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

With regards to the image that Bohdan sent and Eleanor's statements, I'm curious if the splitting of B-factors in Bohdan's image is due to the increased amount of data (which may diminish the extent of uncertainty), due to the diminished ensemble of structures within the crystal, or both. What

[ccp4bb] ATP analogues

? Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program To unsubscribe from the CCP4BB list, click the following link

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

The clash score is also impressively high. Your map may have the incorrect hand. Have you tried flipping it? Best wishes Reza From: CCP4 bulletin board on behalf of Martyn Winn - STFC UKRI <7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> Sent: 10 January 2024 4:5

Re: [ccp4bb] Validation of structure prediction

structure. The structures were predicted with the Robetta server and all have, as expected, geometry better than most experimental structures. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Fwd: [ccp4bb] Validation of structure prediction

has written below. My question was regarding the geometry of the structure. I also understand that outstanding geometry does not indicate an accurately predicted structure -the helix example indicated by Tristian. Nonetheless, the server links sent earlier are extremely helpful. Reza Khayat

[ccp4bb] Validation of structure prediction

minimizes the geometry to improve its statistics. Nonetheless, the journal has asked me for such a report. Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Searching Sequence Motif

?Try using the psi-blast package and search against the PDB. Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Cryo EM Sent: Sunday, September 5

Re: [ccp4bb] poly-dN model

Thank you Robbie. Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Robbie Joosten Sent: Saturday, March 13, 2021 9:09 AM To: CCP4BB

[ccp4bb] poly-dN model

Hi, For DNA/RNA models, is there an equivalent to a poly-Ala model? Something like a poly-dN perhaps? This is in case you don't know the nucleic acid sequence. Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochem

Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

?Does anyone know how AlphaFold performs on sequences with little conservation? Virus and phage proteins are like this. Their structures are homologous, but sequence identity can be less than 10%. Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and

[ccp4bb] Windows binary for probe and reduce

?Hi, Has anyone been able to compile a windows version (non cygwin) of probe and reduce? I'm asking for the windows version of coot. Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Modeling ATP/ADP

fit poses been considered? Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Sent

[ccp4bb] Modeling ATP/ADP

Hi, Can folks suggest programs for objectively docking ATP/ADP molecules into density? Our density is not so good, probably because of occupancy, and we'd like a less subjecting approach for modeling. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New

Re: [ccp4bb] visual mask editor?

?You can generate maps using UCSF Chimera then convert these to binary masks. This means you can drag PDB around to generate a mask where ever you like. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

[ccp4bb] Arp/wARP

Hi, I've installed the entire CCP4 7.1 package (ShelX and arpWarp); however, I can't find the arp/Warp binaries/scripts (e.g. auto_em.sh). Are these not included with the CCP4 package? If not, why not? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College o

Re: [ccp4bb] Searching similar local structural conformations

?Hi Lei, Rosetta uses something very similar to this for designing proteins that bind to ligands/proteins. Perhaps look there. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ITC question -dimer vs monomer

?Isn't the entire idea of using ITC that you are measuring an equilibrium constant? Wouldn't this eliminate the nuances of what you're looking for (i.e. kinetics)? Perhaps you should use SPR to tease out this model? Best wishes, Reza Reza Khayat, PhD Assistant Professor City

Re: [ccp4bb] Reg: water pentagon at dimer interface

?The interface doesn't appear to be extensive. What is the buried surface area? Is the molecule a dimer in solution, or is the dimerization caused by crystal packing? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] challenges in structural biology

freezing conditions become the bottle neck of cryo-EM. ? Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Patrick Shaw Stewart Sent: Tuesday, July 23, 2019 1:35 PM To

[ccp4bb] DNA or RNA

Hi, Sorry for the non-crystallography question. We have a protein complex with nucleic acid and would like to know if the nucleic acid is DNA or RNA. Is there a sensitive method for doing this where we don't need buckets of the sample? Thanks. Best wishes, Reza ? Reza Khayat, PhD Assi

[ccp4bb] Sequence variability mapped on a PDB

Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: Clarke, Oliver Sent: Saturday, March 16, 2019 8:36 PM To: Reza Khayat Subject: [EXTERNAL] Re: CCP4BB Digest - 15 Mar 2019 to 16 Mar 2019 (#2019-81) Hi Reza

[ccp4bb] Sequence variability mapped on a PDB

?Hi, Can someone direct me to a program that can replace the B-factors of a PDB with sequence variability calculated from a sequence alignment? I'm have tried the PVS server, but my sequence alignment is too large for its liking. Thanks. Best wishes, Reza Reza Khayat, PhD Assi

[ccp4bb] Off topic question

?Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2) sequences from a sequence alignment? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department

Re: [ccp4bb] RNA pdb molecular weight

Thanks everyone. I did two things: 1. Extract the MW from the cif file as suggested by David (see below) 2. I extracted the RNA sequence from the cif file and ran it through an oligo calculator with ssRNA as the option Both give similar results. Best wishes, Reza Reza Khayat

[ccp4bb] RNA pdb molecular weight

Hi, I'm not an RNA person. Can anyone suggest a method to calculate the mass of a RNA PDB? I'd like the protons to also be considered in the calculation. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nichol

[ccp4bb] Practices for publishing a crystal structure

wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] Structure of dextran sulfate

wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New York, NY 10031 http://www.khayatlab.org/ 212-650-6070

[ccp4bb] EM voxel size correction

?Hi, Has anyone established a robust method to calibrate the pixel/voxel size of a cryo-EM image reconstructions using a known PDB? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

Re: [ccp4bb] Electrostatic Potential: Poisson-Boltzmann

I think this is an excellent opportunity to combine MD calculations with your structures to see what role(s) this flexible region may play in your structure. Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] RMSD calculation for large assemblies

cally detecting and calculating RMSD, but I'd like to have the spread for each atom in the final graph that Coot generates. Thank you. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] Biotin binding protein

es, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] Unbranched polysaccharide chain

Hi, Is there a server/program that can generate a chemical picture/PDB from the sequence of a polysaccharide and the type of connections? I'm not so interested in the minimized structure at this point. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry

[ccp4bb] Coot no GUI

Hi, Is it possible to run Coot without the use of GUI? We have some Coot scripts for a pipeline and we'd like to do without the GUI. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 2.318 New

Re: [ccp4bb] Weak density of RNA in a complex structure

Dear Chen, Is this an icosahedral virus crystal structure, or a highly symmetric structure where the RNA may have different binding modes to each subunit and thus averaged out in the crystal? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of

[ccp4bb] Rhodamine in FPLC

Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] Refmac5 TLS refinement

0. 0 # Other nonsolvent 0.0. 0 END OF SKTTLS SUMMARY Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Dmytro Gu

Re: [ccp4bb] Structure comparison

t defining such criterion is by no means trivial. Thanks again for the help. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ____ From: Reza Khayat Sent: Sunday, April 9, 2017 6:07 P

[ccp4bb] Structure comparison

one another to warrant a closer look? I think the most important aspect of the analysis would be defining a threshold (possibly based on resolution and structure statistics) that would identify sufficient difference between structures. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant

[ccp4bb] Off topic instrumentation

Hi, Sorry for another non crystallography question. Can someone suggest a fraction collector to collect fractions from a CsCl/glycerol/sucrose/... gradient from an ultracentrifugation run? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of

Re: [ccp4bb] Completely Off-Topic

I don't think this is taught in Biochem101. You didn't miss it. The cytoplasm is quite viscous, like jello. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin boa

Re: [ccp4bb] Off-topic question about SEC

?All these make sense. Protein is very strange cause it goes from 60kDa (globular) to an apparent 360kDa. Process is reversible too. Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin

[ccp4bb] Off-topic question about SEC

elute later because it may interact with the matrix. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031

[ccp4bb] Detecting chlorides in x-tals

Hi, With the hopes of not reigniting the heated "Chloride or water" CCP4 discussion in Jan. 2015, what experimental method is suggested for identifying chlorides in a x-tal? Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry Ne

Re: [ccp4bb] visible side-chains but breaks in main-chain

I would have to agree with Tim. I'm a little surprised that your R/Rf is 27/32. Are the images representative of the entire model/map fits, or a small section of it? Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nic

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

I Agree with Edward. No discussion of politics, religion, or sex at work. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 From: CCP4 bulletin board on behalf of Gloria Borgstahl Sent

Re: [ccp4bb] Superpose program in CCP4

I've done this sort of analysis in the past and it can be very useful depending on your story is. I'm not sure if any software offers this. My solution was to write a script to do the comparison after the superposition was done. Unfortunately I can't find the script. Best wish

[ccp4bb] ssDNA

Hi, Sorry for the non-crystallography question, does anyone know how to produce milligram quantities of single stranded DNA? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 12318 New York, NY 10031

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

That's interesting. Enantiomer differences can be detected at worse than 20Angstrom resolution in EM reconstructions. What do you think is the reason for this? Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York 85 Saint Nicholas Terrace, CDI 12318 New

Re: [ccp4bb] How to fit BioSAXS shape to the Structure

Hi, Follow up question on SAXS. Does SAXS have an enantiomer problem like electron microscopy? In other words, does the calculated model possess the correct handedness or can both handedness of a model fit the scattering profile just as well? Best wishes, Reza Reza Khayat, PhD Assistant

Re: [ccp4bb] Protein precipitation

Hi, Try using 100mM Ammonium Citrate pH 8.5 as the buffer for your lysis -add salts as well. The Citrate will inhibit metalloproteases and is Ni-NTA friendly. It solved our proteolysis problems and may help with yours. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New

Re: [ccp4bb] Cleaved peptide density!

ishes, Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radisky, Evette S., Ph.D. Sent: Wednesday, April 22, 2015 3:40 PM To: C

Re: [ccp4bb] on NCS restraint

Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Victor Lamzin Sent: Tuesday, April 21, 2015 9:07 AM To: CCP4BB@JISCMAIL.

Re: [ccp4bb] [ccp4bb] on NCS restraint

you can define the regions where NCS is applied and thus avoid loops/regions where the NCS is violated. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York 160 Convent Ave, MR-1135 New York, NY 10031 (212) 650-6070 rkha...@ccny.cuny.edu<mailto:rkha...@ccny.cuny.edu

Re: [ccp4bb] Protein expression

Hi, Cultures are being properly cooled prior to induction (water bath supplemented with ice). Reza Reza Khayat, PhD Assistant Professor Department of Chemistry City College of New York New York, NY 10031 http://www.khayatlab.org/ 212-650-6070 From: lieh low [mailto:liehy...@gmail.com] Sent

Re: [ccp4bb] Protein expression

res were lysed with the micro-tip. Same results were observed. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York 160 Convent Ave, MR-1135 New York, NY 10031 (212) 650-6070 rkha...@ccny.cuny.edu<mailto:rkha...@ccny.cuny.edu> On Mar 19, 2015, at 11:15 PM, Jo

[ccp4bb] Protein expression

Hi, We can express quite a bit of soluble protein when growing 3ml cultures. However, the protein becomes insoluble (inclusion bodies) when we scale up to 500ml cultures. Has anyone experienced such a problem, and found a solution to it? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant

Re: [ccp4bb] non-specific disulfide bonds in crystal structures

Hi Todd, A concern of mine is that you may be looking at an artifact of the domain. Whatever assays you decide to do, make sure that they are also performed for the full sized protein. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry

[ccp4bb] cryoprotectant

Hi, Has anyone used citrate as the sole cryoprotectant? If so, what concentration was needed? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org

Re: [ccp4bb] large empty spaces in solved crystal structure

t you have reasonable phases to build a reasonable model. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org Original message >Date: Thu

[ccp4bb] Pipettes

Hi, This is way off topic but relevant. Does anyone routinely use the Rainin Classic Pipet series? If so, what are your thoughts and how often do they need to be calibrated? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135

[ccp4bb] PDB Domain parser

Hi, Can people direct me to programs capable of detecting non- contiguous protein domains from a PDB file? I realize that some structures may be problematic. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue

[ccp4bb] Seeking postdoctoral candidate

Hi, The research group of Dr. Reza Khayat at the City College of New York (www.khayatlab.org) is seeking candidate postdoctoral fellows to study host pathogen interaction using a combination of cryo-electron microscopy (cryo- EM), X-ray crystallography, biophysics and biochemistry. The research

Re: [ccp4bb] Removing PEG3350

on walls next to the FPLC :) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1304934/ Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel

Re: [ccp4bb] Enigmatic electron density attached to Cys residue

Hi, I guessed glycerol by looking at the figs and not reading your text. Having read your text afterwards, you do have glycerol in the solution. My guess is glycerol. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160

[ccp4bb] Removing PEG3350

Hi, Does anyone have a protocol for getting rid of PEG3350 from a protein sample? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org

Re: [ccp4bb] dynapro DLS cuvettes

Hi, A crazy solution may be to make a cuvette with a 3D printer. I'm not sure if the available resins are transparent to DLS. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel.

[ccp4bb] Disrupt beta sheet formation

observe. Are there any chemicals that would disrupt short beta-sheet formation? Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org

[ccp4bb] Solvent channels

pothesized binding site. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org

Re: [ccp4bb] negative density around disulfide bond

What does an omit map look like, if you omit both cysteines? Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org Original message >Date:

[ccp4bb] Imaging Facilities Manager - Research Assistant Professor

CE_JOB_DTL&Action=A&JobOpeningId=10784&SiteId=1&Posti ngSeq=1& Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org

Re: [ccp4bb] HisTrap Trap

ia is not willing to disclose the contents for the media. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 www.khayatlab.org Original message >Date: Mon

[ccp4bb] Seeking postdoctoral candidate

Hi, The research group of Dr. Reza Khayat at the City College of New York (www.khayatlab.org) is seeking candidate postdoctoral fellows to study host pathogen interaction using a combination of cryo-electron microscopy (cryo-EM), X-ray crystallography, biophysics and biochemistry. The

Re: [ccp4bb] First stucture of FCFV

I think fungus dependent crystallization has occurred for some labs. A paper that pops into mind is from my graduate laboratory (not my work though): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2225192/ Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of

Re: [ccp4bb] ITC with unfolded proteins

Hi, I think the experiment is doable, but how would you decouple protein-protein interaction from folding of the unfolded protein due to protein interaction? Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY

Re: [ccp4bb] saving map isovalue surface to file?

USCF Chimera can save maps as a VRML and other formats. You can use 3D animation software to change formats from VRML to anything else. Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070

Re: [ccp4bb] Large Conformational Change Upon Binding Ligand...

Classical case would be Hexokinase. Also, try the various states of Fatty Acid Synthase. Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 Original message >Date: Thu, 27

[ccp4bb] Se-Met and disulfides

to follow in my situation? Here's hoping that the solution is not dumping a bunch of Se-Met into all the purification buffers... Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel.

Re: [ccp4bb] off-topic: bug busting

ot of crap deposits on it with every use. Best wishes, Reza Reza Khayat, PhD Assistant Professor The City College of New York Department of Chemistry, MR-1135 160 Convent Avenue New York, NY 10031 Tel. (212) 650-6070 Original message >Date: Tue, 4 Feb 2014 12:40:51 -0500 >Fro