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

#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:

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

did your input files come from? Cheers -- David On Tue, 12 Mar 2024 at 09:01, Fred Vellieux wrote: Hi folks, I have a simple question: is there an electronic bulletin board for small-molecule crystallography? I have checked the list of CCP projects and there is no CCP

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

Hi folks, I have a simple question: is there an electronic bulletin board for small-molecule crystallography? I have checked the list of CCP projects and there is no CCP-project for small molecule crystallography in the list. I am trying to run SHELXL, and it fails with the cryptic message "*

Re: [ccp4bb] Crystals with DNA

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 09/02/2024 10:59, car

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

Dear all, In case anyone experiences problems with Alma Linux, NVIDIA graphics boards and the NVIDIA graphics driver, here is what worked: somehow, the nouveau graphics driver seems to sneak back in, even if blacklisted. When nouveau is in use, the ugly graphics are obtained with ccp4mg. T

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

Dear Stuart, I did test that (removing the .CCP4MG2 directory and its contents) and it gave the same ugly graphics. There are problems with Alma Linux and the "Secure Boot" on this Hewlett Packard Z4 computer. This I have noticed. The secure boot option wants to load a signed graphics driver

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

Hi, Other people on this BB may run into the same problem. CentOS 7 end of life is announced to happen in July 2024. I have to migrate my Linux box to another Linux "flavour". I've had a look at the possibilities: - migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and "leapp".

[ccp4bb] Question about BIOVIA DiscoveryStudio 2021

Folks, apologies for the non-CCP4 software question. I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact form". I am trying to visualize and perform an analysis on a protein:smaller molecule complex. The smaller molecule

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

Hello Frank, We have to convert betwen file formats very frequently (usually several times daily) and: 1) we didn't need any restraints CIF file for that; 2) the tools we are using are http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html https://datascience.unm.edu/tomca

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

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

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

ture of the complex available) I am 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 -- MedC

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

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

Hi folks, Sorry about the non-ccp4 question. I don't know where to ask. I have to perform MD simulations but I am totally on my own here. The one program that appears to be free (in terms of license) seems to be CHARMM. GROMACS (testing with the examples found in the internet) did not work in

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

Hi folks, I'm trying to run Ligplot on a PDB file that contains a residue with type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 years now (which means that I had to reinstall, with an expired license, and get familiar with it again). I get the following error message (rath

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

Hello there, After running autodock vina on certain small molecules, the graphics software I am using (e.g. Pymol, Coot) draws far too many bonds on the docked small molecule. See enclosed screen capture. Is there any way to prevent this from happening? This isn't very satisfactory of you wi

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

Hi, In addition to all that's been suggested so far: when I was facing such problems I always tried the (commercially available) additive screens (additive kits, whatever they are called nowadays). This means setting up quite a few crystallisation experiments (you already have conditions in w

[ccp4bb] Help needed (input files)

Hello, I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is 1. protein 2. cofactor (FAD) 3. small molecule (either single O2 atom or single Chlorine atom) 4. crystallographic waters The software I can access is either Gromacs (with yum

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

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] superimposition of 3D structures with the DNA part only

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

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

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] current location for the Superimposé web server ?

*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. * ##

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

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

Dear all, I need to run MD calculations in order to follow the trajectories of a very small molecule inside a protein. From previous calculations (not MD) I have starting positions for this small molecule that all seem in agreement with a possible path of motion inside the protein. Now I nee

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

Dear all, These are the replies received so far: Daniel Rigden (U. of Liverpool) suggested to do the conversion using https://www.webqc.org/molecularformatsconverter.php . It didn't work for me, the small molecule may be too complex (error message when reading the .mol file); Petr Kolenko (

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

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,

Re: [ccp4bb] Backup of whole synchrotrons

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] Which Coot for Scientific Linux 6.3

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

Re: [ccp4bb] diagram of dsDNA

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,

Re: [ccp4bb] Changing HETATM to ATOM record

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] NADP binding protein without Rossmann fold.

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 > NADP+ / NADPH.

Re: [ccp4bb] Various OSes and Crystallography

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] Phaser question !!!

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.

[ccp4bb] looking for test data

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] Highest shell standards

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. ===

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

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] CNS v1.2 and unwanted introduction of OXT

d to keep the automatic mainchain break detection because there are some gaps in each chain of the model (12 chains in all). So if there are other suggestions to solve this br of a problem, they are most welcome! Fred. -- Fred. Vellieux, esq. = IBS J.-P.

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

(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] 3 letter code for the Ligand

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