[ccp4bb] off topic: microscope in glove box

Dear all, I want to put one of our microscopes into the glove box. Does anybody know whether some parts of the microscope optics do not like vacuum in the air lock ? Thanks and best regards, Guenter To unsubscribe from

[ccp4bb] Summary: [ccp4bb] off topic: microscope in glove box

ay anywhere between zero and one." https://www.imdb.com/title/tt0584455/characters/nm0921942 - Cosmic Cats approve of this message On Mon, Oct 21, 2019 at 10:00 AM Guenter Fritz <mailto:guenter.fritz.phenix.c...@gmail.com>> wrote: Dear all, I want to put one of our micros

Re: [ccp4bb] Unusual monomer-monomer interface in crystal

Dear Chris, are there any metal ions in your buffer or in your protein. We had a similar looking case. A Zn2+ ion bridged two monomers. Our protein is a Zn2+ binding protein. The Zn2+ originated from some denatured protein in the drop. No extra Zn2+ was in the crystallization buffer. http://w

[ccp4bb] 2 Postdoc positions available

On behalf of Huib Ovaa (h.o...@lumc.nl): We are looking for postdoc candidates with a background in protein chemistry/ structural biology. There are two projects: One project on MHC-T-cell interactions, and diagnostics/ immunotherapy using novel sets of protein reagents that we are developin

[ccp4bb] dimple, skip pointless?

Dear all, I was going through the options in dimple. Is it possible to skip the checking of the space group by pointless? Thanks in advance and best regards, Guenter To unsubscribe from the CCP4BB list, click the follo

Re: [ccp4bb] somewhat off-topic :)

Dear Artem, I am a fan of the former "Superformance" column from Merck. The production / selling  of these columns is sourced out to a small company called Goetec. The columns are not really cheap, but good quality, last forever, suited also for higher pressures, only glas and Teflon in conta

Re: [ccp4bb] Domain Motion Analysis

Dear Antony, similar to the approach Eleanor has described, lsqman will give you rotational matrix and translation vector. http://xray.bmc.uu.se/usf/lsqman_man.html Best regards, Guenter Hi, You can try elNemo server. Regards, Nasrin PhD scholar On Wed, Jul 8, 2020, 10:16 PM Antony Ol

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 w

[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,

Re: [ccp4bb] IUCr committees, depositing images

On the technical feasibility of storage of original data: Sure, running Pilatus for an olympic record, we will go home with several T of data after 24 h (will we?). Yes, we do already. I just checked the number of images from PILATUS 6M we have collected so far this year : ca. 1.7 millions.

Re: [ccp4bb] solvent mask from one crystal form applied to the other second ...

Hi, have a look into the supplement of the paper by Poul Nissen pointed out. There are some shell scripts exactly for that purpose. I had to adapt the scripts a bit, but the instructions are very well to follow. HTH Guenter Hi Pete Thanks for the reply. As for the transformation, I was g

Re: [ccp4bb] High Rmerge with thin frames

ees was actually giving at the end better data. A. -- ******* Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz e-mail: guenter.fr...@uni-konstanz.de e-mail: guenter.fr...@uniklinik-freiburg.de ht

Re: [ccp4bb] expression of Cys-rich small protein

cysteines. Don't really know if that is the problem. Laurie Betts -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz e-mail: guenter.fr...@uni-konstanz.de e-mail: guenter.fr...@uniklinik-f

Re: [ccp4bb] Mg2+ or water

-- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz e-mail: guenter.fr...@uni-konstanz.de e-mail: guenter.fr...@uniklinik-freiburg.de http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html Tel.: +49 761 270

Re: [ccp4bb] Full-screen stereo with Coot/PyMol/etc on 3D LCD displays?

ex.html> Lab: 1-301-594-9229 E-mail: fairman@gmail.com<mailto:fairman@gmail.com> james.fair...@nih.gov<mailto:james.fair...@nih.gov> -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-kon

Re: [ccp4bb] off-topic: LCD monitors

Dear Padmaja, I have use Samsung 2233RZ for stereo running on Linux and Windows systems. Perfomance is great. HTH Guenter Pardon the off-topic query, but I would like to get some feedback about any personal preference for 3D LCD monitors. I am trying to decide between the following 3 monito

Re: [ccp4bb] DSSP server

the very beginning. I want to assign ss to my pdb file in DSSP, but I could not find a server to run it. Does anybody know a webserver where I could run this kind of tasks? I use iMAC. Many thanks! Jane -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie

Re: [ccp4bb] Protein-antibody complex

ng other reducing agents? Your answers and help in this regard will be highly appreciated. Thanks, Jan -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.

Re: [ccp4bb] Is it possible for the Tris buffer to strip the Zn ions from the Zinc Finger motif of a protein?

-- > 搜索本应是彩色的,快来体验新一代搜索引擎-必应,精美图片每天换哦! 立即试 > 用！ <http://cn.bing.com/?form=CRMADS> > ---- > 聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! 立刻下载！ > <http://3g.msn.cn/> -- *

Re: [ccp4bb] protein turns brown

Sandy, like mentioned previously, sounds like FeS. record an optical spectrum. Or even better, check whether there is somebody on the campus running an EPR machine (equipped for helium temperature measurements) Maybe a new FeS protein? FeS is not necessarily required as redox cofactor. It can

Re: [ccp4bb] Setting drops with proteins that are hard to concentrate

n delete it from your system. -- ******* Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: [EMAIL PROTECTED] Tel. Office: +49-(0)7531 88 3205 Tel. Lab : +

Re: [ccp4bb] Bacterial induction at 18C

hen temperature eis decreased by 7 deg C. Godd luck, Guenter I am already playing with lowering and/or doing away with the antibiotics. Any suggestions wrt 18C? The protein is insoluble at 30C. Thanks. Raji -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich B

Re: [ccp4bb] Protein binding to Zn and Ca

insights would be very valuable. thanks, Neeraj -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: [EMAIL

Re: [ccp4bb] pH gradient in Mono Q

rmacy and Pharmaceutical Sciences University of Manchester ---- -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaet

Re: [ccp4bb] coordinates of TCEP

Hi, if a compound is not in the hic-up data base of the USF (http://xray.bmc.uu.se/hicup/) I usually go to NCBI Pubchem database (TCEP e.g. at http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=119411&loc=ec_rcs) , download the sdf file, feed it into a programm that can read it and put ou

Re: [ccp4bb] Concentrating protein

A mild and quick method is to use dry Sephadex G-25. The material will swell and take up all the liquid except molecules larger than ca. 5 kDa. Dear All, we have GCSF protein produced in inclusion bodies. we solubilise it refold it and then concentrate it using proflux system. still the conce

Re: [ccp4bb] how to promote folding for an unfolded protein

t can make some mutations to make it foldable.Any input would be useful. Thanks a lot. Jenny -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10

Re: [ccp4bb] Imidazole's ability to chelate metal ions

Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> *** -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstan

Re: [ccp4bb] Imidazole's ability to chelate metal ions

el: 773.608.9185 email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> ******* -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mai

Re: [ccp4bb] losing zinc during crystallization

Hi Sue, I fully agree with Thierry, you might have to cyrstallize the protein under exclusion of dioxygen. There are many metallo proteins which have to be crystallized that way. But a first attempt might be the TCEP as already suggested by many others. If you need advice regarding crystalliza

Re: [ccp4bb] losing zinc during crystallization

--Original Message- From: CCP4 bulletin board on behalf of Guenter Fritz Sent: Fri 9/26/2008 3:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] losing zinc during crystallization Hi Sue, I fully agree with Thierry, you might have to cyrstallize the protein under exclusion o

Re: [ccp4bb] Semet in non-auxotrophic strains

Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften

Re: [ccp4bb] Offtopic: FAD enzymatic assay: a little bit more about my enzyme

t I didn't. I have several concerns, one is the autooxidisability of FAD, how fast FADH2 would be reoxidized by O2 in the air or by the O2 dissolved in solution. The second cocern is how fast the FAD reaction will go. Please advise. Thank you! Mike -- ****

Re: [ccp4bb] Ordering a cDNA library

from I can order Human and mouse (brain/liver) cDNA library? Any suggestions are welcome. Thanks, Rajan -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz

[ccp4bb] error in startup of ccp4i 6.1

Dear all, I have installed precompiled ccp4 61 (Redhat from download manager) on Centos5 box, X86_64. Running ccp4i gives: [guen...@hypatia ~]$ ccp4i Top level CCP4 directory is /usr/local/software/CCP4/61/ccp4-6.1.0 Using CCP4 programs from /usr/local/software/CCP4/61/ccp4-6.1.0/bin Error in s

Re: [ccp4bb] cryoloops for X-ray data collection from protein crystals at room temperature

thanks -- Dr. Cedric Bauvois Cristallographie des protéines Institut de Recherches Microbiologiques JM Wiame -IRMW Av E. Gryzon 1, 1070 Brussels (Belgium) tél: +32 (0)2 5273634 fax: +32 (0)2 5267273 -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Natur

[ccp4bb] restraints for 4Fe4S in shelxl

*** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fr...@uni-konstanz.de Tel. Office: +49-(0)7531 88 3205 Tel. Lab : +49

[ccp4bb] coot add-residue without map

Dear all, I wanted to use COOT to add a few residues to a the N-term, just simple fantasy building. It should be straight forward with the add-terminal-residue command, however COOT insists on a e-density map. Any idea to overcome this? Thanks in advance, Guenter

Re: [ccp4bb] Angle between two different helices from two different subunits

Hi Peter, you can do that with interhlx: http://nmr.uhnres.utoronto.ca/ikura/resources/data+sw/interhlx/ There is also a way to determine the interhelical angle with molmol, http://hugin.ethz.ch/wuthrich/software/molmol/ defining cylinders for the helices. HTH Guenter Hi all I would be interes

Re: [ccp4bb] Glycerol as metal chelator?

be a weak chelator otherwise it wouldn't be so ubiquitous in protein biochemistry. Has anyone else experienced this before with glycerol? Ho UC Berkeley -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Univers

Re: [ccp4bb] Na/K Phosphate

more practical side of things, if you want to explore an initial hit based on sodium/potassium phosphate, how would you go about it - e.g. what phosphate buffers would you make and at what ratio would you mix them? Thanks in advance, Geoffrey Kong -- *** Priv.

[ccp4bb] Source Ta6Br12 for phasing

Hi, a follow up question: Which supplier offer Ta6Br12? Thanks, Guenter My post-doc recently produced a splendid (for its resolution) ~5A map of a "medium" sized protein-DNA complex using Ta6Br12 clusters. And he's got a good toehold on a ~340kDa complex using the same clusters. So I'm recentl

Re: [ccp4bb] CD spectroscopy sensitivity

idual fold stays intact after removal of one helix. HTH Guenter I would appreciate your opinion All the best Francisco J. Enguita ITQB Oeiras Portugal -- *** PD Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz

Re: [ccp4bb] Pymol

. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fr...@uni-konstanz.de Tel. Office: +49-(0)7531 88 3205 Tel. Lab : +49-(0)7531 88 3687 Fax: +49-(0

Re: [ccp4bb] off topic

+1-410-955-3655 http://web.me.com/bosch_lab/ -- *** Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fr...@uni-konstanz.de Tel.: +49-(0)7531 88

Re: [ccp4bb] off topic

-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.me.com/bosch_lab/ -- *** Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.

Re: [ccp4bb] Zinc or Iron binding protein, that is a question!

Hi Xuan, I guess your protein is not an E.coli protein. There are several examples that eukaryotic Zn-proteins expressed in E.coli contain Fe instead of Zn. I am sceptic whether IMAC with different metal ions will give the solution of the problem. If you really want to get information on the m

Re: [ccp4bb] Zinc or Iron binding protein, that is a question!

- From: CCP4 bulletin board on behalf of Guenter Fritz Sent: Mon 8/6/2007 1:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [Junk Mail] Re: [ccp4bb] Zinc or Iron binding protein, that is a question! Hi Xuan, I guess your protein is not an E.coli protein. There are several examples that eukaryotic Zn

[ccp4bb]

.yahoo.com/ -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: guenter.fr...@uni-konstanz.de Phone Office: +49-(0)75

Re: [ccp4bb] Anomalous map creating

or advice. Thanks. Sergii P.S. Please, find attached mtz and logs. -- ******* Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz Universitaetsstrasse 10 Postfach M665 D

Re: [ccp4bb] Anomalous map creating

v 2009, at 09:24, Guenter Fritz wrote: Hi, I was looking recently for weak anomalous scatterers, when refined model is known. I used phaser as described here: http://www.phenix-online.org/pipermail/phenixbb/2008-July/001136.html or running phaser from the ccp4 gui "SAD with molecular repla

[ccp4bb] TLS refinement refmac

Dear all, one gets different R values, if you re-read in the mtz written out by refmac after TLS refinement. I think this issue had been a while ago in ccp4bb, but I can't find the right track. Here are the details. 1st run: If we do TLS + restr. refinement in refmac we get: InitialFina

Re: [ccp4bb] TLS refinement refmac

Am 17.07.2013 11:59, schrieb Guenter Fritz: Hi Stefan and Gottfried, thanks a lot for the answers. This is the point. Wouldn't it make more sense to add an extra column that contains the changed Fs? Best, Guenter Hi, it is strongly advised to use the original mtz e.g. scala.mtz a

[ccp4bb] Conserved water positions in low resolution refinement?

Dear all, and especially all of you involved in the development of refinement programs, in low resolution refinement we always include structural information we actually do not "see" in the electron density (side chains, riding hydrogens) since we know that these atoms are there. But what about

Re: [ccp4bb] RE : [ccp4bb] Conserved water positions in low resolution refinement?

letin board [CCP4BB@JISCMAIL.AC.UK] de la part de Guenter Fritz [guenter.fr...@uni-konstanz.de] Date d'envoi : samedi 2 novembre 2013 16:04 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Conserved water positions in low resolution refinement? Dear all, and especially all of you involved in the deve

Re: [ccp4bb] How to find the unfound part of a big protein

Dear Sun, I had a similar problem. If you have a good TaBr dataset this should give you good phases. You can combine the TaBr phases and Molrepl phases in SHARP. What worked in my hands very well and is easy to do: SAD using Phaser and the partial Mol Repl Model. You find here a input file f

Re: [ccp4bb] PyMol and Schrodinger

Hi, if one is hesitant to compile it it, pymol is easily installed on a Linux box via "yum" ; enable EPEL repo ( in Redhat derivatives e.g. fedora, Centos, SciLinux) "yum install pymol" will install version 1.6 (latest version by Schrödinger is 1.7) Best, Guenter Hi, I have inquired at Sc

Re: [ccp4bb] Acceptable range of CC1/2

Dear Deepali, the best way to define the resolution cut-off is to check whether the data still contribute to model quality. You can easily check that by the procedure called "paired refinement" as described by Diederichs and Karplus (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/  check

[ccp4bb] Refmac jelly body parameters

Dear Refmac developers, I am trying to reproduce some successful refmac runs but cannot get the previous results despite playing around with the parameters. I did those runs in Feb 2014 (Refmac 5.8.0049) but unfortunately have overwritten the log files in a backup. I still have the pdbs, mtz

Re: [ccp4bb] OT: Nvidia 3D vision 2 glasses with Ubuntu workstation

Dear Adarsh, just an add-on to the instructions of the others. Since GNOME is not anymore compatible with stereo, we use successfully Xubuntu (18.04) with NVIDIA drivers. Best , Guenter Hello everyone We have just purchased a Dell workstation for crystallography data analysis. We were tryin

[ccp4bb] different residues as alternate occupancy?

Dear all, I am refining a multimer and mass spec data of the sample indicate that there is a mixture of two variants which differ in one amino acid residue. The density that we see is therefore most likely an average of both variants. I have created a pdb file with "alternate residues" each w

Re: [ccp4bb] different residues as alternate occupancy?

arc-requ...@jiscmail.ac.uk <mailto:270165b9f4cf-dmarc-requ...@jiscmail.ac.uk>> wrote: A classic case of this is crambin. Residue 25 of 3nir. -James Holton MAD Scientist On 6/24/2019 1:00 AM, Guenter Fritz wrote: Dear all, I am refining a multimer and mass spec data of the sample i

Re: [ccp4bb] Glutathione detection

Dear Avinash, you can use Ellman's reagent (DTNB) for GSH. Have a look here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Thiols_and_disulfides For glutathione you don't have to use a buffer with GuHCl. HTH, Guenter Dear All, Greetings and apology for an off topic query. may requ

[ccp4bb] Aquarius2 ?

Dear colleagues, can somebody give me a hint, whether the program AQUARIUS2 or a similar / successor program is available somewhere? Thanks a lot in advance! Best regards, Guenter

Re: [ccp4bb] Aquarius2 ?

edu) was a replacement. Regards, Tim On 11/07/2014 06:47 PM, Guenter Fritz wrote: Dear colleagues, can somebody give me a hint, whether the program AQUARIUS2 or a similar / successor program is available somewhere? Thanks a lot in advance! Best regards, Guenter

Re: [ccp4bb] Presence of Fe3+ or Fe2+

Hi Monica, what is the reducing agent the protein gets the electron from? Or is it simply unspecific oxidation of protein side chains? Do you know what are the coordinating residues of Fe3+ / Fe2+ ? Dependent on the coordination Fe3+ has some (often very weak) d-d transitions (400-500 nm) whic

[ccp4bb] Configuring updates through a firewall

Hi, I am using CCP4 on Sci Linux machines and running now into some trouble with update manager and our firewall. I connect through a proxy and defined the proxy in the ccp4-setup.sh. Running update-manager gives me an error message; a new window pops up telling me "Downloaded data is corrupt,

Re: [ccp4bb] Off-topic - Crystallisation in anaerobic glove box

Hi Stephen, we crystallized several proteins in a glove box placed in a room with air condition. We checked the temperature all the times and found that is had been quite stable. For one protein that crystallized only at 4 deg C, we setup the crystallization plate within the glove box and pu

[ccp4bb] generating and applying transformation matrix

Dear all, I want to have a closer look at a conformational change in a multidomain protein. We see clear changes from different structures but there is evidence that the conformational changes might be larger than observed. My idea is to get the transformation matrix of each residue (or of each

Re: [ccp4bb] Interesting DNA contamination

Dear Stefan, just saw this after reading post: http://www.nature.com/nature/journal/v522/n7557/full/nature14559.html Best, Guenter Pramod, You already got good suggestions on how to handle DNA contamination in protein preparations. Let me point out briefly that you haven't demonstrated yet tha

Re: [ccp4bb] Disulphide bonds and closed conformation

Hi Jan, you will find some methods for detection of thiols and/or disulfides there: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Thiols_and_disulfides HTH, Guenter Dear all, I am working on a protein where I have to stabilize the closed conformation of the protein using disulp

[ccp4bb] EDSTATS

Dear all, dear Ian, I am trying to run edstats from command line. I have read the previous threads here and I was using the edstats.pl perl script. However I fail. Here is what I type and what I get (same on a centos machine and my mac). $ edstats.pl -hklin paefs_018_dimple_refmac.mtz -pdbin

[ccp4bb] software DS, fconv still available ? contact?

Dear all, does somebody know whom to contact for the software  DSX or fconv of the former group Klebe in Marburg? Many thanks and best regards, Guenter To unsubscribe from the CCP4BB list, click the following link: htt

Re: [ccp4bb] software DS, fconv still available ? contact?

, Manfred Am 14.09.2021 um 14:36 schrieb Guenter Fritz: Dear all, does somebody know whom to contact for the software  DSX or fconv of the former group Klebe in Marburg? Many thanks and best regards, Guenter To unsubscribe

[ccp4bb] update 7.1.016, very poor pyrogen restraints

Dear all, with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision 10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing. I get restraints from the latest version of pyrogen, which do not work in refmac. I added a s

Re: [ccp4bb] update 7.1.016, very poor pyrogen restraints

, Guenter Fritz wrote: Dear all, with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision 10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing. Yes, it's the default now (i.e. without mogul). I get restraints fro

[ccp4bb] freezing in ethane / propane - unipucks ?

Dear all, we have some  delicate crystals which might benefit from freezing in propane. In former times (when I was still travelling to the beamlines) we waited until the propane was solid in the vial and then let the propane thaw in the cryo stream at the beamline. But how can we  do this i

Re: [ccp4bb] freezing in ethane / propane - unipucks ?

/product/combipuck-system/) and some arrangements with your local contact at the other end, perhaps help with using propane remotely? BW, D On 26/01/2022 16:53, Guenter Fritz wrote: Dear all, we have some  delicate crystals which might benefit from freezing in propane. In former times (when I

Re: [ccp4bb] freezing in ethane / propane - unipucks ?

1/26/2022 9:25 AM, Guenter Fritz wrote: Dear Dom, thanks a lot. Yes, this might work sending a combipuck alongside with a good bottle for the local contact. I was wondering whether the grippers can handle a block of propane? Best wishes, guenter Dear Guenter, Would the use of vials inside

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

that hard to build: https://doi.org/10.1107/S0021889894006357 Cheers, -James Holton MAD Scientist On 1/26/2022 9:25 AM, Guenter Fritz wrote: Dear Dom, thanks a lot. Yes, this might work sending a combipuck alongside with a good bottle for the local contact. I was wondering whether the gripper

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] freezing in ethane / propane - unipucks ?

for handling as usual? If you don't have a working N2 gas stream and are on a budget they are not that hard to build: https://doi.org/10.1107/S0021889894006357 Cheers, -James Holton MAD Scientist On 1/26/2022 9:25 AM, Guenter Fritz wrote: Dear Dom, thanks a lot. Yes, this might

Re: [ccp4bb] Se-Met and Se-Cys double labelling

Dear Vito, for SeMet have a look here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Expression_of_SeMet_labeled_proteins Worked like a charm for E.coli and also for other expression hosts with minor modifications (https://www.nature.com/nature/journal/v516/n7529/full/nature14003

[ccp4bb] Postdoctoral position available

should be send to guenter.fr...@uni-hohenheim.de. Please contact me for any further information. Best regards, Guenter Fritz

Re: [ccp4bb] Structure prediction - waiting to happen

Dear all, taking AlphaFold models for " true" experimental structures seems to become a serious problem. I am just returning from a meeting (not a structural biology meeting) and saw one model after other. And the non-structural biologist used terms like "we calculated a structure"  or "a Alph

[ccp4bb] dryshipper, MVE vs. CX100?

Dear all, we  have to "update" our dryshippers. There are two models we are consifering:  the CX100 from Tayler Wharton or the MVE SC4/2. Has anybody experience with the dryshipper from MVE? Thanks a lot in adavance for any insights! Best wishes, Guenter

Re: [ccp4bb] Co-Crystallization with drug molecule

Hi Amit, like Artem wrote below, even despite poor solubility, soaks with dried compounds work well (also in our hands). We adapted it from the work of T. Barthel, J. Wollenhaupt and Manfred Weiss. Also colleagues from industry report good results. We add compound dissolved in DMSO to the crysta

Re: [ccp4bb] Co-Crystallization with drug molecule

n" in the following paper: http://dx.doi.org/10.1107/S1399004715010342 Best wishes, Gerard -- On Fri, Oct 04, 2024 at 05:40:12PM +0200, Guenter Fritz wrote: Hi Amit, like Artem wrote below, even despite poor solubility, soaks with dried compounds work well (also in our

[ccp4bb] acedrg error in gui, command line only cif no pdb output

Dear all, I have a strange acedrg error. I usually run via command line for a set of smiles. If I run it from command line, the job runs, but acedrg writes only a cif and not a pdb anymore. If I run acedrg from the gui (ccp4i old gui) I get for any input (smiles or cif) an error: ..

[ccp4bb] ps, acedrg error in gui, command line only cif no pdb output

just checked across platforms (Windows, OSX, Linux). acedrg version 293 gives this error. acedrg version 277 (last in ccp4 8.0) works fine. Best, Guenter Dear all, I have a strange acedrg error. I usually run via command line for a set of smiles. If I run it from command line, the job run