Re: [ccp4bb] AlphaFold3

Hi Jon, I use AF3 quite often to look at domain boundaries by sequence but not necessarily by their spatial arrangement. This is because protein-protein interactions at least in all cases I’ve tried were not predicted correctly. I have number of Fab-Antigen complexes solved using x-ray crystall

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Yes, it is and I like the definition of shared “trash bin”. It will have more physical meaning if we can separate those contributions into separate bins. Vaheh From: Pavel Afonine Sent: Tuesday, July 30, 2024 1:51 PM To: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

. Vaheh Oganesyan, Ph.D. [cid:image001.png@01DAE281.A8E8D260] R&D | Biologics Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> From: Pavel Afonine Sent: Tuesday, July 30, 2024 11:45 AM To: Oganesyan,

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Early in my Crystallography life I was postdoc with Robert Huber in Munich. We had those gatherings once a week when in very informal way we can ask and answer questions. I remember my question about B factors: how is it possible to have high resolution structure and average B-factor of 100A2. I

Re: [ccp4bb] Difficult Molecular replacement

t; wrote: > > Hi Vaheh, > > for this purpose, I use > > pointless hklin refmacXY.mtz < labin F=FC > eof > > Thus, pointless determines the space group, including the crystallographic > screw axes, from the Fcalc. > > Best wishes, > Kay > > On Wed, 21 Fe

Re: [ccp4bb] Difficult Molecular replacement

Hi All, Interesting discussion as I have a similar case. In my case molecular replacement solution can be found easily in P21, P212121, with very similar looking electron densities. However, R-factors remain relatively high (mid 30s). In P1 completeness suffers (75% completeness), maps look dec

Re: [ccp4bb] Crystallizing a tough target

For what it is worth, human serum albumin has been crystallized initially from 250 mg/ml solution back in ‘90s. When I started working on ternary complex hSA-FcRn-Fc (PDB Id 4N0U) was afraid that such high concentration couldn’t be achieved with amounts of FcRn I can reasonably express. However,

Re: [ccp4bb] Error in "Prepare and validate files for deposition" task"

Nick, What files do you mean when call them CCP4 formatted? Coordinates are accepted only in mmCIF. Experimental data in mtz. What else? Thank you. Vaheh From: CCP4 bulletin board On Behalf Of Nicholas Clark Sent: Wednesday, January 31, 2024 3:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp

Re: [ccp4bb] What could these crystals be?

Run SEC on complex prior to crystallization to remove single entities, provided size difference makes sense. Not too many column options though. Vaheh From: CCP4 bulletin board On Behalf Of careinaedgo...@yahoo.com Sent: Friday, November 24, 2023 4:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] Fragile Crystals

Hi Morgan Elizabeth, In some cases adding 1-2% of cryoprotectant into crystallization drop during setting those drops up helps to introduce 25-30% of the same cryoprotectant during harvest, provided you still can get those crystals to grow. Worked for me in several cases. Vaheh From: CCP4 bul

Re: [ccp4bb] RES: [ccp4bb] About model building

You may as well have fun by manually building your molecule B into 1.9A ed map when R-factors are already in mid 30s. Vaheh From: CCP4 bulletin board On Behalf Of Sam Tang Sent: Monday, November 6, 2023 2:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] RES: [ccp4bb] About model building

Re: [ccp4bb] How to fix ARG planarity outliers?

Whatever it is worth, I agree with Dale. I see those "Major validation issues" all the time. Some structures at medium resolution (2-3A), and some are at high (1.1-1.4A). Not all Arg residues are "in violation". At low and medium resolution cases it is hard to argue. But high resolution electron

Re: [ccp4bb] Ligand superposition!

Hi Rams, Given the ligand is identical in all structures I'd create and object from just the ligand and then write a script to align all 50 structures with that ligand object. I've done that on number of cases. Hope it works in your case as well. Vaheh From: CCP4 bulletin board On Behalf Of

Re: [ccp4bb] To Trim or Not to To Trim

Hi Ben, All copies created by multiplying cell dimensions will act exactly same as the original one, mathematically exactly. Nick’s approach is better. Something similar to what Nick said was published around 2002-2003. I was reviewing it. I did not understand then what the author was trying to

Re: [ccp4bb] off-topic: experience BioRad NGC vs Aekta Pure

Hi Stephan, You’re mostly correct, however, gradients made on instrument with one pump are less reliable. Thank you. Vaheh From: CCP4 bulletin board On Behalf Of Stephan Rempel Sent: Friday, September 16, 2022 7:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] off-topic: experience BioRa

Re: [ccp4bb] Coot sporadically crashes

Thank you, Paul! From: CCP4 bulletin board On Behalf Of Paul Emsley Sent: Friday, July 8, 2022 11:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot sporadically crashes Is there an option to save the session automatically every 10-15 minutes or so? And now to actually answer you

[ccp4bb] Coot sporadically crashes

Hi All, Sorry for posting on CCP4BB. Coot installed together with latest CCP4 on Win10 crashes time to time with no messages/warnings. Is there an option to save the session automatically every 10-15 minutes or so? Thank you. Vaheh

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

So does PISA with great detailed info on interface residues available. VO From: CCP4 bulletin board On Behalf Of Jan Dohnalek Sent: Tuesday, May 31, 2022 2:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i Dear Fred, C

Re: [ccp4bb] ligand binds to one molecule

Well, there is almost nothing left to suggest, but one. Try co-crystallizing. While in solution molecules will have more flexibility to adopt a conformation that fits ligand bound state better. When soaking there might be restrictions on conformational changes needed for better binding due to al

Re: [ccp4bb] Glutaraldehyde and gel filtration

It would probably be safe if you run dialysis first. If you still think that may harm the expensive SEC column then running PD-10 column first would be advised. Hope this helps. Vaheh Oganesyan, Ph.D. [cid:image001.png@01D80EB0.8E5CA9A0] R&D | Biologics Engineering One Medimmune Way, Gaithersbur

Re: [ccp4bb] renaming chains

Dear John Helliwell, I should have been more clear in addressing my email. It was in response to John Berrisford’s answer. Regards, Vaheh From: John R Helliwell Sent: Monday, November 1, 2021 3:13 PM To: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] renaming chains Dear

Re: [ccp4bb] renaming chains

isford Sent: Monday, November 1, 2021 12:53 PM To: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] renaming chains Dear Vaheh Usually we do not rename chains as part of the curation procedure. There are instances when we do, for example when a chain has to be split into two ch

[ccp4bb] renaming chains

Hi All, This question is mostly for RCSB and PDBe: why are you renaming chains in the deposited PDB files? Why does it matter what letter is assigned to the chain? For 1,2 or 3 chain structures it is manageable, but for more chains and/or many complexes per asu this becomes quite a challenge. A

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

How P3221 can be an option if it assumes chain on axis? I guess I'm missing something, but per my belief only those sg will be possible for which there is no axis going through the extra molecule. P1 sg looks the only correct option here in my humble opinion. Democracy (voting) depends on scienc

Re: [ccp4bb] sugestions on weak diffracting protein crystals

Herman's suggestion is very good. But I'd go one step further and try to grow crystals in 30-40% PEG400. Then you definitely do not need any additional cryoprotectant. There is a chance that your crystals are of poor quality to start with. In that case no cryoprotection will help. You can test

Re: [ccp4bb] metal coordination at low resolution - restraints

Hi Jan, They hold nice because of high occupancy or because you have very high resolution and no restraints are necessary at all (even for protein part)? Thank you Vaheh From: CCP4 bulletin board On Behalf Of Jan Dohnalek Sent: Tuesday, September 8, 2020 8:01 AM To: CCP4BB@JISCMAIL.AC.UK Subj

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

book when new one is coming out. And I’m not a hoarder, do not have OCD or ADHD. This is already 4 cents together. Sorry to clutter your mailbox. Vaheh (CCP4 user since 1992) From: Christian Roth Sent: Tuesday, July 7, 2020 12:42 PM To: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re

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

… and how all these changes being justified? From: CCP4 bulletin board On Behalf Of Eleanor Dodson Sent: Tuesday, July 7, 2020 12:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Accessing full list of programs in CCP4I2 Yes - there are things I use all the time which are not part of the CC

Re: [ccp4bb] Flexible C terminus

Hi Chitra Latka, By far the best approach is to find what protein is interacting with the one you have the structure and try co-crystallizing them together. At least there will be some more biology (science) involved in what you will be doing. You may get lucky and get different packing of your

Re: [ccp4bb] nVidia 3D Vision2 glasses

Colleagues, While on stereo issues here is problem I’m trying to resolve with community help: my hardware includes nVidia quadro FX1400, Xpand emiter and NewVision glasses. Driver taken from nVIDIA site specifically for Quadro FX 1400, long lived. On old Linux station these worked together fine

[ccp4bb] RAID array

Hello ccp4-ers, A bit off topic (actually a lot off topic) question regarding RAID array system. On linux box one of two hard drives failed. I've found identical one and replaced it. Can someone point me in the direction where I can get instructions on what to do next to be able to login? Curre

[ccp4bb] "O" executables

Hello Colleagues, A bit off topic, but could someone point me in the direction of Alwyn’s executables for “O”? It doesn’t reside at xray.bmc.uu.se anymore. Regards, Vaheh Oganesyan, Ph.D. Scientist, Biologic Therapeutics Astra

Re: [ccp4bb] Another difficult MR case

Hi Napo, Just in case nobody suggested this option I want to add it. Very recently I’ve solved structure of Fab with 8 molecules per au. It wasn’t easy to do because some of tNCS were dropped by programs. After contacting the developer of MolRep Alexey Vagin and asking him to help understand wh

Re: [ccp4bb] image

Try seeding at lower concentration. From: CCP4 bulletin board On Behalf Of zhangyi19950109 Sent: Friday, March 22, 2019 1:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] image Dear all, A single plus-stranded RNA virus RDRP monomer grows crystals, precipitants (PEG8000) with low concentration

[ccp4bb] R&D Associate II or Associate Scientist I - Protein Engineering

Posting on behalf of colleague (please, do not reply to me): · o § US - Gaithersburg - MD · Apply · Apply with LinkedIn

Re: [ccp4bb] suggestions for cryoprotectant

Firdous, Many crystallographers (if not all) went through case like you describe. So far you’ve got great suggestions that are worth trying. I’ll add one more from my own experience. In all cases I tried it appeared that addition of 0.5 to 1% v/v of glycerol or ethylene glycol to drop (either h

Re: [ccp4bb] Sulphate or phosphate?

Not very elegant way of doing what you want but as a last resort I used distance criteria. P-O distance is 1.6A, S-O distance is 1.4A. Provided your coordinate error is in the range of 0.1A you may cautiously suggest one or the other. However, it may be impossible to prove that what you see is n

[ccp4bb] Arg distorsion during refinement

Dear crystallographers, Lately when refining a structure (at 2.8A) with Refmac5 I've found that nearly all Arg residues get distorted at one angle: NE-CZ-NH1(2). Starting model has 120*, final model 123*(117*), which validation server considers a major issue. May any of you recognize why is th

Re: [ccp4bb] His-6 versus His-10 tag

Hi Herman, I haven't done His-6 versus His-10 for the same protein, but have done that for different ones with success. However, if in His-6 containing protein structure the packing or folding is such that you don't see His-6 then it shouldn't matter it is 6 or 10. Just an opinion. Regards, V

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

James, What you wrote doesn't look like official risk assessment document. However, your essay is very informative and entertaining. Thank you. Regards, Vaheh Oganesyan www.medimmune.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James Ho

Re: [ccp4bb] NMR or Homology Model as a MR model

Percent of identity/similarity is a number that might be often misleading when used as a judgement rule for molecular replacement. Very high or very low numbers are almost always indicative of corresponding outcome. The numbers in twilight zone of 20 to 35%, however, are not. When aligning seque

Re: [ccp4bb] crystallization optimization

What I’m about to write should be referred as a question rather than an answer. However, it might also help to find the answer to crystallization question discussed here. The good old crystallization diagram so far for me was something that I’d look after successful crystallization story and fin

Re: [ccp4bb] Problem with a cell content

1:38 PM To: Oganesyan, Vaheh; Phil Jeffrey; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problem with a cell content Dear Vaheh and Phil, Sorry, I was a bit misleading – antibody fragment I used is a nanobody (VHH, 15kDa). I was worried about the cell content because when I started the pdb

Re: [ccp4bb] Problem with a cell content

Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших кристаллов? Кристаллы бывают разные. First of all Fab by itself is already almost 50 kDa, so complex with antigen should be more than 50 kDa. Because you already solved the structure calculate the molecular mass based on

Re: [ccp4bb] [phenixbb] Asymmetric unit content

Matthews coef. is not made to give you exact answer about number of molecules in the asu. As you rightly say, it is just probability. I’d have been convinced seeing unbiased (before refinement with fifth molecule) diff. electron density map or discontinuous packing in the crystal in the absence

Re: [ccp4bb] Nitrate versus Carbonate

Would this figure answer your question? Cells must have way of feeling the difference in the bond lengths, and strength and nuances in hybridization. At least, I hope they do. Regards, Vaheh Oganesyan www.medimmune.com From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kelle

[ccp4bb] alternative side chain locations

Colleagues, Working at relatively high resolution of 1.5A allows in some cases seeing alternative positions of side chains. After placing those in the coordinate file with occ adding to 1.0 and running refinement (latest REFMAC on Win) I find that occupancies of all atoms in the specific residu

Re: [ccp4bb] AW: [ccp4bb] Rfree below Rwork

ore then unit cells but did not send a correction. Next time, I will check the space group before sending an email. Best regards, Herman Von: Oganesyan, Vaheh [mailto:oganesy...@medimmune.com] Gesendet: Donnerstag, 2. Juli 2015 15:48 An: Schreuder, Herman R&D/DE; CCP4BB@JISCMAIL.AC.UK<mai

Re: [ccp4bb] Rfree below Rwork

Hi Herman, While you're correct regarding increase in number of entities in the asu upon lowering the symmetry, you're not correct for specific case of R32. One molecule per asu in R32 equals 18 molecules per asu in P1. Regards, Vaheh Oganesyan www.medimmune.com From: CCP4 bulletin board [mai

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Hi Robbie and Co, These things are happening now too. Look at the entry 4x4m. The paper got published in January, PDB released coordinates in April. That means reviewers did not have a chance to look even at validation report. In my opinion, whatever it is worth, every journal dealing with crys

Re: [ccp4bb] nVidia quadro

Kay and others, I think Quadro 5000 available @ http://www.amazon.com/PNY-VCQ5000-PB-DisplayPort-Profesional-Graphics/dp/B003X26T7K is a better option both price wise and need of transforming the output into 3-pin mini DIN. Having said that I should mention difference: the memory is 2.5GB for 50

Re: [ccp4bb] nVidia quadro

Colleagues, I’d like to thank everyone who took time to answer my question regarding Quadro cards that support quad buffered stereo. I now hope to build a workstation with Quadro 5000. Regards, Vaheh Oganesyan www.medimmune.com To the extent this electronic communication or any of its attachm

[ccp4bb] nVidia quadro

Graphics gurus, http://www.amazon.com/PNY-DisplayPort-Profesional-Graphics-VCQ6000-PB/dp/B0044XUD1U/ref=sr_1_8?ie=UTF8&qid=1427151570&sr=8-8&keywords=nvidia+quadro Would this card work for quad buffered stereo on Linux workstation? It does have 3-pin mini Din. Regards, Vaheh Oganesyan MedImm

Re: [ccp4bb] Protein expression

Hello everybody, I’m posting this arguably off topic somewhat related to previous query question on behalf of a colleague: Does anyone have experience with Origami cells growing in fermenter? Many searches yield nothing as if these cells have never been used to grow in place other than flasks.

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

I might be completely wrong here but doesn’t it bother that the number of rejected reflections shown in log file is ~83000? It shows, at least to me, that either indexing step is far from being correct or crystal is not really good enough due to defects. Vaheh Oganesyan www.medimmune.com Fro

Re: [ccp4bb] asymmetric homotrimer in the asu

This fact by itself is unusual to say the least (for me): " we have NO rotational symmetry (2, 3, or 4-fold) whatsoever between interacting monomers in the ASU or relating those built up by the crystallographic symmetry" There might be several ways of choosing molecules to represent the asymmetri

Re: [ccp4bb] Challenging Mol.Rep. Problem

Hi Randy, The elbow angle you refer to may be different within one asymmetric unit. The 2FJF has 12 Fab molecules per asymmetric unit with elbow angles ranging between 144 and 192. So, I'd rather think that in a specific case of Fab the search is better off with VH-VL and CH1-CL domain pairs us

Re: [ccp4bb] Off topic: Precast gels

Theresa, Try Genscript. They have probably special now going on, so box of 10 SDS PAGE costs $39. I'm not associated with Genscript in any way and I don't use their SDS PAGE. Vaheh Oganesyan www.medimmune.com -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]

[ccp4bb] migration from monitor to wall mounted screen and projector

Hi all, I'm planning migration from CRT monitor to wall mounted screen with projector that will support stereo. Mid-range emitter like AE125 for small office (4m by 4m) like mine is sufficient. I'm looking for advise on projector and screen. It looks like ViewSonic PJD7820HD ($699) with native

Re: [ccp4bb] Tenure track junior Group Leader Positions in Milan, Italy

It sounds very interesting: "experimental and computational dance biology". Any type of computational dance or there are style limitations? Regards, Vaheh Oganesyan www.medimmune.com [MedI Logo Sig] From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Sebastiano Pasqualato Sen

Re: [ccp4bb] SO4 geometry

: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] SO4 geometry On Monday, 31 March, 2014 19:01:33 Oganesyan, Vaheh wrote: > Colleagues, > > Sorry to bother for something really minor. The Refmac usually always > recognizes tetrahedral SO4 groups and there were no problems re

[ccp4bb] SO4 geometry

Colleagues, Sorry to bother for something really minor. The Refmac usually always recognizes tetrahedral SO4 groups and there were no problems related to its geometry. Two attached files demonstrate SO4 geometry before and after refinement. Would you be able to point me to mistake I’m doing? Th

[ccp4bb] stereo emitter

Colleagues, I was happily using my NuVision 60GX emitter with Quadro FX1400 graphics card for number of years on CRT and recently something went bad and image will flip regularly sending front to back and vice versa. First I thought the card went bad but after installing new one nothing changed

Re: [ccp4bb] high purity imidazole

Thanks to Debanu Das, Pedro J. B. Pereira and Bernhard Rupp for pointing me in the right direction. https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1308&L=ccp4bb&P=R255275&1=ccp4bb&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4 Regards, Vaheh Oganesyan www.medimmune.com To the extent th

[ccp4bb] high purity imidazole

Colleagues, In August of 2013 there was a tread regarding high purity Imidazole and someone posted list of products with absorption values at 280 nm and manufacturer. I can find most of the e-mails from that tread but not the one with list of Imidazoles. Has anyone saved that e-mail for future u

Re: [ccp4bb] Dose anyone see this ligand before?

It actually looks much like pyrophosphate! If your protein is phosphatase and the extra density is in vicinity of the active site it might be the remaining product of reaction. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bo

Re: [ccp4bb] Improve diffraction ...any ideas?

I think this is an advice not to follow. Vaheh -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajiv K Bedi Sent: Friday, May 24, 2013 1:44 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Improve diffraction ...any ideas? Dear Umri, I

Re: [ccp4bb] Etiquette on publishing if there is a crystallization report from someone else.

Herman, I don't know which early days you refer to, but from late 80s until structural genomics era there were relatively few crystallization reports. May be I didn't see them, and then I apologize. But crystallization reports in large started in late 90s through early 21st century and Acta F h

[ccp4bb] UV microscope

Hi All, May I ask opinion of those who currently have standalone UV microscope whether or not they are happy with their choice? Few that I know are from Formulatrix, JanScientific and Corima. Pros and cons of your instument are greatly appreciated. I'll send the summary to the list. Regards,

Re: [ccp4bb] Protein concentration vs Molecular wt...

Number of years ago Jaru Jancarik (the author of Screen I & II sold by HR) while in Berkeley Structural Genomics Center (or may be even earlier) made an observation regarding protein precipitation in condition A6 in that very screen. Based on this observation HR sells now PCT (protein concentrat

Re: [ccp4bb] Death of Rmerge

It wasn't doing well lately. So, it was expected. From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller [j-kell...@fsm.northwestern.edu] Sent: Thursday, May 31, 2012 2:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Death of Rmerge

Re: [ccp4bb] detergent or protein

Alternatively, if you harvest those crystals, wash them well in growth solution and run SDS PAGE you may also get an answer. Vaheh -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, May 04, 2012 8:53 AM To: CCP4BB@JIS

[ccp4bb] water picking

All, For those who still don't use Coot is there an automatic water picking procedure in CCP4? Many years ago there was a peakmax which is now for Patterson peaks only. Then there was routine through Arp/wArp. Now is Coot only. Is this right? Thanks. Vaheh Oganesyan, PhD Antibody Discovery a

[ccp4bb] FW: error

BBers, In my new 6.2.0 installation I'm getting "child killed: segmentation violation" while running Truncate. The /tmp/Vaheh directory does exist and is writable. Below is the message: [Vaheh] === The program run with command: /usr/bin/ccp4-6.2.0/bin/ctru

Re: [ccp4bb] To archive or not to archive, that's the question!

I was hesitant to add my opinion so far because I'm used more to listen this forum rather than tell others what I think. "Why" and "what" to deposit are absolutely interconnected. Once you decide why you want to do it, then you will probably know what will be the best format and vice versa. Whe

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

GE has a policy on Product Obsolescence, which, afaik, means that service contracts will not be issued to those instruments that were discontinued 7 years ago. Among instruments affected by this deadline are "AktaPrime INCL", "AktaPrime EXCL" and "AktaPrime COMPLETE". You have time to service th

Re: [ccp4bb] Cadmium sites and co-ordinations in structure

While I believe there is plenty written about metal coordination, the best approach, IMHO, is to search PDB for metal of your choice at resolution as high as you can get and compare to your case. Vaheh From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

I think that the absolute value of protein concentration is not very important. Some proteins get crystallized at 1 mg/ml, others at 50. What is important is to be able to reproducibly estimate it from prep to prep. You probably want to start at some reasonable value of about 10 mg/ml. If it in

Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.

I completely disagree with Filip's assessment. I've been using nanodrop nearly 5 years and never had inconsistency issues. If you work at reasonable speed (if you put a drop there then lower the lever and click measure before you do anything else) there will be no issues. At very high concentrat

Re: [ccp4bb] Mg2+ or water

Using different web servers on your refined structure is good thing to do. But for distinguishing metal ion, specifically Mg, from water was done unambiguously before these programs existed. The simple rule is two fold: 1. distance; 2. coordination. For Mg ion distances are between 2 and 2.2 A and

[ccp4bb] on the same note

On the same note with Mirek: does anyone know of a source other than GE for resin for purification of FLAG-ed proteins? Thanks. Vaheh -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Mirek Cygler Sent: Tuesday, November 02, 2010 11:47 AM T

Re: [ccp4bb] pdf to text

Thanks go to all who took their time and answered and in some cases did file manipulations. Extremely helpful! Not only for this particular case but many times CCP4BB has proven to be the best. Below are received answers in chronological order: Albert Gluskov: I converted it in adobe acrobat pro,

[ccp4bb] Multiple NCS relations

Dear bb contributors, I would like to refer to your expertise and get advice regarding multiple NCS relations between two macromolecular complexes in asu. Resolution 2.5A, s.g. C2221, R-merge 6%, synchrotron data, 2 complexes per a.s.u. Each complex consist of three polypeptide chains, let's say

Re: [ccp4bb] PEG 1000

Actually it probably would be better ask the supplier of your screen first how they got PEG 1K diluted to 12.5%. If they did hit it then you have to do the same. But even better idea is to order that PEG 1K from the same company that sells the screens. It will insure identical treatment. My 2 c

[ccp4bb] TLSMD server is down.

Are there plans to restore it today? Thanks. Vaheh From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of pos Sent: Wednesday, June 02, 2010 8:26 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Postdoctoral position at the Goethe Unive

Re: [ccp4bb] Fwd: [ccp4bb] Blue color upon X-ray exposure?

Protein crystals grown in Phosphate-Citrate buffer, pH 4.2 behave exactly the way Richard described: they first turn blue then fade through yellow-brown. Vaheh -Original Message- From: CCP4 bulletin board on behalf of Richard Gillilan Sent: Mon 3/15/2010 2:23 PM To: CCP4BB@JISCMAIL.

[ccp4bb] definition file

Colleagues, Do any of you have created a def.site file for LRL-CAT 31-ID-D beamline to be used by HKL2000? I'll appreciate if you can share. __ Oganesyan Vaheh, Ph.D Antibody Discovery MedImmune, Inc. To the extent this electronic communication or any o

Re: [ccp4bb] mammalian cell culture on IMAC

AC after 3X dilution (with properly chosen resin and buffer pH). Your idea works fine: that's why I limit load to 300 ml. Thank you. ___ Vaheh From: Brad Bennett [mailto:bradbennet...@gmail.com] Sent: Thursday, October 08, 2009 4:43 PM To: Oga

Re: [ccp4bb] mammalian cell culture on IMAC

In case of cell lysates this may be a good idea since you can adjust the salt concentration in your sample. In case of secreted proteins it is probably not so good since the media contains ~150 mM NaCl. In my case this salt prevents protein from bindinq to Q column. Thank you anyway.

Re: [ccp4bb] mammalian cell culture on IMAC

Dear All, When mammalian cell culture is being loaded to GE HisTrap resin Ni ions are being stripped off the resin, at least in my hands. Did any of you have similar experience and if so what kind of work-around was found? Volume is fairly large (3L) and concentration/dialysis have proven to ca

[ccp4bb] shape complementarity calculations

Colleagues, Would some one kindly suggest software that calculates shape complementarity of two interacting proteins based on co-crystal structure? I've seen number of reports with "sc" parameter included but none of those mention how it was done. Among non-runnable programs in CCP4 there is the s

[ccp4bb] Planar Systems monitor

I came across this LCD monitor with DVI connection. Would experts in the field recommend this monitor for stereo viewing? http://www.pcconnection.com/IPA/Shop/Product/Detail.htm?sku=6220485 Thank you. ___ Vaheh To the extent this electronic communication or any of its attachments contain

Re: [ccp4bb] ccp4 database error

Thanks to all replied. I'm back on track. ___ Vaheh -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Friday, October 17, 2008 2:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ccp4 database error -- Matthew Franklin , P

[ccp4bb] ccp4 database error

Dear CCP4 community, Due to power failure during ccp4i session the database file got locked (according to message from ccp4i). This prevents me from seeing previously run jobs and from running new jobs in that same project directory. I would appreciate a help on how to overcome this condition and

Re: [ccp4bb] cryo-cooling

version of TLSMD. I'm writing to you to find out if there was any progress in that direction and how to make carbohydrates to be recognized. Regards, Vaheh Oganesyan ___ Vaheh -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Kay Diederichs

[ccp4bb] HEK293S

Please, forgive my partially off-topic question. I'm looking for commercial or cell bank source for GnTI-deficient HEK293S cells and will appreciate any suggestions on how to get them. P.S. It's partially off-topic since the cells will be used to produce protein for crystallography. Thanks. ___

[ccp4bb] Research Associate I/II position

s not required. To apply, please visit http://www.medimmune.appone.com/ and search by Req. Number 00616. __ Oganesyan Vaheh, Ph.D Antibody Discovery MedImmune, Inc. To the extent this electronic communication or any of its attachments contain information that is not in the p

[ccp4bb] negative LLG in Phaser run

=-44 RFZ=3.8 TFZ=5.8 PAK=19 LLG=-908 Thank you in advance. __ Oganesyan Vaheh, Ph.D Antibody Discovery MedImmune, Inc. To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is

Re: [ccp4bb] crystallisation robot

Mark, What was the state of the larger drops when tiny counterparts had crystals? My guess - they all precipitated. I'm trying to understand why some proteins or some conditions require change in protein concentration while others do not when migrating from smaller drops to larger ones. If it

Re: [ccp4bb] crystallisation robot

I have been using Phoenix for more than two years and so far there were no issues with maintenance. Wash the needles and nano-dispenser before and after the runs and you are good to go. Electrostatic effects have been seen in a way of drops being positioned on the side of the flat bottom plate, but

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