Re: [ccp4bb] Pymol Map range

[Gerard Kleywegt]

Hi all,

By popular demand (yeah, me too) the HTML versions of the old USF manuals have 
been kindly added to the GitHub site (link below) by Martyn Winn.


Also, the machine in Uppsala that used to serve them has finally given up the 
ghost so GitHub is now the only source of USF source code and documentation.


--Gerard

PS: I managed to mistype the word "GitHub" twice while composing this email, 
as GutHub and HitHub...



On Thu, 4 Mar 2021, Gerard DVD Kleywegt wrote:


Hi all,

Following up on this: some time ago, Martyn Winn was kind enough to put the 
source of a bunch of old Uppsala Software Factory programs in GitHub:


  https://github.com/martynwinn/Uppsala-Software-Factory

It's all unsupported now (I haven't compiled anything in 12 years...) but 
free to do with whatever you like.


(The website in Uppsala has unfortunately not been accessible for several 
months already. This means that the manuals are not online. If there is 
interest I could post a tgz file with -as far as I can determine- the latest 
version of all manuals in HTML format (0.8 MB total).)


--Gerard


On Wed, 3 Mar 2021, James Holton wrote:


Yes, I stand corrected. "mapmask" is the CCP4 program.

mapman is still around.  I even found a way to get it to work on 64-bit!
https://git.bl831.als.lbl.gov/jamesh/map-bender/-/blob/master/mapman_regression_test.csh

-James Holton
MAD Scientist


On 3/3/2021 9:10 AM, Jon Cooper wrote:

 For old-schoolers, mapmask (once known as extend) in ccp4 does this.
 Mapman was from the Upsala suite and became XDLmapman in ccp4, but then
 became unusable and disappeared. I liked the original mapman as you had 
to

 actually give a name for your map, like 'jim' or 'jon'.

 Best wishes, Jon Cooper


 Sent from ProtonMail mobile



  Original Message 
 On 1 Mar 2021, 21:19, James Holton < jmhol...@lbl.gov> wrote:


 The CCP4 program you are looking for is called "mapman", and the
 option you need is "border".

 -James Holton
 MAD Scientist


 On 2/26/2021 8:07 AM, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:


 Hello BB,

 I’m trying to make an image of some electron density in pymol but
 am running into a problem, my atoms are half in and half out of
 the unit cell so I only get half the density.

 Has anyone ran into this problem previously, and if so, is there
 a way to shift the origin, extend the map, or something so
 everything is covered?

 I realise this is not a ccp4 problem exactly, so I am ready for
 the inevitable replies, but I imagine a program in ccp4 might be
 the answer.

 Cheers,

 Sam

 --
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Best wishes,

--Gerard

**
  Gerard J. Kleywegt

 http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
  The opinions in this message are fictional.  Any similarity

Re: [ccp4bb] Pymol Map range

[Edward A. Berry]

On 03/04/2021 10:42 AM, Gerard DVD Kleywegt wrote:

If there is interest I could post a tgz file with -as far as I can determine- 
the latest version of all manuals in HTML format (0.8 MB total).)

Yes, I would like to grab a copy of the manuals.
Ed



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Re: [ccp4bb] Pymol Map range

[Gerard DVD Kleywegt]

Hi all,

Following up on this: some time ago, Martyn Winn was kind enough to put the 
source of a bunch of old Uppsala Software Factory programs in GitHub:


   https://github.com/martynwinn/Uppsala-Software-Factory

It's all unsupported now (I haven't compiled anything in 12 years...) but free 
to do with whatever you like.


(The website in Uppsala has unfortunately not been accessible for several 
months already. This means that the manuals are not online. If there is 
interest I could post a tgz file with -as far as I can determine- the latest 
version of all manuals in HTML format (0.8 MB total).)


--Gerard


On Wed, 3 Mar 2021, James Holton wrote:


Yes, I stand corrected. "mapmask" is the CCP4 program.

mapman is still around.  I even found a way to get it to work on 64-bit!
https://git.bl831.als.lbl.gov/jamesh/map-bender/-/blob/master/mapman_regression_test.csh

-James Holton
MAD Scientist


On 3/3/2021 9:10 AM, Jon Cooper wrote:

 For old-schoolers, mapmask (once known as extend) in ccp4 does this.
 Mapman was from the Upsala suite and became XDLmapman in ccp4, but then
 became unusable and disappeared. I liked the original mapman as you had to
 actually give a name for your map, like 'jim' or 'jon'.

 Best wishes, Jon Cooper


 Sent from ProtonMail mobile



  Original Message 
 On 1 Mar 2021, 21:19, James Holton < jmhol...@lbl.gov> wrote:


 The CCP4 program you are looking for is called "mapman", and the
 option you need is "border".

 -James Holton
 MAD Scientist


 On 2/26/2021 8:07 AM, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:


 Hello BB,

 I’m trying to make an image of some electron density in pymol but
 am running into a problem, my atoms are half in and half out of
 the unit cell so I only get half the density.

 Has anyone ran into this problem previously, and if so, is there
 a way to shift the origin, extend the map, or something so
 everything is covered?

 I realise this is not a ccp4 problem exactly, so I am ready for
 the inevitable replies, but I imagine a program in ccp4 might be
 the answer.

 Cheers,

 Sam

 -- 


 This e-mail and any attachments may contain confidential,
 copyright and or privileged material, and are for the use of the
 intended addressee only. If you are not the intended addressee or
 an authorised recipient of the addressee please notify us of
 receipt by returning the e-mail and do not use, copy, retain,
 distribute or disclose the information in or attached to the e-mail.
 Any opinions expressed within this e-mail are those of the
 individual and not necessarily of Diamond Light Source Ltd.
 Diamond Light Source Ltd. cannot guarantee that this e-mail or
 any attachments are free from viruses and we cannot accept
 liability for any damage which you may sustain as a result of
 software viruses which may be transmitted in or with the message.
 Diamond Light Source Limited (company no. 4375679). Registered in
 England and Wales with its registered office at Diamond House,
 Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11
 0DE, United Kingdom


 

 To unsubscribe from the CCP4BB list, click the following link:
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Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
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   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**



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Re: [ccp4bb] Pymol Map range

[Emilia Arturo]

There is also a pymol mailing list you might like to ping:
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/info.html

Emilia ("Emily") C Arturo
Postdoctoral associate
Laboratory of Dr. Erica Ollmann Saphire
Division of Structural Biology & Infectious Diseases
La Jolla Institute for Immunology, California USA
Twitter @moonlighterturo @ljiresearch @EOSpahire




On Fri, Feb 26, 2021 at 8:35 AM Horrell, Sam (DLSLtd,RAL,LSCI) <
sam.horr...@diamond.ac.uk> wrote:

> Thanks Paul, that has worked just fine.
>
>
>
> Cheers,
>
>
>
> Sam
>
>
>
> *From:* CCP4 bulletin board  *On Behalf Of *Paul
> Emsley
> *Sent:* 26 February 2021 16:12
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Pymol Map range
>
>
>
>
>
> On 26/02/2021 16:07, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
>
> Hello BB,
>
>
>
> I’m trying to make an image of some electron density in pymol but am
> running into a problem, my atoms are half in and half out of the unit cell
> so I only get half the density.
>
> Has anyone ran into this problem previously, and if so, is there a way to
> shift the origin, extend the map, or something so everything is covered?
>
> I realise this is not a ccp4 problem exactly, so I am ready for the
> inevitable replies, but I imagine a program in ccp4 might be the answer.
>
>
>
>
>
> You can do it in Coot.  Do the masking or whatever, then File -> Export
> Map Fragment
>
> Then use that map in PyMOL
>
> 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 e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Pymol Map range

[Horrell, Sam (DLSLtd,RAL,LSCI)]

Thanks Paul, that has worked just fine.

Cheers,

Sam

From: CCP4 bulletin board  On Behalf Of Paul Emsley
Sent: 26 February 2021 16:12
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Pymol Map range



On 26/02/2021 16:07, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:
Hello BB,

I'm trying to make an image of some electron density in pymol but am running 
into a problem, my atoms are half in and half out of the unit cell so I only 
get half the density.
Has anyone ran into this problem previously, and if so, is there a way to shift 
the origin, extend the map, or something so everything is covered?
I realise this is not a ccp4 problem exactly, so I am ready for the inevitable 
replies, but I imagine a program in ccp4 might be the answer.




You can do it in Coot.  Do the masking or whatever, then File -> Export Map 
Fragment

Then use that map in PyMOL

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 e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] Pymol Map range

[Paul Emsley]

On 26/02/2021 16:07, Horrell, Sam (DLSLtd,RAL,LSCI) wrote:


Hello BB,

I’m trying to make an image of some electron density in pymol but am 
running into a problem, my atoms are half in and half out of the unit 
cell so I only get half the density.


Has anyone ran into this problem previously, and if so, is there a way 
to shift the origin, extend the map, or something so everything is 
covered?


I realise this is not a ccp4 problem exactly, so I am ready for the 
inevitable replies, but I imagine a program in ccp4 might be the answer.




You can do it in Coot.  Do the masking or whatever, then File -> Export 
Map Fragment


Then use that map in PyMOL

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 
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