Re: [ccp4bb] Coot under WSL2
Hi all, If anyone is interested in the question, coot (and any graphical application I tried) is now fully functional in Windows 11 and the newest WSLg. No configuration is needed, everything works out of the box, with full hardware acceleration. Clément On Wed, 25 Mar 2020 at 15:58, Clement Degut wrote: > Update to my update > > It is possible to have coot fully functional under WSL2 with the native > openGL on. > The caveat is : > - You need a full linux desktop environment installed (xfce4 for me) > - You need to use the host X server (VcSrv in my case) as single window, > so you lose a bit of the seamless integration with windows in that case, > but you have to do that only with coot (or any openGL software) > after starting the DE, coot will work normally with very decent speed, the > upcoming direct hardware access for the VM may also improve performance. > > In these conditions full CCP4 (or everything I tried at least) can work > relatively seamlessly in windows while using the linux version. > (it actually works better than the actual windows version imho) > > Clément > > > On Thu, 19 Mar 2020 at 14:56, Clement Degut > wrote: > >> Immediate update : >> >> If you use VcXserv, you need to start it with all default option, and >> generate a config file. >> Then change in the file wgl to False. >> Restart computer (yes) >> And start VcXserv with the modified config. >> If you simply deactivate native openGl via the gui nothing is working >> anymore for some reason, it must change another option somewhere. >> >> doing that the display of coot is perfectly fine, just a bit laggy, as i >> guess it's full software render, but usable (with a beefy CPU). >> >> Clément >> >> On Thu, 19 Mar 2020 at 14:48, Clement Degut >> wrote: >> >>> The performance are massively improved in WSL2 versus WSL1, so maybe >>> it's why you had bad memory of it ? >>> WSL2 is currently only available in insider fast ring, but will be for >>> everyone with next major update (v2004) in few weeks. >>> >>> The main problem is, while you can use the right toolbar by simply >>> detaching it, selecting residues is almost impossible as the pointer is >>> still using the main UI as reference, but the 3D display is away, so you >>> need to click far from the residus you try to select. >>> >>> I am playing around with the xserver options, but am not sure what I am >>> doing with that windows X server. >>> I'll update if I find a solution. >>> >>> Clément >>> >>> On Thu, 19 Mar 2020 at 13:31, Paul Emsley >>> wrote: >>> >>>> On 19/03/2020 12:43, Clement Degut wrote: >>>> > >>>> > I have been recently trying to use ccp4 in windows subsystem for >>>> Linux 2 (Ubuntu distribution), everything i >>>> > tried run perfectly smoothly, including graphical interfaces. >>>> >>>> I am pleasantly surprised - when I tried that (some time ago) the >>>> graphics performance as terrible. Perhaps >>>> you have better hardware. >>>> >>>> > My only problem is with coot (latest build), the interface is working >>>> fine, as well as the 3D graphical. The >>>> > only problem is that the graphical window is offset from the rest of >>>> the UI (see screenshot). >>>> > So although it looks like everything would work smoothly it's not >>>> really usable. >>>> >>>> What, would you say, is the biggest problem? >>>> >>>> > I guess it comes from the absence of GPU access under WSL2 and so no >>>> proper display driver, but does anyone >>>> > had this problem? (and managed to solve it). >>>> >>>> FWIW, I have not seen this problem before (and don't know how to fix it) >>>> >>>> It seems to me an X server problem (or configuration issue). Have you >>>> tweaked or disabled the native OpenGL >>>> options on the X server? >>>> >>>> > Would be very useful for people working from home without a full >>>> linux dual boot. >>>> >>>> Hmm. >>>> >>>> > In a more general note, it seems that WSL2 will be able to replace >>>> windows specific build very effectively >>>> > in the very near future. >>>> >>>> For everything other than OpenGL graphics (and maybe the Cloud would >>>> also be problematic), yes, it seems so. >>>> >>>> Paul. >>>> >>> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Coot 0.9 Released
At the moment I am struggling a bit to have it to compile under WSL2-ubuntu18.04 But the pre release version included in the ccpem nightly 20200327 is working well, it is a bit laggy when showing maps and you end up having to decrease the map radius a bit. but overall it is perfectly usable. The compatibility is great, but WSL2 is not meant for graphics and is not happy when openGL is involved. Clément On Sat, 4 Apr 2020 at 20:52, Kay Diederichs wrote: > has anybody tried to run coot-0.9 on Windows under WSL2 ( > https://pureinfotech.com/install-windows-subsystem-linux-2-windows-10/ ) > ? WSL2 is supposed to provide good compatibility between Windows and Linux. > To try this, one needs to become participant of the Windows Insider Program > ( https://insider.windows.com ). > > HTH, > Kay > > On Thu, 2 Apr 2020 16:59:22 +0100, Aleksandr Sverzhinsky < > aleksandr.sverzhin...@umontreal.ca> wrote: > > >This is great! Do you have an idea when this version will be available > for WinCoot? > > > > > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Coot under WSL2
Update to my update It is possible to have coot fully functional under WSL2 with the native openGL on. The caveat is : - You need a full linux desktop environment installed (xfce4 for me) - You need to use the host X server (VcSrv in my case) as single window, so you lose a bit of the seamless integration with windows in that case, but you have to do that only with coot (or any openGL software) after starting the DE, coot will work normally with very decent speed, the upcoming direct hardware access for the VM may also improve performance. In these conditions full CCP4 (or everything I tried at least) can work relatively seamlessly in windows while using the linux version. (it actually works better than the actual windows version imho) Clément On Thu, 19 Mar 2020 at 14:56, Clement Degut wrote: > Immediate update : > > If you use VcXserv, you need to start it with all default option, and > generate a config file. > Then change in the file wgl to False. > Restart computer (yes) > And start VcXserv with the modified config. > If you simply deactivate native openGl via the gui nothing is working > anymore for some reason, it must change another option somewhere. > > doing that the display of coot is perfectly fine, just a bit laggy, as i > guess it's full software render, but usable (with a beefy CPU). > > Clément > > On Thu, 19 Mar 2020 at 14:48, Clement Degut > wrote: > >> The performance are massively improved in WSL2 versus WSL1, so maybe it's >> why you had bad memory of it ? >> WSL2 is currently only available in insider fast ring, but will be for >> everyone with next major update (v2004) in few weeks. >> >> The main problem is, while you can use the right toolbar by simply >> detaching it, selecting residues is almost impossible as the pointer is >> still using the main UI as reference, but the 3D display is away, so you >> need to click far from the residus you try to select. >> >> I am playing around with the xserver options, but am not sure what I am >> doing with that windows X server. >> I'll update if I find a solution. >> >> Clément >> >> On Thu, 19 Mar 2020 at 13:31, Paul Emsley >> wrote: >> >>> On 19/03/2020 12:43, Clement Degut wrote: >>> > >>> > I have been recently trying to use ccp4 in windows subsystem for Linux >>> 2 (Ubuntu distribution), everything i >>> > tried run perfectly smoothly, including graphical interfaces. >>> >>> I am pleasantly surprised - when I tried that (some time ago) the >>> graphics performance as terrible. Perhaps >>> you have better hardware. >>> >>> > My only problem is with coot (latest build), the interface is working >>> fine, as well as the 3D graphical. The >>> > only problem is that the graphical window is offset from the rest of >>> the UI (see screenshot). >>> > So although it looks like everything would work smoothly it's not >>> really usable. >>> >>> What, would you say, is the biggest problem? >>> >>> > I guess it comes from the absence of GPU access under WSL2 and so no >>> proper display driver, but does anyone >>> > had this problem? (and managed to solve it). >>> >>> FWIW, I have not seen this problem before (and don't know how to fix it) >>> >>> It seems to me an X server problem (or configuration issue). Have you >>> tweaked or disabled the native OpenGL >>> options on the X server? >>> >>> > Would be very useful for people working from home without a full linux >>> dual boot. >>> >>> Hmm. >>> >>> > In a more general note, it seems that WSL2 will be able to replace >>> windows specific build very effectively >>> > in the very near future. >>> >>> For everything other than OpenGL graphics (and maybe the Cloud would >>> also be problematic), yes, it seems so. >>> >>> Paul. >>> >> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Coot under WSL2
Immediate update : If you use VcXserv, you need to start it with all default option, and generate a config file. Then change in the file wgl to False. Restart computer (yes) And start VcXserv with the modified config. If you simply deactivate native openGl via the gui nothing is working anymore for some reason, it must change another option somewhere. doing that the display of coot is perfectly fine, just a bit laggy, as i guess it's full software render, but usable (with a beefy CPU). Clément On Thu, 19 Mar 2020 at 14:48, Clement Degut wrote: > The performance are massively improved in WSL2 versus WSL1, so maybe it's > why you had bad memory of it ? > WSL2 is currently only available in insider fast ring, but will be for > everyone with next major update (v2004) in few weeks. > > The main problem is, while you can use the right toolbar by simply > detaching it, selecting residues is almost impossible as the pointer is > still using the main UI as reference, but the 3D display is away, so you > need to click far from the residus you try to select. > > I am playing around with the xserver options, but am not sure what I am > doing with that windows X server. > I'll update if I find a solution. > > Clément > > On Thu, 19 Mar 2020 at 13:31, Paul Emsley > wrote: > >> On 19/03/2020 12:43, Clement Degut wrote: >> > >> > I have been recently trying to use ccp4 in windows subsystem for Linux >> 2 (Ubuntu distribution), everything i >> > tried run perfectly smoothly, including graphical interfaces. >> >> I am pleasantly surprised - when I tried that (some time ago) the >> graphics performance as terrible. Perhaps >> you have better hardware. >> >> > My only problem is with coot (latest build), the interface is working >> fine, as well as the 3D graphical. The >> > only problem is that the graphical window is offset from the rest of >> the UI (see screenshot). >> > So although it looks like everything would work smoothly it's not >> really usable. >> >> What, would you say, is the biggest problem? >> >> > I guess it comes from the absence of GPU access under WSL2 and so no >> proper display driver, but does anyone >> > had this problem? (and managed to solve it). >> >> FWIW, I have not seen this problem before (and don't know how to fix it) >> >> It seems to me an X server problem (or configuration issue). Have you >> tweaked or disabled the native OpenGL >> options on the X server? >> >> > Would be very useful for people working from home without a full linux >> dual boot. >> >> Hmm. >> >> > In a more general note, it seems that WSL2 will be able to replace >> windows specific build very effectively >> > in the very near future. >> >> For everything other than OpenGL graphics (and maybe the Cloud would also >> be problematic), yes, it seems so. >> >> Paul. >> > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Coot under WSL2
The performance are massively improved in WSL2 versus WSL1, so maybe it's why you had bad memory of it ? WSL2 is currently only available in insider fast ring, but will be for everyone with next major update (v2004) in few weeks. The main problem is, while you can use the right toolbar by simply detaching it, selecting residues is almost impossible as the pointer is still using the main UI as reference, but the 3D display is away, so you need to click far from the residus you try to select. I am playing around with the xserver options, but am not sure what I am doing with that windows X server. I'll update if I find a solution. Clément On Thu, 19 Mar 2020 at 13:31, Paul Emsley wrote: > On 19/03/2020 12:43, Clement Degut wrote: > > > > I have been recently trying to use ccp4 in windows subsystem for Linux 2 > (Ubuntu distribution), everything i > > tried run perfectly smoothly, including graphical interfaces. > > I am pleasantly surprised - when I tried that (some time ago) the graphics > performance as terrible. Perhaps > you have better hardware. > > > My only problem is with coot (latest build), the interface is working > fine, as well as the 3D graphical. The > > only problem is that the graphical window is offset from the rest of the > UI (see screenshot). > > So although it looks like everything would work smoothly it's not really > usable. > > What, would you say, is the biggest problem? > > > I guess it comes from the absence of GPU access under WSL2 and so no > proper display driver, but does anyone > > had this problem? (and managed to solve it). > > FWIW, I have not seen this problem before (and don't know how to fix it) > > It seems to me an X server problem (or configuration issue). Have you > tweaked or disabled the native OpenGL > options on the X server? > > > Would be very useful for people working from home without a full linux > dual boot. > > Hmm. > > > In a more general note, it seems that WSL2 will be able to replace > windows specific build very effectively > > in the very near future. > > For everything other than OpenGL graphics (and maybe the Cloud would also > be problematic), yes, it seems so. > > Paul. > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] CC work / free
Did not knew about that trick !
But I second that a well made script (i.e. not my homemade one) included in
software for paired refinement would be a great addition.
On Thu, 8 Nov 2018 at 20:13, Georg Mlynek wrote:
> Dear Frank,
>
> pdb_redo webserver does. However you have to cheat to provoke it: The
> resolution remark in the PDB has to be 0.10A beyond what it was used
> before. You can use also use the command line version of pdb-redo to tweak
> settings for your calculation (the expert option).
>
> However it would be nice to have the option also in ccp4 and phenix. Doing
> this without a script is painful.
>
> Br, Georg.
>
> Am 11/8/2018 um 17:52 schrieb Frank von Delft:
>
> Does any refinement software automatically do the CC* resolution
> exploration ("paired refinement") that Kay did in the original paper? Now
> that *would* be fantastically useful.
>
>
> On 08/11/2018 12:44, Pavel Afonine wrote:
>
> Clément,
> I'm guessing this is because it isn't clear what CCwork/CCfree can tell
> you that Rwork/Rfree can not. Needless to say we all more or less have a
> good idea about what the ok values for Rwork, Rfree and Rfree-Rwork (as
> function of resolution) while it is much less clear (to me at least) when
> it comes to CCwork/CCfree.
> I think phenix.refine used to report CCwork/CCfree in some releases but I
> removed it as useless.
> All the best,
> Pavel
>
> On Thu, Nov 8, 2018 at 8:16 PM Clement Degut <
> 26de0a160250-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hi all,
>>
>> This probably have already be discussed, but can't find trace of it :
>> Is there any reason I am not aware of that refinement software (thinking
>> of both phenix and refmac) do not output CC work / free ?
>> We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which
>> tend to lead to high Rfree ( last shells having very poor phases), at least
>> high overall R free in regard to the majority same resolution structures as
>> they been refined with I/sig > 3.
>> Which in return push people to cut resolution AFTER refinement which
>> obviously drastically decrease the R free and catapult your structure from
>> worst of the PDB to best of the PDB. It should never be done but it is
>> nonetheless.
>> How to blame a "non expert" to do that when changing the resolution from
>> 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the
>> idea).
>> Now it seems to me -but I may be very wrong as I am far from expert in
>> the arcane math of these- that CC work and free would be more agnostic to
>> this resolution cut off problem, as we compare it to the CC* value anyway ?
>> thought it will never start to be used if refinement software don't output
>> it as a standard (not talking about completely replacing Rfree here as it
>> is obviously useful).
>> Would CC work/free be a bad appreciation of the refinement process ?
>>
>> Thanks
>>
>> Clément
>>
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>>
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>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
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[ccp4bb] CC work / free
Hi all, This probably have already be discussed, but can't find trace of it : Is there any reason I am not aware of that refinement software (thinking of both phenix and refmac) do not output CC work / free ? We all accepted CC 1/2 for resolution cut (whether it's 30 or 10 %) which tend to lead to high Rfree ( last shells having very poor phases), at least high overall R free in regard to the majority same resolution structures as they been refined with I/sig > 3. Which in return push people to cut resolution AFTER refinement which obviously drastically decrease the R free and catapult your structure from worst of the PDB to best of the PDB. It should never be done but it is nonetheless. How to blame a "non expert" to do that when changing the resolution from 1.49 to 1.5 change your Rfree by 2% (yes it exaggerated but you get the idea). Now it seems to me -but I may be very wrong as I am far from expert in the arcane math of these- that CC work and free would be more agnostic to this resolution cut off problem, as we compare it to the CC* value anyway ? thought it will never start to be used if refinement software don't output it as a standard (not talking about completely replacing Rfree here as it is obviously useful). Would CC work/free be a bad appreciation of the refinement process ? Thanks Clément To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
