Re: [ccp4bb] sugestions on weak diffracting protein crystals

Hi Deepak, If this is a metalloprotein, include higher concentration of the metal in the crystallization drop. It may act as a glue in the interfaces and give you a good crystal. Jackie Vitali Cleveland State University On Tue, May 18, 2021 at 6:20 AM Deepak Deepak wrote: > Dear all, > > I

Re: [ccp4bb] Anisotropic Scaling

There is an anisotropy server from ucla that I think you can use over the internet, Just google it and try it to see if it helps with your data. I think the data is better afterwards, Jackie Vitali Cleveland State University On Sat, Jan 13, 2018 at 5:53 AM, Zhang Foggy

Re: [ccp4bb] Modeling protein tertiary structure

The easiest is modeller via chimera. You can use I-TASSER server but it decides for itself what to do... You have some control too. You can use the sec structure from itasser and then go to modeller in chimera You can use modeller in the interfaces it provides in the web (mod web ...) or

Re: [ccp4bb] Model parts rearrangement

coot, lsq command i have not checked chimera but it may have too. (I think so) For coot. I used it recently for a small molecule. And pymol Finally the superpose server may do it. On Jul 8, 2015, at 3:41 PM, Bernhard Rupp (Hofkristallrat a.D.) hofkristall...@gmail.com wrote: Hi Fellows,

[ccp4bb] what happens when freezer goes down

Dear colleagues, I know this is not related to ccp4 but I am in need of an answer and many of you work with cells etc. My building had a major malfunction of electricity and the power backup did not kick in. My -80C freezer was without power for over 24 hours until I found out. Because it is

Re: [ccp4bb] I/sigmaI or I/sigmaI

Phil Jeffrey has a small program to calculate avg. I/sig for Table 1 including for resolution ranges. Jackie Vitali On Wed, Feb 12, 2014 at 11:20 AM, Ronald E Stenkamp stenk...@u.washington.edu wrote: How did people get I/sigmI when using HKL2000? Ron On Wed, 12 Feb 2014, Phil Evans

Re: [ccp4bb] structural homologs as cross seeds

I do not have experience with this but it is worth trying. On Fri, Dec 27, 2013 at 2:29 PM, Mahesh Lingaraju mxl1...@psu.edu wrote: Dear all, I was wondering if it sounds logical to use the crystals from a possible structural homolog as seeds to induce nucleation ? (in terms of overall

Re: [ccp4bb] Align linux version

Mintu Chandra, align is gerson cohen's program. Unless you talk about another align. I googled align for linux Gerson Cohen and here is what I found -- the linux version http://software.compbio.washington.edu/ramp/ramp/src/other_source/align.save.f Test it and see if it works. If not, there

[ccp4bb] use only companies that you know to purchase chemicals

Dear all, I used the guidechem chemical network to obtain a compound that is not sold in US. Many people responded and I was persuaded to try to buy it from SHANGHAI JIEKE BIOTECHNOLOGY LIMITED COMPANY Adress：NO.1008 Qigangroad,FengXianZone,ShangHai,China Tel ：+86-031-97265503 Fax

[ccp4bb] question about arginine sepharose 4B

Dear all, Arginine sepharose 4B is an affinity column. If you have used it please let me know where you purchased it. GE Lifesciences used to sell it but discontinued it. I found it in China in the site http://www.pharmaceutical-sales.net and I corresponded with their sales representative

[ccp4bb] Fwd: request for reprint

Dear Colleagues, Does anyone have access to this article? It is not in my library and they cannot find it via interlibrary loan. I know the limitations and that it is best not to ask papers via the newsgroup but I have even tried to ask the author for a reprint and my email was returned to me.

Re: [ccp4bb] offtopic: AKTA prime

Yes, it has happened to me more than once. It is not a good pump. Acta Prime Plus has a better one. They still have parts. Call GE technical support and they will tell you what to do. The part costs some money (it is not cheap - probably $500). I think the Akta Prime will keep on running as

Re: [ccp4bb] Monomers in COOT

try file search monomer library. Hit search without typing anything. It will give you what it has. Jackie Vitali 2011/10/12 Dr. STEPHEN SIN-YIN, CHUI chui...@hkucc.hku.hk Dear All, For all monomers (3 letter) used in COOT, where can i find the full names of the whole library? Many thanks

[ccp4bb] Linux vs MacOS for crystallographic software

Dear colleagues, I need some advice for a new computer. (1) I have the option of an HP Z210 8 GB with a low end Quadro Nvidia 400 512 MB. --How does Coot run with this card? --I am happy with any Linux. However, the system needs updates for security purposes (the University requires it). Do

[ccp4bb] glycerol on three-fold axis

Dear colleagues, Has anyone seen glycerol on a three-fold axis? THis is possible as the glycerol can be disordered but I want to know if there is an actual case. Any information would be greatly appreciated. Jackie Vitali

[ccp4bb] cryosleeves with ID 22 mm

Dear colleagues, I needed cryo -sleeves 22 mm ID so that I could put standard epitubes in cryo canes and protect them. The epitubes do not hold as good as the cryo vials in the cryo canes. All commercially available cryo sleeves are 16 mm ID and are made for cryo vials. Some of us put cultures

Re: [ccp4bb] Off topic question. NACCESS

I think one of the options of PISA is to calculate accessibilities -- I recall when I was learning how to use pisa that I saw this option. Also DSSP outputs accessibilities per residue Areaimol in ccp4 does too. I have seen many programs in the internet, google accessibilities, accessible

Re: [ccp4bb] diverging Rcryst and Rfree

Hi, I have seen this happening when I had NCS and did not include it in refinement. Rwork drops and Rfree increases. In this case the difference became small when I included the NCS. Also if your Rmerge is high and you include all reflections in refinement, Rfree is high. In my experience, by

Re: [ccp4bb] molecule on symmetry axis

Dear colleagues, Thank you for your suggestions. I was able to do the refinement of the sulfates and tartaric acid in phenix by changing the occupancies to 0.33 and 0.5, It appears to me (from the log file and from graphics afterwards) that the program automatically turns off the interaction

[ccp4bb] molecule on symmetry axis

Dear colleagues, I have a tartaric acid on a two fold axis with its two halves related by the two fold. How do I refine this in Phenix? Also I have a SO4 on a 3 fold with S and one O on tthe 3 fold. The other 3 oxygens are related by the 3-fold. How do I refine this in phenix? I can put S

[ccp4bb] question on the effect of a fire alarm on crystallization

Dear all, Does anyone know the effect of a fire alarm placed in the same room where one grows crystals? (1) On trays placed inside styrofoam boxes (2) On trays placed inside an incubator which has not been tested as vibration free. Thank you. Jackie Vitali

[ccp4bb] effect of high mosaicity on atomic coordinates

Dear all, I have a high mosaic spread for a structure (1.2 deg). It refines well to low R values. The temp factors become very high in this structure. I assume the reason is the high mosaicity. Are the coordinates also affected by high mosaicity? I would appreciate any input. Thanks.

[ccp4bb] question on Akta Prime

Dear colleagues, I have an Akta Prime. I have always had problem with the reproducibility of the peak heights of the various peaks. Recently the pump is breaking. Does anyone have an idea what can cause the pump to break? It is more than once. Jackie Vitali

[ccp4bb] MSCAN or DSCAN

Dear colleagues, Does anyone have a copy of the old program DSCAN or MSCAN by S.T. Rao? It calculates torsion angles in small molecules. Alternatively, does anyone have a program to calculate torsion angles and their ESD's for small molecules? Thanks. Jackie Vitali

[ccp4bb] cuvette for dynapro 99-CP

Dear colleagues, I am trying to find a cuvette for Dynapro 99-CP. Wyatt does not seem to have these cuvettes. If anyone knows where I can get one please let me know. Thanks. Jackie Vitali

Re: [ccp4bb] about anisotrophic diffraction

Look at the paper (search in pubmed) by B. M. Schick and F. Jurnak on cryoprotection of TuTs. He changes the reservoir in 24 steps using a 24 well cryschem plate. There are some references there that are important too. Jackie Vitali On Mon, Jun 23, 2008 at 8:14 PM, Ji lee [EMAIL PROTECTED]

[ccp4bb] dissolving L-alanosine

Dear colleagues: I added a few lamdas of NaOH and dissolved it. Thank you all for the responses. Jackie Vitali