Re: [ccp4bb] MR for coiled coil structure

Dear All, Thank you very much for your valued suggestions. I am trying them out and will let you know how they work ASAP. If successful I will write a summary and post to ccp4bb. Best, Shengyang From: Conners, Becky [mailto:r.conn...@exeter.ac.uk] Sent: 10 July 2019 16:29 To: Shengyang Jin

[ccp4bb] Two postdoctoral positions at the Walter and Eliza Hall Institute, Melbourne

Dear colleagues, We are seeking two talented and enthusiastic postdocs to join teams within the Inflammation Division of the Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia: one focused on structural biology+cell biology; and another postdoc to study protein-protein

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Hi Lumbini, There are couple of queries I have before commenting on this issue. 1) how many Cysteine residues are there in your protein 2) have you calculated their solvent accessible surface area ? 3) What is the final concentration of Sodium dithionite ? Cysteine is highly prone to get

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Hi Jakob, If there is radiation damage, for every "new" positive density there should be a negative density in the original position. From the pictures we've seen, it seems unlikely. Best, Nukri On Wed, Jul 10, 2019 at 10:21 AM Keller, Jacob wrote: > How about radiation-damaged/smashed Sulphur?

Re: [ccp4bb] Fo-Fc density close to cysteine residue

How about radiation-damaged/smashed Sulphur? You could test this by refining occupancy of the cys S. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Dear Lumbini, Certainly not a proof but your density looks like (di)methyl-arsinoyl-cysteine (PDB residue type CAF). This modification can happen when the protein has been exposed to cacodylate buffer. You can find such residues (and maps) in the PDB entries 3LPT or 5MDI. Best wishes,

Re: [ccp4bb] Error in data reduction!

I think Helen’s answer is absolutely right. I asked Phil Evans about this when I saw him yesterday, and he said that error usually arises when it is not possible to write the xml file, either because a disk is full, or because you do not have permission to write to that area. Andrew > On 3

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Thank you for the valuable input On Wed, Jul 10, 2019 at 4:25 PM Eleanor Dodson wrote: > Well - that more or less proves the residue is a CYS - there is a peak in > the PHAN map right on the S. > And that the extra density does not contain an anomalous scatterer so is > probably not a metal or

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Well - that more or less proves the residue is a CYS - there is a peak in the PHAN map right on the S. And that the extra density does not contain an anomalous scatterer so is probably not a metal or a sulphate or... But that still doesnt explain WHAT it is . Sorry not to be more help.. Eleanor

Re: [ccp4bb] Fo-Fc density close to cysteine residue

No I am using ccp4i. I tried doing SAD refinement in refmac and the output image is attached below . I do not seen density near cysteine that was visible in Fo-Fc map On Wed, Jul 10, 2019 at 3:40 PM Eleanor Dodson wrote: > The key word for refmac is ANOM MAPONLY > Are you using GUI2? > Eleanor

Re: [ccp4bb] Fo-Fc density close to cysteine residue

The key word for refmac is ANOM MAPONLY Are you using GUI2? Eleanor On Wed, 10 Jul 2019 at 09:32, Lumbini Yadav wrote: > I have soaked my crystals in sodium dithionite a reducing agent. I have > not done mass spec but sequence is confirmed > > On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel >

Re: [ccp4bb] Error in Aimless task!

Hello Mike, This is just a guess. From the error message it seems that it’s trying to write to the root directory of your filesystem. I am assuming you are using the old ccp4i interface. It might be because the ccp4i project directory you’re running it under has been set to / or is empty. If

[ccp4bb] PostDoc Position at the Wohl Institute of King’s College London

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[ccp4bb] Research Fellow Position in Singapore

We are seeking an enthusiastic and self-motivated postdoctoral research fellow to study proteins involved in maintaining genome stability and the Hippo signaling pathway. We take a combinatorial approach of molecular biology, biochemical and biophysical methods, and structural biology

Re: [ccp4bb] MR for coiled coil structure

Dear Mark and Shengyang, indeed, as Mark pointed out, we have a special mode in ARCIMBOLDO_LITE devised to tackle coiled-coil structures. Trough the ccp4i interface this will be available as an option you can tick when running an ARCIMBOLDO_LITE job. A tutorial is available on our website (

Re: [ccp4bb] MR for coiled coil structure

This sounds like a case for the Arcimboldo program developed by the Uson group (http://chango.ibmb.csic.es/ ), of which three versions are in CCP4 (Borges, Lite and Shredder). This will use short secondary structure elements in a mixed MR/ab initio approach. We

[ccp4bb] Problems in installing XDSapp in macOS Moiave 10.14.5

Dear all, I am using OS Moiave 10.14.15, and after installing XDS I would need also XDSAPP. Did anyone successfully installed XDSAPP on Moiave? Following the installation instructions, I faced some problems with linkapps and with the installation of pyqwt. Do you have any suggestions on how to

Re: [ccp4bb] MR for coiled coil structure

Dear Shengyang We'll be happy to help you sort this out. I suggest we discuss it between the two of us and then post a summary to the bulletin board. Could you please tell me, privately not to the board, which gui you are using, which version of CCP4 and which options you are trying to

Re: [ccp4bb] Fo-Fc density close to cysteine residue

I have soaked my crystals in sodium dithionite a reducing agent. I have not done mass spec but sequence is confirmed On Tue, Jul 9, 2019 at 9:26 PM Bonsor, Daniel wrote: > Have you mass-speced the protein before crystallization to make sure it > wasn’t derivatized during expression and/or

[ccp4bb] MR for coiled coil structure

Dear all, We recently acquired a data set (2.0 A, P222) for a coiled coil protein (according to Itasser, QUARK, Robetta, and Phaser). Matthews coefficient indicates 1 copy of protein per ASU. Sequence of the protein is quite novel with no apparent homolog in PDB. We tried to to MR with various

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Lumbini, 2.5A is close to the coordination bond length of sulfur-metal. Did you use IMAC during purification? ср, 10 июл. 2019 г. в 08:44, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>: > I am serious about checking the anomalous map!! > (trivial from REFMAC - key word anom

Re: [ccp4bb] Fo-Fc density close to cysteine residue

I am serious about checking the anomalous map!! (trivial from REFMAC - key word anom map on) Then do a peak search and just check first that the rogue residue IS CYS first - you should see the S as a peak..) Eleanor On Wed, 10 Jul 2019 at 07:38, Lumbini Yadav wrote: > Thanks for the reply. >

Re: [ccp4bb] Fo-Fc density close to cysteine residue

Thanks for the reply. The distance between sulphur and centre of Fo-Fc map is around 2.5A. The density does not appear to be of hydrogen (attached image) anisotropy refinement also does not help. On Tue, Jul 9, 2019 at 5:13 PM Anthony Addlagatta wrote: > Lumbini, > > It would useful to know