 41 rue Jules Horowitz 38027 Grenoble Cedex 01 France Tel: +33 438789605

[ccp4bb] Different residue type with same number in refmac?

2012-10-29 Thread Fred Kerff
your help. Fred - Frédéric Kerff Chercheur qualifié F.R.S.-FNRS Cristallographie des protéines Centre d'Ingénierie des Protéines Université de Liège 17, Allée du 6 Août - Bat B5a 4000 Liège (Belgium) Tel.: +32 (0)4 3663620 Fax: +32 (0)4 3663772

[ccp4bb] Post-doctoral position at York Structural Biology Laboratory / Closing date: 15 January 2013

2013-01-09 Thread Fred Antson
. Closing date for this post is Tuesday 15 January. Additional information and full details about the application process can be found at https://jobs.york.ac.uk/ Please don't hesitate to contact me directly for further information. Fred Antson / YSBL

Re: [ccp4bb] Suggestions to improve resolution of protein crystals

2021-03-24 Thread Fred Vellieux
uld be the cause of the problems with the current crystals etc but who cares? It may be that (for example) a small molecule inserts itself in the right place to give you the desired result. Worth trying. HTH, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czec

[ccp4bb] coot & other graphics programs draw too many bonds

2021-04-01 Thread Fred Vellieux
f you wish to produce figures for a presentation or for publication. Ta, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, click the following link:

[ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

2021-04-06 Thread Fred Vellieux
awings ? At some stage I ran PRODRG, introduced the cif file in the file components.cif used by LigPlot (LigPlus). I also replaced the coordinate files by those returned by the PRODRG run. Always with the same cryptic error message provided by the software (oops, app). Thanks, Fred. -- Med

[ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

2021-05-21 Thread Fred Vellieux
-terminus: fails. It complains about the ACE cap. Removing the cap solves that problem but then CHARMM fails because of "HIS". If CHARMM fails because it doesn't like any amino-acids then I don't know how I can use the program. But still I'd like to use it because I have to.

[ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

2022-05-30 Thread Fred Vellieux
looking for a method allowing me to identify and display the interface forming residues of one of the protein components. Plus a surface representation of that part, for the 3D structure. Thanks in advance for any tips. Regards, Fred. Vellieux -- MedChem, 1st F. Medicine, Charles University

[ccp4bb] SUMMARY: displaying residues (as a surface perhaps) for one component of a p-p-i

2022-05-31 Thread Fred Vellieux
play of the proteins appears with the residues involved in the interface. This is followed by a PISA calculation from within CCP4MG. The surface of only one of the components in the p-p-i can be displayed, which is exactly what I was looking for. Thanks for all the suggestions. Regards, Fred. On

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

2022-08-23 Thread Fred Vellieux
Hello Pavel, You may want to have a look at PDB structure 6YCR: the macrocyclic peptide inhibitor is modelled as two conformations. The entire peptide. HTH, Fred. On 8/24/22 00:02, Pavel Afonine wrote: Dear community, I’m looking for an example of a crystal structure where a large group

Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

2023-05-19 Thread Fred Vellieux
m.edu/tomcat/biocomp/convert Sometimes the conversion doesn't take place and I have no idea why. HTH, Fred. On 5/19/23 11:28, Frank von Delft wrote: Hello - as in the subject line, does anybody know of, or have, code that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the rest

[ccp4bb] Question about BIOVIA DiscoveryStudio 2021

2023-07-03 Thread Fred Vellieux
idea of how to specify that a part of a coordinate file is the ligand, so that DiscoveryStudio 2021 recognises it as such and allows me to proceed? Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec,

[ccp4bb] CentOS 7 end of life (july 2024)

2023-08-18 Thread Fred Vellieux
igurations)? If so I'd like to know what was successful. Thank you. Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, click the following link: http

Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

2024-01-17 Thread Fred Vellieux
Linux. I don't know how many times I've had to re-install Alma Linux... Jan Dohnalek mentioned that the ugly graphics could be due to a lack of memory problem. I am investigating that. Cheers, Fred. On 1/17/24 11:47, Stuart McNicholas wrote: Dear Fred,   Many apologies for yo

Re: [ccp4bb] Solution to [ccp4bb] problem running ccp4mg: ugly and useless graphics

2024-01-22 Thread Fred Vellieux
nd saved). Just in case. Fred. On 17/01/2024 10:17, Frederic Vellieux wrote: Dear all, Perhaps a reader of the bb will have a solution for this problem. ccp4 is version 8.0 and is up to date. All graphics programs (coot, but also other non-ccp4 software such as chimeraX, Pymol...) run fine on

Re: [ccp4bb] Crystals with DNA

2024-02-09 Thread Fred Vellieux
Hello, Overhanging "sticky" ends are mentioned frequently when it comes to obtaining infinite helices that are useful in crystallization. For example in https://home.ccr.cancer.gov/csb/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf . Cheers, Fred. On 09/02/

[ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux
know if this is feasible or even advised. Probably not. Thanks, Fred. -- MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech Republic To unsubscribe from the CCP4BB list, click the following link: https://www

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux
machine and not the latest v1.5). However, olex2 (the installation program) does not come with Shelx program executables, and I could not locate the installers for the shelx software on Windows. Hence I am running SHELXL in line command mode on my Linux box. Thank you again, Fred. On 12/03

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

2024-03-12 Thread Fred Vellieux
#x27;t remember (the Linux flavour here is Alma Linux 9, not Debian). Fred. On 12/03/2024 10:56, David Waterman wrote: Hi Fred, CCP4 distributes the shelxl binary on Linux. I've not checked yet, but perhaps it is also part of CCP4 on Windows? Cheers -- David On Tue, 12 Mar 2024 at 09: