Re: [ccp4bb] pymol 2.5 GUI font size too small

Hi, Ursula, I have the same problem on my Pymol version 2.5.1 on the Mac Mojave system, I posted a solution from an old thread below that solved the problem. "This looks like missing shader support, which is unexpected on modern Mac hardware. Can you try to set the "use_shaders" setting? PyMOL>

Re: [ccp4bb] generate symmetry mates of EM structures

ao On Fri, May 21, 2021 at 9:07 AM Stefano Trapani wrote: > Le 2021-05-21 13:54, Xiao Lei a écrit : > > Thank you for your help. It seems the problem is due to the Pymol program. > > Hi Xiao > which version of PyMOL are you using ? > > > I could only see 3 chains in P

Re: [ccp4bb] generate symmetry mates of EM structures

gz)" would give you the full structure. > > Kind Regards, > David Armstrong > > On 21/05/2021 11:33, Xiao Lei wrote: > > Dear Community, > > I wonder if there is a way to generate symmetry mates of EM structures? > For example for PDB code 5L93, I tried PISA assembl

[ccp4bb] generate symmetry mates of EM structures

Dear Community, I wonder if there is a way to generate symmetry mates of EM structures? For example for PDB code 5L93, I tried PISA assembly server and Pymol to generate assembly (18 chains) but failed because it is not a crystal structure. I tried to download assembly directly from RCSB databank

Re: [ccp4bb] Lost extension bar in Coot

Hi, Kahkashan, Does Coot 0.9 bundle with CCP4 7.1 installation?I install CCP4 7.1 and I did not see Coot installed. Best, Xiao On Thu, Jun 11, 2020 at 8:27 AM Firdous Tarique wrote: > Hi > > Just downloaded the new CCP4-7.1. Wondering where the extension bar in > Coot 0.9 has gone. Please

Re: [ccp4bb] [Off-Topic] 3D Vision stereo with Ubuntu 18.04

I used to use Ubuntu Mate OS to get 3D work for coot and pymol. I am not sure if the latest version still works. Regards Xiao On Fri, Nov 8, 2019, 7:19 AM Chris Richardson wrote: > Apologies for the only slightly relevant question. > > Does anyone know the correct incantations to get nVidia 3D

[ccp4bb] Offtopic: Is there a way to search protein-protein interface structural similarity in database ?

Hi All, I wonder if there is a way to search protein-protein interaction interface similarities in PDB database? For example, I have two proteins proA and proB, part of proA and part of proB contact with each other in a crystal structure, I want to search if there are similar interaction interfac

Re: [ccp4bb] Off-topic, protein in dye-front (ion front?) on native-PAGE

Hi All, Sorry to bring this old topic up again. I planned to run tricine gels but I found a possible error in table 2 (4% stacking gel formula) in Hermann Schägger protocol (Nature Protocols volume 1, pages 16–22 (2006), the author wrote 3ml 3X gel buffer in a total of 12 ml solution, it should b

[ccp4bb] Postdoc position available

*Postdoctoral Scholar Position on Investigating CRISPR Mechanism at University of Southern California, Los Angeles, California, USA* The Qin Laboratory in the Chemistry Department of the University of Southern California invites applications for postdoctoral scholar positions supported by fundin

[ccp4bb] Postdoc Position available at Dr. Peter Qin lab at University of Southern California

*Postdoctoral Scholar Position on Investigating CRISPR Mechanism at University of Southern California, Los Angeles, California, USA* The Qin Laboratory in the Chemistry Department of the University of Southern California invites applications for postdoctoral scholar positions supported by fundin

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

I see. Thanks Eleanor! On Thu, Dec 7, 2017 at 4:33 AM, Eleanor Dodson wrote: > Rf_used is the R factor for the non-free reflections. > > If you do the plot the 4SSQ/L**2 is converted to As.. > > E > > On 7 December 2017 at 11:50, Xiao Lei wrote: > >> Thanks Eleano

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

47.737.5 0.43 0.43 42848.037.6 > 0.47 0.48 > 0.2888611 98.2440.932.1 0.42 0.42 45041.832.1 > 0.50 0.50 > $$ > > > > On 7 December 2017 at 01:07, Bernhard Rupp > wrote: > >> You can find these numbers in the header

Re: [ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

This works. Thanks a lot Bernhard. On Wed, Dec 6, 2017 at 5:07 PM, Bernhard Rupp wrote: > You can find these numbers in the header of the output model coordinate > file. > > > > BR > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *

[ccp4bb] How to find the Rfree and R in the highest resolution bin in Refmac 5?

Dear All, I am asking how to find the Rfree and R in the highest resolution bin in Refmac 5 output? I used Refmac5 in refinement of protein structure at 3A resolution. Output of Refmac5 gives Rfee and R as: InitialFinal R factor0.2900 0.2052

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear All, Thanks. I tried PDBemotif, indeed, it works very well! On Thu, Oct 26, 2017 at 10:04 AM, Andrew Lovering < andrewleelover...@googlemail.com> wrote: > The backbone psi phi angle option in pdbemotif should limit hits to a > particular secondary structure. > > Good luck! > Andy > > On 26

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear All, Thanks for the suggestions! I tried MPI pattern search, MOTIF2 as Andrew suggested, they worked fine to pull out of the PDB containing short sequences. What I need to do is a little bit more, I'd also like to know my hit region's secondary structure (helix, sheet, or loop), MPI and MOTI

[ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear CCP4BB members, Sorry this post is off-topic. I am asking is there a way to blast pdb for a very short sequence like 2 or 3 amino acids? I tried this for a positive control in pdb database but returned that "Your search parameters were adjusted to search for a short input sequence." and "No

[ccp4bb] How to search 2 models (ensembles) in Molrep

Dear Crystallographers, How to search 2 models (ensembles) in Molrep for molecular replacement? It seems there is just one model input place in Molrep GUI. In Phaser MR, this can be done with clicking the "add ensemble" button to add another ensemble, but I am not sure how to do it in Molrep.

[ccp4bb] align structure in Pymol based on dsDNA helix

Dear All, I was wondering in Pymol is there a way to align various NCS protein dsDNA complex structure in asymmetric unit based on the double helix of DNA? I can do the align with the protein part with action-->align--> to molecule or to selection. But this way does not work out if I select dsDNA

Re: [ccp4bb] Coot label on symmetric residue not working consistent

wrote: > On 10/04/17 18:39, Xiao Lei wrote: > >> Hi All, >> >> I am using Coot 0.8.3 EL on Mac OS X 10.10. After I generate symmetric >> molecule by Draw---> Cell & Symmetry. I found double click a residue in >> symmetric molecules will give me a label

[ccp4bb] Coot label on symmetric residue not working consistent

Hi All, I am using Coot 0.8.3 EL on Mac OS X 10.10. After I generate symmetric molecule by Draw---> Cell & Symmetry. I found double click a residue in symmetric molecules will give me a label sometime but not always. I do not know if anyone has similar experience.

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

everything works great! On Thu, Mar 2, 2017 at 4:15 PM, Xiao Lei wrote: > Hi All, > > Just share my experience, Windows 10 works for pymol 3D under Quadro M4000 > with Nvidia 3D kit (no need to connect the 3 pin MINI DIN, Quadro M4000 > does not have 3 pin Mini DIN connections)

Re: [ccp4bb] Large number of outliers in the dataset

This case is encouraging to me that a structure can be solved with such high mosaicity (in your report is 1.9). I wonder how the diffraction looks like (I imagine spots smearing or streak). With such high mosaicity, the unit cell dimension and space group determination is highly likely not accurate

Re: [ccp4bb] Coot render tool missing

yourwincootinstallationdrirectory\python27\lib\site-packages\coot\* *4. Done. Works!* Thanks Bernhard! On Wed, Mar 29, 2017 at 11:58 AM, Xiao Lei wrote: > Hello B., > > Works.Thank you very much! > > On Wed, Mar 29, 2017 at 8:14 AM, B.Lohkamp wrote: > >> >

Re: [ccp4bb] Coot render tool missing

7, 2017 at 2:18 PM, Ethan A Merritt wrote: > On Monday, 27 March, 2017 22:12:22 Paul Emsley wrote: > > On 27/03/17 21:55, Xiao Lei wrote: > > > > > > > > > Because the picture quality from Coot>>Draw>>Screenshot>>Simple is > > > v

[ccp4bb] Coot render tool missing

Hi All, Because the picture quality from Coot>>Draw>>Screenshot>>Simple is very low, I tried Coot>>Draw>>Screenshot>>Povray or Raster3D to export high quality picture, but I had an error of "render tool missing" and Coot tried automatically find the render tool but failed. I use Wincoot 0.8 versio

Re: [ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

Thanks Pavel, is there a command that can tell secondary structure assignment based on Rama plot of each residue beside phi and psi? for example : A 2 ASN:56.93:-60.58:141.19:Favored:General alpha helix A 3 ASN:48.44:-119.25:125.15:Favored:General alpha helix On Fri, Mar 24, 2017 at 1:

Re: [ccp4bb] Positive densities map on selective residues on Coot

Hi Paul, Thanks for the instructions! Works in my case. On Mon, Mar 20, 2017 at 6:05 AM, Paul Emsley wrote: > On 17/03/17 14:41, Xiao Lei wrote: > > > > In Coot, I could adjust the densities of map (2Fo-Fc in my case) > > radius, but I'd like to show the density

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

t; > www.mrc-mbu.cam.ac.uk > > > > > > > On 18 Mar 2017, at 10:43, Eleanor Dodson > wrote: > > I think CCP4MG does this very selectively? > > Eleanor Dodson > > On 17 March 2017 at 17:03, Xiao Lei wrote: > >> Dear All, >> >> Thanks for

Re: [ccp4bb] Positive densities map on selective residues on Coot or Pymol

generated output map. After open by pymol, only a unit cell sign is shown (I attach here), no map is displayed.. I use Pymol 1.8.X in Win7. Any further input is appreciated. . On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei wrote: > Dear All, > > In Coot, I could adjust the densities of ma

[ccp4bb] Positive densities map on selective residues on Coot or Pymol

Dear All, In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, but I'd like to show the density on selective residues, not on the unselected part of structure, is there a way to do it? I am using WinCoot 0.81. In addition, could Pymol do it? Thanks ahead!

[ccp4bb] Refmac twin refine works for Amplitude based but not Intensity based

Dear CCP4bb members, I have a dataset of 3A, twinned data (twin fraction 0.15) set of space group P6222, I solved the structure by phaser (TFZ>10, LLG>1000) with space group P32 and build model to Rfree/R 30% 26%. I then tried twin refinement in Refmac, after I tried amplitude based refine the Rf

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

the graphics card > and the monitor. > > > > Yong > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao > Lei > *Sent:* Monday, January 30, 2017 11:50 PM > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* Re: [ccp4bb] Coot and Pym

[ccp4bb] Phaser MR pairwise percent packing criterion

Dear CCP4bb members, I found in the newer CCP4 Phaser MR version (I use CCP4 7.0.0 in Win7), there is no "allow maximal clash..." option anymore. There are only two options "pairwise percent packing" and "accept all solutions". I used to increase the number in the "allow maximal clash" (let's say

Re: [ccp4bb] iMosflm twist large variance and specific space group scale output

ut. > > Try it and see if the merging stats look better... > > Harry > -- > Dr Harry Powell > Chairman of International Union of Crystallography Commission on > Crystallographic Computing > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing

[ccp4bb] iMosflm twist large variance and specific space group scale output

Dear CCP4bb members, I have two questions about imosflm integration and scaling process (my data is 3A resolution and 0.5 degree mosaicity): 1. I have warnings after integration saying the twist variance is too large (from -0.26 to 0.33, which is larger than 0.5), suggesting that cell parameters

Re: [ccp4bb] Coot and pymol 3D for Centos 7?

for Linux you need the 3-pin mini Din connectors On Tue, Jan 31, 2017 at 8:29 AM, Jun Dong wrote: > I have made coot and pymol 3D work with NVIDIA Quadro K5200 under Windows > 7 but I could not make it work under Centos 7. WinCoot was not able to load > big virus maps, it crashed all the time. I

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

ater. On Mon, Jan 30, 2017 at 7:50 PM, wrote: > Xiao, > > > > If you connect the board and monitor by DisplayPort cable directly, it > should work. > > I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not > tested on Windows. > > > > Tak

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

er, even with a DVI dual link cable. If you used an > adapter come with the board, it's probably passive. > > > > Taka > > > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > ] *On Behalf Of *Xiao Lei > *Sent:* Tuesday, January 31, 2017 9:

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

OK thanks, I'll update! On Mon, Jan 30, 2017 at 4:57 PM, wrote: > Dear Xiao, > > > > I think it would work, though I'm not sure because it's smaller and > cheaper than what I used (https://www.amazon.co.uk/ > Dell-BizLink-DisplayPort-Adapter-Powered/dp/B003XYBA72), which have > worked well since

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao > Lei > *Sent:* Tuesday, January 31, 2017 9:10 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under > Windows 10 > > > > Dear All, &g

[ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

Dear All, I tried to make Coot and Pymol 3D working for a HP Workstation with Quadro M4000 graphics card, the card has four displayport. I also has a Asus 24 inch 3D monitor. I tried to connect the graphics card with the monitor through displayport to displayport connection and displayport to DVI

Re: [ccp4bb] Ubuntu Mate for Pymol and Coot 3D

Thanks Nicolas and Paul! I am using active 3D with Quadro 5000 graphics card and Nvidia 3D kit in Fedora system (Fedora 23). Everytime I update the kernel (dnf update), I lost the 3D in both the updated new kernel and the old kernel, I have to reinstall the driver again, but can not make every rei

[ccp4bb] Ubuntu Mate for Pymol and Coot 3D

Hi All, I am asking if anyone used Ubuntu Mate operating system and is this system good for Pymol and Coot 3D?

Re: [ccp4bb] Refmac5 update water option

criteria. That you have to do manually. You can > always try to automatically add new waters, which is done by this option in > later refinement runs of course, but that doesn't "touch" the waters > previously added to the model. > > Cheers > > Christian &g

[ccp4bb] Refmac5 update water option

Dear CCP4bb members, Does Refmac5 in CCP4i have an option of adding waters to the refined structure (the input coordinate does not have any water)? I see in Phenix refine there is an option of "update water", I tried to look for this option in Refmac5 but I could not find it. I am using CCP4i 7.0

[ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

Hi All, I have an x ray diffraction dataset of protein and dna complex processed with pointless and I am trying to get the resolution cut for this data, the result is below, I do not know why in the N=23 (Dmid=3.68) bin, there is no statistic of CC(1/2), N_cc, CCfit, etc? The program just put a

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

We are using Fedora system for pymol and coot 3D. I prefer Mac OSX, but I have no way of making 3D environment for pymol and coot 3D, I'd like to know if any lab make the 3D environment work for Mac OS X system. On Sat, Oct 15, 2016 at 7:45 AM, Robert Oeffner wrote: > We build Phenix on all thre

[ccp4bb] Alternative ways to get electron density map other than EDS server

Hi All, I am trying to get electron density map of some pdb structures, I know there is a database called "Electron density server" (EDS http://eds.bmc.uu.se/eds). But somehow these days I can not connect to the website and I keep getting the "This webpage is not available" message in my browser (

Re: [ccp4bb] OS X yosemite

Hi Mirek, I have to reinstall xquartz to get my ccp4 and coot working after upgrading to Yosemite from Mavericks. Xiao On Tue, Mar 17, 2015 at 4:30 PM, Cygler, Miroslaw wrote: > Hi, > I am thinking of upgrading the os on my mac to Yosemite. Are there any > known issues for crystallographic so

Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop

Hi Marc, I have a Macbook pro Mid 2009 model (with integrated graphics card) and I can run coot and pymol without any problem ( I haven't tested on Chimera), I do not think a discrete graphics is needed. However, for pymol I can not use the "stereo" function. I do not know if the discrete graphic

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

orrect or crystal is not > really good enough due to defects. > > > > > > > > *Vaheh Oganesyan* > > *www.medimmune.com <http://www.medimmune.com>* > > > > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Xiao >

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

the data through Pointless, Aimless ctruncate (though > I had to fix Aimless) suggests > > 1. the data are not very good > 2. the space group may be C2 > 3. it may be twinned (or just some spot overlap with the long 288A c axis) > > Phil > > On 13 Jan 2015, at 00:34, Xiao Lei wro

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

te for Medical ResearchTel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 13 Jan 2015, at 00:34, Xiao Lei wrote: > > > Hi Eleanor,

[ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

Dear All, I tried to convert my x-ray diffraction sca data from HKL200 (.sca file) to mtz in CCP4 using Scalepack2mtz and it failed, I do not know what should I supposed to do next to correct the problem, any suggestions are appreciated. I pasted the message from part of log file below: ANISOTRO