Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi Folks, Re: docs for elderly programs cd $CBIN/html In here you will find the ccp4 program docs probably going back ~ 20+ years for the old programs - for _your_ version of ccp4 It’s probably got greater coverage on the old command line stuff than the newfangled i2 things Cheers Graeme (wh

Re: [ccp4bb] Domain Motion Analysis

Hello Tony, I think CueMol gives you the screw rotation and translation when you fit domains. Jon CooperOn 8 Jul 2020 18:53, Eleanor Dodson <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:Well - I use standard software.Use GESANT or some such program to fit Structure 2 A to Structure ! A only

Re: [ccp4bb] Looking for suggestions with protein expression

Hello Umar, I would not pin down your difficulties solely due to an Fe-S proteins. I have produced some with no fusion partners and they work wonderfully. They were expressed in an aerobic environment and then reduced in an anaerobic one before usage in reactions. 1) On the Fe-S side, there ar

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Hi, Just in case nobody has pointed this out yet (which I doubt) "google ccp4 documentaion" or just "doc" will give you several lists+docs  of current and old ccp4 programs, included and absent from ccp4i2. Cheers, Boaz Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion Unive

Re: [ccp4bb] Accessing full list of programs in CCP4I2

I didn’t expect it to be so lively! I completely understand the reasons why there are changes, it looks quite good and I think it benefits new users greatly. Its just for us “old-fashioned” folk it just becomes a bit tedious to find out where the programs are now, as long as they are there! Ho

Re: [ccp4bb] Domain Motion Analysis

Well - I use standard software. Use GESANT or some such program to fit Structure 2 A to Structure ! A only - output wilh have all A B C but only A has been fitted// Now fit Structure 2 B from fitted structure to Structur 1 B . It will give you a PHI CHI Kappa needed to rotate B2 to B1 Is that clear

Re: [ccp4bb] AcTEV protease

AcTEV protease is a TEV protease catalytic domain with a stabilizing mutation. There is a patent on the mutation, although most people ignore the patent. We have TurboTEV (http://accelagen.com/TurboTEV.htm) which is not stabilized by the patented mutations. It costs a fraction of the price of

Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

Exactly, on point David. All programs are still there and accessible, but maybe not actively supported or developed. Similar to Moleman I used from time to time. However they are not in the interface list (i2) because they are not with an interface and therefore cannot be used in that way. But th

[ccp4bb] Time-Resolved Structural Biology workshop

*Time Resolved Structural Biology – Seeing the structure of motions* The workshop in Time Resolved Structural Biology organized by LINXS and originally planned for this spring will be held in Lund, S

[ccp4bb] AcTEV protease

Another protein purification question: Does anyone know what is AcTEV protease that is sold by Thermofisher Scientific? Is this the same as SuperTEV? It works well but is so expensive. Thanks for any advice, Gloria To unsu

Re: [ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

Hi all, Please be reassured that there are no plans at the moment to remove programs from CCP4, at least none of which I am aware. The newer GUIs might not provide interfaces to run all of these programs, but they are still there to run from the command line. There is currently no good reason to r

Re: [ccp4bb] Commercial source of His-tagged protein

Dear All, many thanks to you all for your suggestions and help! I learned about some interesting small companies producing proteins and had other useful suggestions, some already shared with the list. Another example of the wonderful CCP4bb community. In the end it looks like we will go for His

[ccp4bb] AW: [ccp4bb] Accessing full list of programs in CCP4I2

I fully agree, I have some old scripts I infrequently use. Making these programs inaccessible would break these scripts, forcing me to reinvent a couple of wheels. My 2 cnts worth of junk to your mailbox, Herman Von: CCP4 bulletin board Im Auftrag von Oganesyan, Vaheh Gesendet: Mittwoch, 8. Ju

Re: [ccp4bb] Accessing full list of programs in CCP4I2

Thank you for explanation. There are many small programs in CCP4 that have not been updated for years and they still work despite being in unsupported folder. By making them inaccessible (or more difficult to access) nobody gets easier/cheaper life. Even if there are newer programs that may do t

Re: [ccp4bb] adding external planar restraint in refmac5

On 08/07/2020 12:39, Laurent wrote: I am currently refinining an enzyme structure obtained in the presence of a substrate analog : the catalytic serine is acylated and form an ester bond with the ligand. I have added a LINK record in the PDB file to specify the newly created covalent bond b

[ccp4bb] adding external planar restraint in refmac5

Dear CCP4 users, I am currently refinining an enzyme structure obtained in the presence of a substrate analog : the catalytic serine is acylated and form an ester bond with the ligand. I have added a LINK record in the PDB file to specify the newly created covalent bond between OG atom of Serin

Re: [ccp4bb] Twin law definition in REFMAC5

Dear Petr Both questions, on twin law and R-factors, are mainly questions about definitions and standards. From Online Dictionary of Crystallography: "The twin law is the SET of twin operations mapping two individuals of a twin." In your P 21 21 21 example with a=b, the set contains four oper

[ccp4bb] PhD position (or Research Associate) opportunity

Posted on behalf of Dr. Xinlai Cheng In the Department of Biochemistry, Chemistry and Pharmacy - Institute of Pharmaceutical Chemistry in the field of Medicinal Chemistry - Dr. Xinlai Cheng offers a position starting instantly of a PhD-Student/ Research Associate (E13 TV-G-U, 50 % part-time).

[ccp4bb] Postdoctoral position in Structural Biology, Cambridge UK

Dear CCP4 community, I am looking to hire a Postdoctoral Scientist to join our team at the Cambridge Institute for Medical Research (UK) studying molecular mechanisms driving neurodegenerative disease. If you are a biochemist/structural biologist with experience in protein crystallography and/or c

Re: [ccp4bb] Accessing full list of programs in CCP4I2

As a longtime user few comments. I have also started with writing scripts and have seen a couple of changes in ccp4. Each time I briefly think "do I have to learn another script, gui, ...?" but I get used to it and appreciate it, once I can see the new rationale. Some older procedure are still usef